European Bioinformatics Institute

Pattern Recognition in Bioinformatics. 7th IAPR International Conference, PRIB 2012, Tokyo, Japan, November 8-10, 2012. Proceedings. Volume 7632 LNBI, (2012), p.14-25 doi: 10.1007/978-3-642-34123-6_2

Revisiting the training of logic models of protein signaling networks with ASP

Videla, S., Guziolowski C., EDUATI F., Thiele S., Grabe N., SAEZ-RODRIGUEZ J., and Siegel A.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Volume 7605 LNBI, (2012), p.342-361

Delivering ICT infrastructure for biomedical research

Nyrönen, Tommi Henrik, Laitinen Jarno, Tourunen Olli, Sternkopf Danny, Laurikainen Risto, ster Per Ö., Lehtovuori Pekka T., Miettinen Timo A., Simonen Tomi, Perheentupa Teemu, et al.

Proceedings of the WICSA/ECSA 2012 Companion Volume. (2012), New York, NY, USA, p.37–44 doi: 10.1145/2361999.2362006

Diachronic linked data: towards long-term preservation of structured interrelated information

Auer, S., Dalamagas T., Parkinson H., Bancilhon F., Flouris G., Sacharidis D., Buneman P., Kotzinos D., Stavrakas Y., Christophides V., et al.

Proceedings of the First International Workshop on Open Data. (2012), New York, NY, USA, p.31-39

MetaboLights–an open-access general-purpose repository for metabolomics studies and associated meta-data

HAUG, K., Salek R. M., Conesa P., HASTINGS J., De Matos P., Rijnbeek M., Mahendraker T., Williams M., Neumann S., Rocca-Serra P., et al.

Nucleic Acids Research. Volume 41, Number D1, (2012), p.D781–D786 doi: 10.1093/nar/gks1004

The International Nucleotide Sequence Database Collaboration

Karsch-mizrachi, I., Nakamura Y., Cochrane G., and Collaboration International Nucleotide Sequence Database

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D33-7 doi:

PSI-Search: iterative HOE-reduced profile SSEARCH searching

Li, Weizhong, McWilliam Hamish, Goujon Mickael, Cowley Andrew, Lopez Rodrigo, and Pearson William R.

Bioinformatics. Volume 28, Number 12, (2012), p.1650–1651

Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies

Fusi, N., Stegle O., and Lawrence N. D.

PLoS computational biology. Volume 8, Number 1, (2012), p.e1002330

Toward community standards in the quest for orthologs.

Dessimoz, Christophe, Gabaldón Toni, Roos David S., Sonnhammer Erik L. L., Herrero Javier, and the for Consortium Quest Orthologs

Bioinformatics. 3, Volume 28, Number 6, (2012), p.900-904 doi: 10.1093/bioinformatics/bts050

BLUEPRINT to decode the epigenetic signature written in blood.

Adams, David, Altucci Lucia, Antonarakis Stylianos E., Ballesteros Juan, Beck Stephan, Bird Adrian, Bock Christoph, Boehm Bernhard, Campo Elias, Caricasole Andrea, et al.

Nat Biotechnol. Volume 30, Number 3, (2012), United States, p.224-6 doi: 10.1038/nbt.2153

The Worldwide Protein Data Bank

Berman, H. M., Henrick K., KLEYWEGT G. J., Nakamura H., and Markley J. L.

International Tables for Crystallography. Volume F, Number ch. 24.1, (2012), p.827-832 doi: 10.1107/97809553602060000896

Integration of the Anatomical Therapeutic Chemical Classification System and DrugBank using OWL and text-mining

Croset, S., Hoehndorf R., and REBHOLZ-SCHUHMANN D.

GI WORKGROUP “ONTOLOGIES IN BIOMEDICINE AND LIFE SCIENCES”(OBML). (2012),

Potential 2-aminosuccinimide structures in mollusc proteins

GARAVELLI, J., and Hirshberg M.

Protein Science. Volume 21, (2012), p.130 doi: 10.1002/pro.2113

Global Analysis of Small Molecule Binding to Related Protein Targets

KRUGER, F. A., and OVERINGTON J. P.

PLoS Computational Biology. Volume 8, Number 1, (2012), p.e1002333

Modeling gene expression using chromatin features in various cellular contexts

Dong, X., Greven M. C., Kundaje A., Djebali S., Brown J. B., Cheng C., Gingeras T. R., Gerstein M., Guigó R., Birney E., et al.

Genome biology. Volume 13, Number 9, (2012), p.R53

ArrayExpress update–trends in database growth and links to data analysis tools

RUSTICI, G., KOLESNIKOV N., BRANDIZI M., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., ISON J., KEAYS M., et al.

Nucleic acids research. Nov 27, Volume Article in press, (2012),

Genome content of uncultivated marine _Roseobacters_ in the surface ocean

Luo, H., Löytynoja A., and Moran M. A.

Environmental Microbiology. Volume 14, (2012), p.41-51

MicroRNA-9 inhibition of cell proliferation and identification of novel miR-9 targets by transcriptome profiling in breast cancer cells

Selcuklu, S. D., Donoghue M. T. A., Rehmet K., de Souza Gomes M., Fort A., Kovvuru P., Muniyappa M. K., Kerin M. J., Enright A. J., and Spillane C.

Journal of Biological Chemistry. Volume 287, Number 35, (2012), p.29516–29528

The interface of protein structure, protein biophysics, and molecular evolution

Liberles, D. A., Teichmann S. A., Bahar I., Bastolla U., Bloom J., Bornberg-Bauer E., Colwell L. J., de Koning AP, Dokholyan N. V., Echave J., et al.

Protein Science. (2012),

Bioinformatics training network (BTN): A community resource for bioinformatics trainers

Schneider, M. V., Walter P., Blatter M. C., Watson J., Brazas M. D., Rother K., Budd A., Via A., van Gelder C. W. G., Jacob J., et al.

Briefings in Bioinformatics. Volume 13, Number 3, (2012), p.383-389

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity'?

Lentini, Giovanni

Nat Rev Drug Discov. Sep, Volume 11, Number 9, (2012), p.730; author reply 730 doi: 10.1038/nrd3503-c1

Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma

Caldas, J., GEHLENBORG N., Kettunen E., Faisal A., Rönty M., Nicholson A. G., Knuutila S., BRAZMA A., and Kaski S.

Bioinformatics. Volume 28, Number 2, (2012), p.246–253

Comparative Interaction Networks: Bridging Genotype to Phenotype

Beltrao, P., Ryan C., and Krogan N. J.

Evolutionary Systems Biology. (2012), p.139–156

HSM–a hybrid system based approach for modelling intracellular networks

BRAZMA, A., Cerans K., Ruklisa D., Schlitt T., and Viksna J.

Gene. (2012),

Toward interoperable bioscience data

Sansone, Susanna-Assunta, Rocca-Serra Philippe, Field Dawn, Maguire Eamonn, Taylor Chris, Hofmann Oliver, Fang Hong, Neumann Steffen, Tong Weida, Amaral-Zettler Linda, et al.

Nat Genet. Volume 44, Number 2, (2012), p.121–126 doi: 10.1038/ng.1054

InterPro in 2011: new developments in the family and domain prediction database

Hunter, Sarah, Jones Philip, Mitchell Alex, Apweiler Rolf, Attwood Teresa K., Bateman Alex, Bernard Thomas, Binns David, Bork Peer, Burge Sarah, et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D306–D312

AntiFam: a tool to help identify spurious ORFs in protein annotation

Eberhardt, R. Y., Haft D. H., Punta M., MARTIN M., O'Donovan C., and Bateman A.

Database: The Journal of Biological Databases and Curation. Volume 2012, (2012), doi:

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

BURGE, S., Kelly E., Lonsdale D., MUTOWO-MUELLENET P., MCANULLA C., Mitchell A., SANGRADOR-VEGAS A., YONG S. Y., Mulder N., and HUNTER S.

Database: the journal of biological databases and curation. Volume 2012, (2012),

Annotating human P-glycoprotein bioassay data

Zdrazil, B., Pinto M., Vasanthanathan P., Williams A. J., Balderud L. Z., Engkvist O., Chichester C., HERSEY A., OVERINGTON J. P., and Ecker G. F.

Molecular Informatics. Volume 31, Number 8, (2012), p.599-609

TraML a standard format for exchange of selected reaction monitoring transition lists

Deutsch, E.W., Chambers M., Neumann S., Levander F., Binz P.A., Shofstahl J., Campbell D.S., Mendoza L., Ovelleiro D., Helsens K., et al.

Molecular & Cellular Proteomics. Volume 11, Number 4, (2012),

Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis

Windram, O., Madhou P., McHattie S., Hill C., Hickman R., Cooke E., Jenkins D. J., Penfold C. A., Baxter L., Breeze E., et al.

The Plant Cell Online. Volume 24, Number 9, (2012), p.3530–3557

Analysis of variation at transcription factor binding sites in Drosophila and humans.

Spivakov, Mikhail, Akhtar Junaid, Kheradpour Pouya, Beal Kathryn, Girardot Charles, Koscielny Gautier, Herrero Javier, Kellis Manolis, Furlong Eileen Em, and Birney Ewan

Genome Biol. Volume 13, Number 9, (2012), England, p.R49 doi: 10.1186/gb-2012-13-9-r49

An integrated map of genetic variation from 1,092 human genomes.

Consortium, Genomes Project 1000

Nature. 11, Volume 491, Number 7422, (2012), England, p.56-65 doi: 10.1038/nature11632

Qualitative translation of relations from BioPAX to SBML qual

BUCHEL, F., Wrzodek C., MITTAG F., Drager A., Eichner J., Rodriguez N., NOVERE LE N., and Zell A.

Bioinformatics (Oxford, England). Oct 15, Volume 28, Number 20, (2012), p.2648-2653

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Schulz, M. H., Zerbino D. R., Vingron M., and Birney E.

Bioinformatics. Volume 28, Number 8, (2012), p.1086–1092

Harmonization of gene/protein annotations: towards a gold standard MEDLINE

Campos, D., Matos S., Lewin I., Oliveira J. L., and REBHOLZ-SCHUHMANN D.

Bioinformatics. Volume 28, Number 9, (2012), p.1253–1261

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

Doreleijers, J. F., VRANKEN W. F., Schulte C., Markley J. L., Ulrich E. L., Vriend G., and Vuister G. W.

Nucleic acids research. Jan 1 (e-pub 1 D, Volume 40, Number D1, (2012), p.D519-D524

The mzIdentML data standard for mass spectrometry-based proteomics results

Jones, A. R., Eisenacher M., Mayer G., Kohlbacher O., Siepen J., Hubbard S. J., Selley J.N., Searle B. C., Shofstahl J., Seymour S.L., et al.

Molecular & Cellular Proteomics. Volume 11, Number 7, (2012),

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

Schroder, K., Irvine K. M., Taylor M. S., Bokil N. J., Cao K. - A. L., Masterman K. - A., Labzin L. I., Semple C. A., Kapetanovic R., Fairbairn L., et al.

Proceedings of the National Academy of Sciences U.S.A.. Volume 109, (2012), p.E944-E953

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

Gonzalez-Galarza, F. F., Lawless C., Hubbard S. J., Fan J., Bessant C., Hermjakob H., and Jones A. R.

OMICS: A Journal of Integrative Biology. (2012),

ELIXIR: a distributed infrastructure for European biological data.

Crosswell, Lindsey C., and Thornton Janet M.

Trends Biotechnol. May, Volume 30, Number 5, (2012), p.241–242 doi: 10.1016/j.tibtech.2012.02.002

InterPro in 2011: new developments in the family and domain prediction database

HUNTER, S., Jones P., Mitchell A., Apweiler R., Attwood T. K., Bateman A., Bernard T., Binns D., Bork P., BURGE S., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D306–D312 doi:

PSI-Search: iterative HOE-reduced profile SSEARCH searching

Li, W., McWilliam H., GOUJON M., Cowley A., Lopez R., and Pearson W. R.

Bioinformatics. Volume 28, Number 12, (2012), p.1650–1651

NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment

Reynolds, N., Latos P., Hynes-Allen A., Loos R., Leaford D., O'Shaughnessy A., Mosaku O., Signolet J., Brennecke P., Kalkan T., et al.

Cell Stem Cell. May, Volume 10, Number 5, (2012), p.583–594

WormBase: Annotating many nematode genomes

Howe, K., Davis P., Paulini M., Tuli M. A., Williams G., Yook K., Durbin R., Kersey P., and Sternberg P.

Worm. Volume 1, Number 1, (2012), p.15–21

Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters

Conrad, Thomas, Cavalli Florence MG, Vaquerizas Juan M., Luscombe Nicholas M., and Akhtar Asifa

Science. Volume 337, Number 6095, (2012), p.742–746

Process attributes in bio-ontologies

Andrade, André Q., Blondé Ward, Hastings Janna, and Schulz Stefan

BMC Bioinformatics. Volume 13, Number 1, (2012), p.217 doi: 10.1186/1471-2105-13-217

Bioimage informatics: a new category in Bioinformatics

Peng, H., Bateman A., Valencia A., and Wren J. D.

Bioinformatics. Volume 28, Number 8, (2012), p.1057

MouseFinder: candidate disease genes from mouse phenotype data.

Chen, Chao-Kung K., Mungall Christopher J., Gkoutos Georgios V., Doelken Sandra C., Köhler Sebastian, Ruef Barbara J., Smith Cynthia, Westerfield Monte, Robinson Peter N., Lewis Suzanna E., et al.

Hum Mutat. 2, Volume 33, Number 5, (2012), p.858-866 doi: 10.1002/humu.22051

Rare copy number variants contribute to congenital left-sided heart disease.

Hitz, Marc-Phillip P., Lemieux-Perreault Louis-Philippe P., Marshall Christian, Feroz-Zada Yassamin, Davies Robbie, Yang Shi Wei, Lionel Anath Christopher, D'Amours Guylaine, Lemyre Emmanuelle, Cullum Rebecca, et al.

PLoS Genet. 9, Volume 8, Number 9, (2012), United States, p.e1002903 doi: 10.1371/journal.pgen.1002903

Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON

MATTIONI, M., Cohen U., and NOVERE N. L.

Frontiers in neuroinformatics. Volume 6, (2012), p.20

CING: an integrated residue-based structure validation program suite

Doreleijers, J. F., SILVA SOUSA DA A. W., Krieger E., Nabuurs S. B., Spronk C. A., Stevens T. J., VRANKEN W. F., Vriend G., and Vuister G. W.

Journal of Biomolecular NMR. Volume 54, Number 3, (2012), p.267-283 doi: 10.1007/s10858-012-9669-7

Paralogous annotation of disease-causing variants in long QT syndrome genes

Ware, J. S., Walsh R., Cunningham F., Birney E., and Cook S. A.

Human Mutation. (2012),

ELIXIR: a distributed infrastructure for European biological data

Crosswell, Lindsey C., and Thornton Janet M.

Trends in biotechnology. Volume 30, (2012), p.241–242 doi:

Chemogenomics, Introduction to Cheminformatics: Data management, manipulation and properties,

OVERINGTON, J. P.

(2012),

On the need for an international effort to capture, share and use crystallization screening data

Newman, J., Bolton E. E., Muller-Dieckmann J., Fazio V. J., Gallagher D. T., Lovell D., Luft J. R., Peat T. S., Ratcliffe D., Sayle R. A., et al.

Acta Crystallographica Section F. Volume 68, Number Pt 3, (2012), p.253-258 doi: 10.1107/S1744309112002618

HUPO 2011: The New Cardiovascular Initiative-Integrating Proteomics and Cardiovascular Biology in Health and Disease

Lam, M. P. Y., Vivanco F., Scholten A., Hermjakob H., Van Eyk J., and Ping P.

Proteomics. Volume 12, Number 6, (2012), p.749–751

Ten Years of Standardizing Proteomic Data: A Report on the HUPO-PSI Spring Workshop

Orchard, S., Binz P.A., Borchers C., Gilson M. K., Jones A. R., Nicola G., Vizcaino J.A., Deutsch E.W., and Hermjakob H.

Proteomics. Volume 12, Number 18, (2012), p.2767–2772

Serotonin: from top to bottom.

Fidalgo, Sara, Ivanov Dobril K., and Wood Shona H.

Biogerontology. Oct, (2012), doi: 10.1007/s10522-012-9406-3

Protein–RNA interactions: new genomic technologies and perspectives

König, Julian, Zarnack Kathi, Luscombe Nicholas M., and Ule Jernej

Nature Reviews Genetics. Volume 13, Number 2, (2012), p.77–83

Self-organizing ontology of biochemically relevant small molecules.

Chepelev, Leonid L., Hastings Janna, Ennis Marcus, Steinbeck Christoph, and Dumontier Michel

BMC Bioinformatics. Volume 13, (2012), p.3 doi: 10.1186/1471-2105-13-3

The Pfam protein families database

Punta, M., Coggill P. C., Eberhardt R. Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D290–D301

The future of sequence archiving

Cochrane, G., Cook C. E., and Birney E.

GigaScience. Volume 1, (2012), doi:

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing.

Xue, Yali, Chen Yuan, Ayub Qasim, Huang Ni, Ball Edward V., Mort Matthew, Phillips Andrew D., Shaw Katy, Stenson Peter D., Cooper David N., et al.

Am J Hum Genet. 12, Volume 91, Number 6, (2012), p.1022-1032 doi: 10.1016/j.ajhg.2012.10.015

Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes.

Uhlenhaut, Henriette N., Barish Grant D., Yu Ruth T., Downes Michael, Karunasiri Malith, Liddle Christopher, Schwalie Petra, Hübner Norbert, and Evans Ronald M.

Mol Cell. 11, (2012), doi: 10.1016/j.molcel.2012.10.013

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Kersey, P. J., Staines D. M., Lawson D., Kulesha E., Derwent P., Humphrey J. C., Hughes D. S. T., Keenan S., Kerhornou A., Koscielny G., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D91–D97

Text-mining solutions for biomedical research: enabling integrative biology

REBHOLZ-SCHUHMANN, D., Oellrich A., and Hoehndorf R.

Nature Reviews Genetics. (2012),

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Cheng, C., Alexander R., Min R., Leng J., Yip K. Y., Rozowsky J., Yan K. K., Dong X., Djebali S., Ruan Y., et al.

Genome research. Volume 22, Number 9, (2012), p.1658–1667

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

Mallon, A. M., Iyer V., Melvin D., Morgan H., Parkinson H., Brown S. D., Flicek P., and Skarnes W. C.

Mammalian genome : official journal of the International Mammalian Genome Society. Sep 19, Volume 23, Number 9-10, (2012), p.641-652

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Orchard, S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F., Cesareni G., et al.

Nature Methods. Volume 9, Number 4, (2012), p.345–350

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Löytynoja, A., Vilella A. J., and Goldman N.

Bioinformatics. Volume 28, (2012), p.1684-1691

Large-scale analysis of microRNA evolution

GUERRA-ASSUNÇÃO, J. A., and Enright A. J.

BMC genomics. Volume 13, Number 1, (2012), p.218

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

Lewis, S., Csordas A., Killcoyne S., Hermjakob H., Hoopmann M. R., Moritz R.L., Deutsch E.W., and Boyle J.

BMC bioinformatics. Volume 13, Number 1, (2012), p.324

Looking for Darwin in genomic sequences –- validity and success of statistical methods

Zhai, W., Nielsen R., Goldman N., and Yang Z.

Molecular Biology and Evolution. Volume 29, (2012), p.2889-2893

The BioSample Database (BioSD) at the European Bioinformatics Institute

GOSTEV, M., FAULCONBRIDGE A., BRANDIZI M., FERNANDEZ-BANET J., Sarkans U., BRAZMA A., and Parkinson H.

Nucleic acids research. Volume 40, Number D1, (2012), p.D64–D70

Systematic Functional Prioritization of Protein Posttranslational Modifications

Beltrao, P., Albanèse V., Kenner L. R., Swaney D. L., Burlingame A., Villén J., Lim W. A., Fraser J. S., Frydman J., and Krogan N. J.

Cell. Volume 150, Number 2, (2012), p.413–425

Bioinformatics Meets User-Centred Design: A Perspective

Pavelin, Katrina, Cham Jennifer A., De Matos Paula, Brooksbank Cath, Cameron Graham, and Steinbeck Christoph

PLoS Computational Biology. Volume 8, Number 7, (2012), p.e1002554 doi: 10.1371/journal.pcbi.1002554

Biocurators and Biocuration: surveying the 21st century challenges

BURGE, S., Attwood T. K., Bateman A., Berardini T. Z., Cherry M., O'Donovan C., and others

Database: the journal of biological databases and curation. Volume 2012, (2012), doi:

Cheminformatics

Wegner, J. K., Sterling A., Guha R., Bender A., Faulon, HASTINGS J., O'Boyle N., OVERINGTON J., Vlijmen Van H., and Willighagen E.

Commun.ACM. nov, Volume 55, Number 11, (2012), p.65-75

Isoelectric point optimization using peptide descriptors and support vector machines

Perez-Riverol, Y., Audain E., Millan A., Ramos Y., Sanchez A., Vizcaino J.A., Wang R., Müller M., Machado Y. J., Betancourt L. H., et al.

Journal of proteomics. (2012),

CreZOO–the European virtual repository of Cre and other targeted conditional driver strains.

Chandras, Christina, Zouberakis Michael, Salimova Ekaterina, Smedley Damian, Rosenthal Nadia, and Aidinis Vassilis

Database (Oxford). 1, Volume 2012, (2012), England, p.bas029 doi: 10.1093/database/bas029

An integrated encyclopedia of DNA elements in the human genome.

Consortium, ENCODE Project

Nature. 9, Volume 489, Number 7414, (2012), England, p.57-74 doi: 10.1038/nature11247

The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

Adams, R. R., Tsorman N., Stratford K., Akman O. E., Gilmore S., JUTY N., NOVERE LE N., and A.J. Millar MILLAR A. J.

Journal of Biological Rhythms. Aug, Volume 27, Number 4, (2012), p.328-332

A transcription factor collective defines cardiac cell fate and reflects lineage history

Junion, G., Spivakov M., Girardot C., Braun M., Gustafson E. H., Birney E., and Furlong E. E. M.

Cell. Volume 148, Number 3, (2012), p.473–486

Improving Disease Gene Prioritization by Comparing the Semantic Similarity of Phenotypes in Mice with Those of Human Diseases

Oellrich, A., Hoehndorf R., Gkoutos G. V., and REBHOLZ-SCHUHMANN D.

PloS one. Volume 7, Number 6, (2012), p.e38937

Toxicogenomics Investigation Under the eTOX Project

Taboureau, O., HERSEY A., Audouze K., Gautier L., Jacobsen UP, Akhtar R., F A., and Brunak S O. J. P.

J Pharmacogenom Pharmacoproteomics. Volume 7, (2012), p.2153–0645

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

Griss, J., Reisinger F., Hermjakob H., and Vizcaino J.A.

Proteomics. Volume 12, Number 6, (2012), p.795–798

Targeted Deletion of MicroRNA-22 Promotes Stress-Induced Cardiac Dilation and Contractile DysfunctionClinical Perspective

Gurha, P., ABREU-GOODGER C., Wang T., Ramirez M. O., Drumond A. L., Van Dongen S., Chen Y., BARTONICEK N., Enright A. J., Lee B., et al.

Circulation. Volume 125, Number 22, (2012), p.2751–2761

A neuronal transcriptome response involving stress pathways is buffered by neuronal microRNAs

MANAKOV, S. A., Morton A., Enright A. J., and Grant S. G. N.

Frontiers in Neuroscience. Volume 6, (2012),

Insights into hominid evolution from the gorilla genome sequence

Scally, Aylwyn, Dutheil Julien Y., Hillier LaDeana W., Jordan Gregory E., Goodhead Ian, Herrero Javier, Hobolth Asger, Lappalainen Tuuli, Mailund Thomas, Marques-Bonet Tomas, et al.

Nature. Volume 483, (2012), p.169-175

PomBase: a comprehensive online resource for fission yeast

Wood, V., Harris M. A., McDowall M. D., Rutherford K., Vaughan B. W., Staines D. M., Aslett M., Lock A., Bähler J., Kersey P. J., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D695–D699

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells

Hebenstreit, D., Deonarine A., Babu M. M., and Teichmann S. A.

Current Opinion in Cell Biology. (2012),

European initiative towards quality standards in education and training for discovery, development and use of medicines

Klech, H., Brooksbank C., Price S., Verpillat P., Buhler F. R., Dubois D., Haider N., Johnson C., Linden H. H., Payton T., et al.

European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences. Volume 45, Number 5, (2012), p.520-520

Epigenomic and transcriptional effects of Dnmt3b mutations in human ICF syndrome-derived B cell lines.

Gatto, S., Angelini C., Leppert S., Proserpio V., Teichmann S., D’Esposito M., and R Matarazzo M.

EMBnet. journal. Volume 17, Number B, (2012), p.p–33

Toward community standards in the quest for orthologs

Dessimoz, C., Gabaldón T., Roos D.S., Sonnhammer E. L. L., Herrero J., and others

Bioinformatics. Volume 28, Number 6, (2012), p.900–904

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors

Metzakopian, E., Lin W., Salmon-Divon M., Dvinge H., Andersson E., Ericson J., Perlmann T., Whitsett J.A., Bertone P., and Ang S.L.

Development. Jul, Volume 139, Number 14, (2012), p.2625–2634

The Gene Ontology: enhancements for 2011

Chan, J., Kishore R., Sternberg P., and Van Auken K.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D559–D564

The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex

Conrad, Thomas, Cavalli Florence MG, Holz Herbert, Hallacli Erinc, Kind Jop, Ilik Ibrahim, Vaquerizas Juan M., Luscombe Nicholas M., and Akhtar Asifa

Developmental cell. Volume 22, Number 3, (2012), p.610–624

Requirements for semantic biobanks.

Andrade, André Q., Kreuzthaler Markus, Hastings Janna, Krestyaninova Maria, and Schulz Stefan

Studies in health technology and informatics. Volume 180, (2012), p.569–573

Reactome-a curated knowledgebase of biological pathways: megakaryocytes and platelets

Jupe, S., Akkerman J. W., Soranzo N., and Ouwehand W.H.

Journal of Thrombosis and Haemostasis. (2012),

Genome-wide meta-analysis of common variant differences between men and women.

Boraska, Vesna, Jerončić Ana, Colonna Vincenza, Southam Lorraine, Nyholt Dale R., Rayner Nigel William, Perry John R. B., Toniolo Daniela, Albrecht Eva, Ang Wei, et al.

Hum Mol Genet. 11, Volume 21, Number 21, (2012), England, p.4805-15 doi: 10.1093/hmg/dds304

Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

Mitsos, A., Melas I. N., Morris M. K., SAEZ-RODRIGUEZ J., Lauffenburger D. A., and Alexopoulos L. G.

PloS one. Volume 7, Number 11, (2012), p.e50085

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Kersey, Paul J., Staines Daniel M., Lawson Daniel, Kulesha Eugene, Derwent Paul, Humphrey Jay C., Hughes Daniel S. T., Keenan Stephan, Kerhornou Arnaud, Koscielny Gautier, et al.

Nucleic Acids Res. 1, Volume 40, Number Database issue, (2012), England, p.D91-7 doi: 10.1093/nar/gkr895

Calcium Input Frequency, Duration and Amplitude Differentially Modulate the Relative Activation of Calcineurin and CaMKII

Li, L., STEFAN M. I., and NOVERE LE N.

PloS one. Volume 7, Number 9, (2012), p.e43810

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level

Dalby, A. R., EMAM I., and Franke R.

PLoS ONE. Volume 7, Number 11, (2012),

The genomic basis of adaptive evolution in threespine sticklebacks

Jones, F. C., Grabherr M. G., Chan Y. F., Russell P., Mauceli E., Johnson J., Swofford R., Pirun M., Zody M. C., White S., et al.

Nature. Volume 484, Number 7392, (2012), p.55–61

Three Hybrid Classifiers for the Detection of Emotions in Suicide Notes

Liakata, M., Kim J. H., Saha S., HASTINGS J., and REBHOLZ-SCHUHMANN D.

Biomedical informatics insights. Volume 5, Number Suppl. 1, (2012), p.175

The 2010 Cryo-EM Modeling Challenge

Ludtke, S. J., Lawson C. L., KLEYWEGT G. J., Berman H., and Chiu W.

Biopolymers. Volume 97, Number 9, (2012), p.651-654 doi: 10.1002/bip.22081

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

Rosato, A., Aramini J. M., Arrowsmith C., Bagaria A., Baker D., Cavalli A., Doreleijers J. F., Eletsky A., Giachetti A., Guerry P., et al.

Structure. Volume 20, Number Issue 2, (2012), p.227-236. doi: 10.1016/j.str.2012.01.002

Analyzing Protein–Protein Interaction Networks†

Koh, G. C. K. W., Porras P., Aranda B., Hermjakob H., and Orchard S. E.

Journal of proteome research. Volume 11, Number 4, (2012), p.2014–2031

Quality of computationally inferred Gene Ontology annotations

Škunca, N., Altenhoff A., and Dessimoz C.

PLoS Computational Biology. Volume 8, (2012), p.e1002533

Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing.

Papatheodorou, Irene, Ziehm Matthias, Wieser Daniela, Alic Nazif, Partridge Linda, and Thornton Janet M.

PLoS One. Volume 7, Number 12, (2012), p.e50881 doi: 10.1371/journal.pone.0050881

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription

Kahramanoglou, Christina, Prieto Ana I., Khedkar Supriya, Haase Bettina, Gupta Ankur, Benes Vladimir, Fraser Gillian M., Luscombe Nicholas M., and Seshasayee Aswin S. N.

Nature Communications. Volume 3, (2012), p.886

A Database for Chemical Proteomics: ChEBI.

De Matos, P., ADAMS N., HASTINGS J., MORENO P., and Steinbeck C.

Methods Mol Biol. Volume 803, (2012), p.273–296

Major submissions tool developments at the European Nucleotide Archive

Amid, C., Birney E., Bower L., Cerdeno-Tárraga A., Cheng Y., Cleland I., Faruque N., Gibson R., Goodgame N., Hunter C., et al.

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D43-7 doi:

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Goncalves, A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, and Marioni JC

Genome Research. Volume 22, (2012), p.2376 doi: 10.1101/gr.142281.112

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans.

Mallon, Ann-Marie M., Iyer Vivek, Melvin David, Morgan Hugh, Parkinson Helen, Brown Steve D. M., Flicek Paul, and Skarnes William C.

Mamm Genome. 10, Volume 23, Number 9-10, (2012), United States, p.641-52 doi: 10.1007/s00335-012-9428-9

Mapping the human phosphatome on growth pathways

Sacco, F., Gherardini P. F., Paoluzi S., SAEZ-RODRIGUEZ J., Helmer-Citterich M., Ragnini-Wilson A., Castagnoli L., and Cesareni G.

Molecular systems biology. Aug 14, Volume 8, (2012), p.603

The BioSample Database (BioSD) at the European Bioinformatics Institute

GOSTEV, M., FAULCONBRIDGE A., BRANDIZI M., FERNANDEZ-BANET J., Sarkans U., BRAZMA A., and Parkinson H.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D64-D70

Analyzing genomic data: understanding the genome

Fernández-Suárez, X. M.

Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery. 3, Volume 2, Number 2, (2012), p.116-137 doi: 10.1002/widm.54

Towards virtual know ledge broker services for semantic integration of life science literature and data sources

Harrow, I., Filsell W., Woollard P., DIX I., Braxtenthaler M., Gedye R., Hoole D., Kidd R., Wilson J., and REBHOLZ-SCHUHMANN D.

Drug Discovery Today. (2012),

Gene Expression Atlas update - Value-added database of microarray and sequencing-based functional genomics experiments

KAPUSHESKY, M., ADAMUSIAK T., BURDETT T., CULHANE A., FARNE A., FILIPPOV A., HOLLOWAY E., KLEBANOV A., KRYVYCH N., KURBATOVA N., et al.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D1077-D1081

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Yip, K. Y., Cheng C., Bhardwaj N., Brown J. B., Leng J., Kundaje A., Rozowsky J., Birney E., Bickel P., Snyder M., et al.

Genome biology. Volume 13, Number 9, (2012), p.R48

Gene Expression Atlas update–a value-added database of microarray and sequencing-based functional genomics experiments

KAPUSHESKY, M., ADAMUSIAK T., BURDETT T., CULHANE A., FARNE A., FILIPPOV A., HOLLOWAY E., KLEBANOV A., KRYVYCH N., KURBATOVA N., et al.

Nucleic acids research. Nov 7, Volume 40, Number Database issue, (2012), p.D1077-D1081

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

Altenhoff, A. M., Studer R. A., Robinson-Rechavi M., and Dessimoz C.

PLoS Computational Biology. Volume 8, (2012), p.e1002514

ACPYPE - AnteChamber PYthon Parser interfacE

SILVA, SOUSA DA A. W., and VRANKEN W. F.

BMC Research Notes. Volume 5, (2012), p.367-374 doi: 10.1186/1756-0500-5-367

Towards Generating a Corpus Annotated for Prokaryote-Drug Relations

Ying, Y., Kafkas S., Conroy M., and REBHOLZ-SCHUHMANN D.

Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine. (2012), doi: 10.5167/uzh-64476

Improvements in the protein identifier cross-reference service

Wein, S. P., Côté R.G., Dumousseau M., Reisinger F., Hermjakob H., and Vizcaino J.A.

Nucleic acids research. Volume 40, Number W1, (2012), p.W276–W280

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

Parts, L., Hedman K., Keildson S., Knights A. J., ABREU-GOODGER C., van de Bunt M., GUERRA-ASSUNÇÃO J. A., BARTONICEK N., Van Dongen S., Mägi R., et al.

PLoS Genetics. Volume 8, Number 5, (2012), p.e1002704 doi:

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs

Brookes, E., de Santiago I., Hebenstreit D., Morris K. J., Carroll T., Xie S. Q., Stock J. K., Heidemann M., Eick D., Nozaki N., et al.

Cell stem cell. Volume 10, Number 2, (2012), p.157–170

From Proteomics Data Representation to Public Data Flow: A Report on the HUPO-PSI Workshop September 2011, Geneva, Switzerland

Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Binz P.A., Martinez-Bartolomé S., Vizcaino J.A., and Hermjakob H.

Proteomics. Volume 12, Number 3, (2012), p.351–355

The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

Côté, R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H. W. P., van Breukelen B., Heck A.J.R., Hulstaert N., Martens L., et al.

Molecular & Cellular Proteomics. Volume 11, Number 12, (2012), p.1682–1689

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology

Hoehndorf, Robert, Harris Midori A., Herre Heinrich, Rustici Gabriella, and Gkoutos Georgios V.

Bioinformatics (Oxford, England). Volume 28, (2012), p.1783–1789 doi:

Hierarchical Modularity and the Evolution of Genetic Interactomes across Species

Ryan, C. J., Roguev A., Patrick K., Xu J., Jahari H., Tong Z., Beltrao P., Shales M., Qu H., Collins S. R., et al.

Molecular Cell. Volume 46, Number 5, (2012), p.691–704

Tools for mapping high-throughput sequencing data

FONSECA, N. A., Rung J., BRAZMA A., and MARIONI J. C.

Bioinformatics. Volume 28, Number 24, (2012), p.3169–3177

MetaboLights: towards a new COSMOS of metabolomics data management

Steinbeck, Christoph, Conesa Pablo, Haug Kenneth, Mahendraker Tejasvi, Williams Mark, Maguire Eamonn, Rocca-Serra Philippe, Sansone Susanna-Assunta, Salek Reza M., and Griffin Julian L.

Metabolomics. Volume 8, Number 5, (2012), p.757–760 doi: 10.1007/s11306-012-0462-0

Bioinformatics Advance Access published March 6, 2012

Peng, H., Bateman A., Valencia A., and Wren J. D.

(2012),

Global analysis of small molecule binding to related protein targets

KRUGER, F. A., and OVERINGTON J. P.

PLoS computational biology. Jan, Volume 8, Number 1, (2012), p.e1002333

ApiNATOMY: A novel toolkit for visualizing multiscale anatomy schematics with phenotype-related information

de Bono, B., Grenon P., and Sammut S.J.

Human Mutation. (2012),

Patterns of cis regulatory variation in diverse human populations

Stranger, B. E., Montgomery S. B., Dimas A. S., Parts L., Stegle O., Ingle C. E., Sekowska M., Smith G. D., Evans D., Gutierrez-Arcelus M., et al.

PLoS genetics. Volume 8, Number 4, (2012), p.e1002639

Genome sequencing and analysis of the tasmanian devil and its transmissible cancer.

Murchison, Elizabeth P., Schulz-Trieglaff Ole B., Ning Zemin, Alexandrov Ludmil B., Bauer Markus J., Fu Beiyuan, Hims Matthew, Ding Zhihao, Ivakhno Sergii, Stewart Caitlin, et al.

Cell. 2, Volume 148, Number 4, (2012), United States, p.780-91 doi: 10.1016/j.cell.2011.11.065

Systematic identification of genomic markers of drug sensitivity in cancer cells

Garnett, M. J., Edelman E. J., Heidorn S. J., Greenman C. D., Dastur A., Lau King W., Greninger P., Thompson I. R., Luo X., Soares J., et al.

Nature. 03/29, Volume 483, Number 7391, (2012), p.570-575

Insights into hominid evolution from the gorilla genome sequence.

Scally, Aylwyn, Dutheil Julien Y., Hillier LaDeana W., Jordan Gregory E., Goodhead Ian, Herrero Javier, Hobolth Asger, Lappalainen Tuuli, Mailund Thomas, Marques-Bonet Tomas, et al.

Nature. 3, Volume 483, Number 7388, (2012), England, p.169-75 doi: 10.1038/nature10842

Modeling Signaling Networks Using High-throughput Phospho-proteomics

TERFVE, C., and SAEZ-RODRIGUEZ J.

Advances in Experimental Medicine and Biology. Volume 736, (2012), p.19-57

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Lee, B. K., Bhinge A. A., Battenhouse A., McDaniell R. M., Liu Z., Song L., Ni Y., Birney E., Lieb J. D., Furey TS, et al.

Genome research. Volume 22, Number 1, (2012), p.9–24

Poseidon: An information retrieval and extraction system for metagenomic marine science

Radom, M., Rybarczyk A., Kottman R., Formanowicz P., Szachniuk M., Glöckner F. O., REBHOLZ-SCHUHMANN D., and Błażewicz J.

Ecological Informatics. (2012),

Shouldn't enantiomeric purity be included in the'minimum information about a bioactive entity? Response from the MIABE group

Orchard, S., Al-Lazikani B., Bryant S., Clark D., Calder E., DIX I., Engkvist O., Forster M., GAULTON A., Gilson M., et al.

Nature Reviews Drug Discovery. Volume 11, Number 9, (2012), p.730–730 doi:

The Protein Data Bank at 40: reflecting on the past to prepare for the future

Berman, H. M., KLEYWEGT G. J., Nakamura H., and Markley J. L.

Structure . Volume 20, Number 3, (2012), p.391-396 doi: 10.1016/j.str.2012.01.010

Metric distances derived from cosine similarity and Pearson and Spearman correlations

Van Dongen, S., and Enright A. J.

arXiv preprint arXiv:1208.3145. (2012),

European initiative towards quality standards in education and training for discovery, development and use of medicines

Klech, H., Brooksbank C., Price S., Verpillat P., Bühler F. R., Dubois D., Haider N., Johnson C., Lindén H. H., Payton T., et al.

European Journal of Pharmaceutical Sciences. Volume 45, Number 5, (2012), p.515-520

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.

VAQUERIZAS, J. M., Teichmann S. A., and Luscombe N. M.

Methods in molecular biology (Clifton, NJ). Volume 786, (2012), p.3–19

Reorganizing the protein space at the Universal Protein Resource (UniProt)

Consortium, Uniprot, and others

Nucleic Acids Res. Volume 40, (2012), p.D71–D75

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

Engström, P. G., Tommei D., Stricker S. H., Ender C., Pollard S. M., and Bertone P.

Genome Med. Oct, Volume 4, Number 10, (2012), p.76

Taking the next step: Building an Arabidopsis Information Portal

Baerenfaller, K., and Müller H. M.

Plant Cell. Volume 24, Number 6, (2012), p.2248–2256

Toxicology ontology perspectives.

Hardy, Barry, Apic Gordana, Carthew Philip, Clark Dominic, Cook David, Dix Ian, Escher Sylvia, Hastings Janna, Heard David J., Jeliazkova Nina, et al.

ALTEX. Volume 29, Number 2, (2012), p.139–156

Integrating knowledge representation and quantitative modelling in physiology

de Bono, B., and Hunter P.

Biotechnology Journal. Volume 7, Number 8, (2012), p.958–972

A Combined Functional Annotation Score for Non-Synonymous Variants.

Lopes, Margarida C., Joyce Chris, Ritchie Graham R. S., John Sally L., Cunningham Fiona, Asimit Jennifer, and Zeggini Eleftheria

Hum Hered. 1, Volume 73, Number 1, (2012), p.47-51 doi: 10.1159/000334984

State-time spectrum of signal transduction logic models

MACNAMARA, A., TERFVE C., HENRIQUES D., BERNABE B. P., and SAEZ-RODRIGUEZ J.

Physical biology. Aug, Volume 9, Number 4, (2012), p.045003

Ensembl 2012.

Flicek, Paul, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Carvalho-Silva Denise, Clapham Peter, Coates Guy, Fairley Susan, Fitzgerald Stephen, et al.

Nucleic Acids Res. 1, Volume 40, Number 1, (2012), England, p.D84-90 doi: 10.1093/nar/gkr991

Centroids: Gold Standards with Distributional Variations

Lewin, I., Kafkas S., and REBHOLZ-SCHUHMANN D.

Proceedings of the International Conference on Language Resources and Evaluation. (2012),

Validation of protein crystal structures

KLEYWEGT, G. J.

International Tables for Crystallography. Volume F, Issue ch.21.1, Number ch.21.1, (2012), p.649-661 doi: 10.1107/97809553602060000879

Mapping small molecule binding data to structural domains

KRUGER, F. A., Rostom R., and OVERINGTON J. P.

BMC Bioinformatics. Volume 13, Number Suppl 17, (2012), p.S11

WeNMR: Structural Biology on the Grid

Wassenaar, T. A., van Dijk M., Loureiro-Ferreira N., van der Schot G., de Vries S. J., Schmitz C., van der Zwan J., Boelens R., Giachetti A., Ferella L., et al.

Journal of Grid Computing. Volume 10, (2012), p.743-767 doi: 10.1007/s10723-012-9246-z

PRIDE Inspector: a tool to visualize and validate MS proteomics data

Wang, R., Fabregat A., R{\'ıos D., Ovelleiro D., Foster J.M., Côté R.G., Griss J., Csordas A., Perez-Riverol Y., Reisinger F., et al.

Nature biotechnology. Volume 30, Number 2, (2012), p.135–137

PRIDE: Quality control in a proteomics data repository

Csordas, A., Ovelleiro D., Wang R., Foster J.M., R{\'ıos D., Vizcaino J.A., and Hermjakob H.

Database: The Journal of Biological Databases and Curation. Volume 2012, (2012),

Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification.

Ballester, Pedro J., Mangold Martina, Howard Nigel I., Robinson Richard L. Marchese, Abell Chris, Blumberger Jochen, and Mitchell John B. O.

J R Soc Interface. Dec, Volume 9, Number 77, (2012), p.3196–3207 doi: 10.1098/rsif.2012.0569

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and Next Generation Sequencing

Sipos, B., Massingham T., Stütz A. M., and Goldman N.

PLoS ONE. Volume 7, (2012), p.e43359

MyDas, an Extensible Java DAS Server

Salazar, G. A., Garc{\'ıa L. J., Jones P., Jimenez R.C., Quinn A. F., Jenkinson A.M., Mulder N., Martin M., Hunter S., and Hermjakob H.

PLOS ONE. Volume 7, Number 9, (2012), p.e44180

Probing the diverse landscape of protein flexibility and binding

Marsh, J. A., Teichmann S. A., and Forman-Kay J. D.

Current Opinion in Structural Biology. (2012),

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Martincorena, Iñigo, Seshasayee Aswin S. N., and Luscombe Nicholas M.

Nature. Volume 485, Number 7396, (2012), p.95–98

Accessing and using chemical property databases.

HASTINGS, J., Josephs Z., and Steinbeck C.

Methods in molecular biology (Clifton, NJ). Volume 929, (2012), p.193

InterPro in 2011: new developments in the family and domain prediction database

HUNTER, S., Jones P., Mitchell A., Apweiler R., Attwood T. K., Bateman A., Bernard T., Binns D., Bork P., BURGE S., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D306–D312

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

Gaudet, P., ARIGHI C., Bastian F., Bateman A., Blake J. A., Cherry M. J., D’Eustachio P., Finn R., Giglio M., Hirschman L., et al.

Database: The Journal of Biological Databases and Curation. Volume 2012, (2012), doi:

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Schneider, Maria V., Walter Peter, Blatter Marie-Claude, Watson James, Brazas Michelle D., Rother Kristian, Budd Aidan, Via Allegra, van Gelder Celia W. G., Jacob Joachim, et al.

Briefings in bioinformatics. Volume 13, Number 3, (2012), p.383–389

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma.

Nelson, Andrew C., Pillay Nischalan, Henderson Stephen, Presneau Nadège, Tirabosco Roberto, Halai Dina, Berisha Fitim, Flicek Paul, Stemple Derek L., Stern Claudio, et al.

J Pathol. 7, Volume 228, Number 3, (2012), England, p.274-85 doi: 10.1002/path.4082

Graph2tab, a library to convert experimental workflow graphs into tabular formats

BRANDIZI, M., KURBATOVA N., Sarkans U., and Rocca-Serra P.

Bioinformatics. Volume 28, Number 12, (2012), p.1665-1667

A systematic survey of loss-of-function variants in human protein-coding genes.

MacArthur, Daniel G., Balasubramanian Suganthi, Frankish Adam, Huang Ni, Morris James, Walter Klaudia, Jostins Luke, Habegger Lukas, Pickrell Joseph K., Montgomery Stephen B., et al.

Science. 2, Volume 335, Number 6070, (2012), United States, p.823-8 doi: 10.1126/science.1215040

A Computational Study on Altered Theta-Gamma Coupling during Learning and Phase Coding

Zhang, X., Kendrick K. M., Zhou H., ZHAN Y., and Feng J.

PLoS ONE. 06/21, Volume 7, Number 6, (2012), p.e36472

Analysis of variation at transcription factor binding sites in Drosophila and humans

Spivakov, M., Akhtar J., Kheradpour P., Beal K., Girardot C., Koscielny G., Herrero J., Kellis M., Furlong E. E. M., and Birney E.

Genome biology. Volume 13, Number 9, (2012), p.R49

The BioSample Database (BioSD) at the European Bioinformatics Institute

GOSTEV, M., FAULCONBRIDGE A., BRANDIZI M., FERNANDEZ-BANET J., Sarkans U., BRAZMA A., and Parkinson H.

Nucleic acids research. Nov 16, Volume 40, Number Database issue, (2012), p.D64-D70

Protein Structure Validation Using Side-Chain Chemical Shifts

Sahakyan, Aleksandr B., Cavalli Andrea, Vranken Wim F., and Vendruscolo Michele

The Journal of physical chemistry. B. Volume 116, Number 16, (2012), p.4754–4759

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

Vizcaino, J.A., Côté R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., Griss J., Alpi E., Birim M., Contell J., et al.

Nucleic Acids Research. (2012),

Current challenges in genome annotation through structural biology and bioinformatics.

Furnham, Nicholas, de Beer Tjaart A. P., and Thornton Janet M.

Curr Opin Struct Biol. Oct, Volume 22, Number 5, (2012), p.594–601 doi: 10.1016/j.sbi.2012.07.005

Bioimage informatics: a new category in Bioinformatics

Peng, H., Bateman A., Valencia A., and Wren J. D.

Bioinformatics. Volume 28, Number 8, (2012), p.1057–1057

Open data for drug discovery: learning from the biological community

HERSEY, A., Senger S., and OVERINGTON J. P.

Future medicinal chemistry. Oct, Volume 4, Number 15, (2012), p.1865-1867

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

Stegle, O., Parts L., Piipari M., Winn J., and Durbin R.

Nature protocols. Volume 7, Number 3, (2012), p.500–507

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.

Schmidt, Dominic, Schwalie Petra C., Wilson Michael D., Ballester Benoit, Gonçalves Angela, Kutter Claudia, Brown Gordon D., Marshall Aileen, Flicek Paul, and Odom Duncan T.

Cell. 1, Volume 148, Number 1-2, (2012), United States, p.335-48 doi: 10.1016/j.cell.2011.11.058

Integrating literature-constrained and data-driven inference of signalling networks

EDUATI, F., Rivas De Las J., Camillo Di B., Toffolo G., and SAEZ-RODRIGUEZ J.

Bioinformatics (Oxford, England). Sep 15, Volume 28, Number 18, (2012), p.2311-2317

The 1000 Genomes Project: data management and community access.

Clarke, Laura, Zheng-Bradley Xiangqun, Smith Richard, Kulesha Eugene, Xiao Chunlin, Toneva Iliana, Vaughan Brendan, Preuss Don, Leinonen Rasko, Shumway Martin, et al.

Nat Methods. Volume 9, Number 5, (2012), p.459-462 doi: 10.1038/nmeth.1974

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

TERFVE, C., COKELAER T., HENRIQUES D., MACNAMARA A., GONCALVES E., Morris M. K., IERSEL MV, Lauffenburger D. A., and SAEZ-RODRIGUEZ J.

BMC systems biology. Oct 18, Volume 6, (2012), p.133-0509-6-133

Major submissions tool developments at the European nucleotide archive

Amid, C., Birney E., Bower L., Cerdeño-Tárraga A., Cheng Y., Cleland I., Faruque N., Gibson R., Goodgame N., Hunter C., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D43–D47

Systems Biology and Bioinformatics in Aging Research: A Workshop Report

Fuellen, G., Dengjel J., Hoeflich A., Hoeijmakers J., Kestler H. A., Kowald A., Priebe S., REBHOLZ-SCHUHMANN D., Schmeck B., Schm{\'ıtz U., et al.

Rejuvenation Research. Number ja, (2012),

Annotating Human P-Glycoprotein Bioassay Data

Zdrazil, B., Pinto M., Vasanthanathan P., Williams A. J., Balderud L. Z., Engkvist O., Chichester C., HERSEY A., OVERINGTON J. P., and Ecker G. F.

Molecular Informatics. Volume 31, Number 8, (2012), p.599–609

OMERO: flexible, model-driven data management for experimental biology

Allan, C., Burel J. M., Moore J., Blackburn C., Linkert M., Loynton S., Macdonald D., Moore W. J., Neves C., Patterson A., et al.

Nature Methods. Volume 9, Number 3, (2012), p.245-253 doi: 10.1038/nmeth.1896

The HUPO initiative on Model Organism Proteomes, iMOP

Jones, A. M. E., Aebersold R., Ahrens C. H., Apweiler R., Baerenfaller K., Baker M., Bendixen E., Briggs S., Brownridge P., Brunner E., et al.

Proteomics. Volume 12, Number 3, (2012), p.340–345

Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines

Davis, M. P. A., ABREU-GOODGER C., Van Dongen S., Lu D., Tate P. H., BARTONICEK N., Kutter C., Liu P., Skarnes W. C., Enright A. J., et al.

PloS one. Volume 7, Number 8, (2012), p.e41762

Experimental design in phylogenetics: testing predictions from expected information

San Mauro, D., Gower D. J., Cotton J. A., Zardoya R., Wilkinson M., and Massingham T.

Systematic Biology. Volume 61, (2012), p.661-674

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

Levy, E. D., De S., and Teichmann S. A.

Proceedings of the National Academy of Sciences. Volume 109, Number 50, (2012), p.20461–20466

FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.

Furnham, Nicholas, Sillitoe Ian, Holliday Gemma L., Cuff Alison L., Rahman Syed A., Laskowski Roman A., Orengo Christine A., and Thornton Janet M.

Nucleic Acids Res. Jan, Volume 40, Number Database issue, (2012), p.D776–D782 doi: 10.1093/nar/gkr852

Bioinformatics meets user-centred design: a perspective

Pavelin, K., Cham J. A., De Matos P., Brooksbank C., Cameron G., and Steinbeck C.

PLoS computational biology. Volume 8, Number 7, (2012), p.e1002554 doi:

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Schneider, M. V., Walter P., Blatter M. C., Watson J., Brazas M. D., Rother K., Budd A., Via A., van Gelder C. W. G., Jacob J., et al.

Briefings in bioinformatics. Volume 13, Number 3, (2012), p.383–389

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

Dasmahapatra, K. K., Walters J. R., Briscoe A. D., Davey J. W., Whibley A., Nadeau N. J., Zimin A. V., Hughes D. S. T., Ferguson L. C., Martin S. H., et al.

Nature. Volume 487, (2012), p.94–98

Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases

Lahti, L., Torrente A., Elo L. L., BRAZMA A., and Rung J.

arXiv preprint arXiv:1212.5932. (2012),

Food for thought ... A toxicology ontology roadmap.

Hardy, Barry, Apic Gordana, Carthew Philip, Clark Dominic, Cook David, Dix Ian, Escher Sylvia, Hastings Janna, Heard David J., Jeliazkova Nina, et al.

ALTEX. Volume 29, Number 2, (2012), p.129–137

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks

Buljan, M., Chalancon G., Eustermann S., Wagner G. P., Fuxreiter M., Bateman A., and Babu M. M.

Molecular cell. Volume 46, Number 6, (2012), p.871–883

Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells

Haudek-Prinz, V., Klepeisz P., Slany A., Griss J., Meshcheryakova A., Paulitschke V., Mitulovic G., Stöckl J., and Gerner C.

Journal of Proteomics. (2012),

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Goncalves, Angela, Leigh-Brown Sarah, Thybert David, Stefflova Klara, Turro Ernest, Flicek Paul, Brazma Alvis, Odom Duncan T., and Marioni John C.

Genome Res. 8, Volume 22, Number 12, (2012), United States, p.2376-84 doi: 10.1101/gr.142281.112

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Kirouac, D. C., SAEZ-RODRIGUEZ J., Swantek J., Burke J. M., Lauffenburger D. A., and Sorger P. K.

BMC systems biology. May 1, Volume 6, (2012), p.29

Integrative annotation of chromatin elements from ENCODE data.

Hoffman, Michael M., Ernst Jason, Wilder Steven P., Kundaje Anshul, Harris Robert S., Libbrecht Max, Giardine Belinda, Ellenbogen Paul M., Bilmes Jeffrey A., Birney Ewan, et al.

Nucleic Acids Res. 12, (2012), doi: 10.1093/nar/gks1284

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

JUTY, N., NOVERE LE N., and LAIBE C.

Nucleic acids research. Dec 2, Volume 40(1):D580-6, Number Database issue, (2012), p.D580-D583

Introductory editorial

Pestian, J. P.

Biomedical Informatics Insights. Volume 5, Number Suppl. 1, (2012), p.1

Cheminformatics

Wegner, J. K., Sterling A., Guha R., Bender A., Faulon J. L., HASTINGS J., O'Boyle N., OVERINGTON J., Van Vlijmen H., and Willighagen E.

Communications of the ACM. Volume 55, Number 11, (2012), p.65–75

An integrated encyclopedia of DNA elements in the human genome

ENCODE Project Consortium, The, Dunham I., Birney E., Lajoie B. R., Sanyal A., Dong X., Greven M., Lin X., Wang J., Whitfield T. W., et al.

(2012),

Outcome of the First Electron Microscopy Validation Task Force Meeting

Henderson, R., Sali A., Baker M. L., Carragher B., Devkota B., Downing K. H., Egelman E. H., Feng Z., Frank J., Grigorieff N., et al.

Structure . Volume 20, Number 2, (2012), p.205-214 doi: 10.1016/j.str.2011.12.014

Error-correcting properties of the SOLiD Exact Call Chemistry

Massingham, T., and Goldman N.

BMC Bioinformatics. Volume 13, (2012), p.145

The PRIDE Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

Côté, R.G., Griss J., Dianes J.A., Wang R., Wright J.C., van den Toorn H. W. P., van Breukelen B., Heck A.J.R., Hulstaert N., Martens L., et al.

Molecular & Cellular Proteomics. (2012),

The UniProt-GO annotation database in 2011

Dimmer, E.C., Huntley R.P., Alam-Faruque Y., Sawford T., O'Donovan C., Martin M. J., Bely B., Browne P., Chan W.M., Eberhardt R., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D565–D570 doi:

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Kersey, P. J., Staines D. M., Lawson D., Kulesha E., Derwent P., Humphrey J. C., Hughes D. S. T., Keenan S., Kerhornou A., Koscielny G., et al.

Nucleic Acids Research. Volume 40, Number D1, (2012), p.D91–D97

m: Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence

Reimand, Jüri, Aun Anu, Vilo Jaak, Vaquerizas Juan, Sedman Juhan, and Luscombe Nicholas

Genome Biology. Volume 13, Number 6, (2012), p.R55

Structure-based classification and ontology in chemistry.

Hastings, Janna, Magka Despoina, Batchelor Colin, Duan Lian, Stevens Robert, Ennis Marcus, and Steinbeck Christoph

Journal of cheminformatics. Volume 4, (2012), p.8 doi: 10.1186/1758-2946-4-8

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors

Rawlings, N. D., Barrett A. J., and Bateman A.

Nucleic acids research. Volume 40, Number D1, (2012), p.D343–D350

Paralogous annotation of disease-causing variants in long QT syndrome genes.

Ware, James S., Walsh Roddy, Cunningham Fiona, Birney Ewan, and Cook Stuart A.

Hum Mutat. 5, Volume 33, Number 8, (2012), p.1188-1191 doi: 10.1002/humu.22114

Toxicology ontology perspectives.

Hardy, B., Apic G., Carthew P., Clark D., Cook D., DIX I., Escher S., HASTINGS J., Heard D. J., Jeliazkova N., et al.

Altex. Volume 29, Number 2, (2012), p.139

Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines.

Davis, Matthew P. A., Abreu-Goodger Cei, van Dongen Stijn, Lu Dong, Tate Peri H., Bartonicek Nenad, Kutter Claudia, Liu Pentao, Skarnes William C., Enright Anton J., et al.

PLoS One. Volume 7, Number 8, (2012), United States, p.e41762 doi: 10.1371/journal.pone.0041762

Software support for SBGN maps: SBGN-ML and LibSBGN

IERSEL, VAN M. P., Villeger A. C., Czauderna T., Boyd S. E., Bergmann F. T., Luna A., Demir E., Sorokin A., Dogrusoz U., Matsuoka Y., et al.

Bioinformatics (Oxford, England). May 10, Volume 28, Number 15, (2012), p.2016-2021

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Wang, J., Zhuang J., Iyer S., Lin X. Y., Whitfield T. W., Greven M. C., Pierce B. G., Dong X., Kundaje A., Cheng Y., et al.

Genome research. Volume 22, Number 9, (2012), p.1798–1812

PDBe: Protein Data Bank in Europe

VELANKAR, S., ALHROUB Y., BEST C., CABOCHE S., CONROY M. J., DANA J. M., MONTECELO FERNANDEZ M. A., GINKEL VAN G., Golovin A., GORE S. P., et al.

Nucleic Acids Research. Volume 40 , Issue Database issue, Number Database issue, (2012), p.D445-D452 doi: 10.1093/nar/gkr998

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)| Macquarie University ResearchOnline

Kinsinger, C. R., Apffel J., Gorman J., Grimm R., Hancock W., Hermjakob H., Horn D., Hunter C., Kolar P., Kraus H.J., et al.

(2012),

Tools for mapping high-throughput sequencing data

Fonseca, NA, Rung J, Brazma A, and Marioni JC

Bioinformatics. Volume 28, (2012), p.3169–3177 doi: 10.1093/bioinformatics/bts605

The EBI enzyme portal

Alcántara, R., Onwubiko J., Cao H., De Matos P., Cham J.A., Jacobsen J., Holliday G.L., Fischer J.D., Rahman S.A., Jassal B., et al.

Nucleic Acids Research. (2012),

DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

Charoensawan, V., Janga S. C., Bulyk M. L., Babu M. M., and Teichmann S. A.

Molecular Cell. Volume 47, Number 2, (2012), p.183–192

MageComet—web application for harmonizing existing large-scale experiment descriptions

Xue, V., BURDETT T., Lukk M., TAYLOR J., BRAZMA A., and Parkinson H.

Bioinformatics. Volume 28, Number 10, (2012), p.1402–1403

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

Hastings, Janna, De Matos Paula, Dekker Adriano, Ennis Marcus, Harsha Bhavana, Kale Namrata, Muthukrishnan Venkatesh, Owen Gareth, Turner Steve, Williams Mark, et al.

Nucleic Acids Research. Volume 41, Number D1, (2012), p.D456–D463 doi: 10.1093/nar/gks1146

Making your database available through Wikipedia: the pros and cons

Finn, R. D., Gardner P. P., and Bateman A.

Nucleic acids research. Volume 40, Number D1, (2012), p.D9–D12

The Sequence Read Archive: explosive growth of sequencing data

Kodama, Y., Shumway M., Leinonen R., and International Nucleotide Sequence Database Collaboration

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D54-6 doi:

ChEMBL: a large-scale bioactivity database for drug discovery

GAULTON, A., BELLIS L. J., BENTO A. P., CHAMBERS J., DAVIES M., HERSEY A., LIGHT Y., MCGLINCHEY S., Michalovich D., Al-Lazikani B., et al.

Nucleic acids research. Sep 23, Volume 40, Number Database issue, (2012), p.D1100-D1107

ShapePheno: unsupervised extraction of shape phenotypes from biological image collections

Karaletsos, T., Stegle O., Dreyer C., Winn J., and Borgwardt K. M.

Bioinformatics. Volume 28, Number 7, (2012), p.1001–1008

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.

Löytynoja, Ari, Vilella Albert J., and Goldman Nick

Bioinformatics. 7, Volume 28, Number 13, (2012), England, p.1684-91 doi: 10.1093/bioinformatics/bts198

De novo assembly and genotyping of variants using colored de Bruijn graphs.

Iqbal, Zamin, Caccamo Mario, Turner Isaac, Flicek Paul, and McVean Gil

Nat Genet. Volume 44, Number 2, (2012), United States, p.226-32 doi: 10.1038/ng.1028

Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network

Serra-Musach, J., Aguilar H., IORIO F., Comellas F., Berenguer A., Brunet J., SAEZ-RODRIGUEZ J., and Pujana M. A.

Integrative biology : quantitative biosciences from nano to macro. Sep, Volume 4, Number 9, (2012), p.1038-1048

Ensembl 2012

Flicek, P., Amode M. R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., Fitzgerald S., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D84–D90

Automatically transforming pre-to post-composed phenotypes: EQ-lising HPO and MP

Oellrich, A., Grabmüller C., and REBHOLZ-SCHUHMANN D.

GI WORKGROUP “ONTOLOGIES IN BIOMEDICINE AND LIFE SCIENCES”(OBML). (2012),

The IntAct molecular interaction database in 2012

Kerrien, S., Aranda B., Breuza L., Bridge A., Broackes-Carter F., Chen C., Duesbury M., Dumousseau M., Feuermann M., Hinz U., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D841–D846

The making of ENCODE: Lessons for big-data projects

Birney, E.

Nature. Volume 489, Number 7414, (2012), p.49–51

MageComet–web application for harmonizing existing large-scale experiment descriptions

Xue, V., BURDETT T., Lukk M., TAYLOR J., BRAZMA A., and Parkinson H.

Bioinformatics (Oxford, England). May 15, Volume 28, Number 10, (2012), p.1402-1403

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

Reisinger, F., Krishna R., Ghali F., R{\'ıos D., Hermjakob H., Antonio Vizcaino J., and Jones A. R.

Proteomics. Volume 12, Number 6, (2012), p.790–794

MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs

Lu, D., Davis M. P. A., ABREU-GOODGER C., Wang W., Campos L. S., Siede J., Vigorito E., Skarnes W. C., Dunham I., Enright A. J., et al.

PloS one. Volume 7, Number 8, (2012), p.e40938

Evolution of oligomeric state through geometric coupling of protein interfaces

Perica, T., Chothia C., and Teichmann S. A.

Proceedings of the National Academy of Sciences. Volume 109, Number 21, (2012), p.8127–8132

Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.

Furnham, Nicholas, Sillitoe Ian, Holliday Gemma L., Cuff Alison L., Laskowski Roman A., Orengo Christine A., and Thornton Janet M.

PLoS Comput Biol. Volume 8, Number 3, (2012), p.e1002403 doi: 10.1371/journal.pcbi.1002403

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Schneider, M. V., Walter P., Blatter M. C., Watson J., Brazas M. D., Rother K., Budd A., Via A., van Gelder C. W., Jacob J., et al.

Briefings in bioinformatics. Volume 13, Number 3, (2012), p.383-389

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes

Teichmann, S. A., Wigge P. A., and Charoensawan V.

Cell Cycle. Volume 11, Number 24, (2012), p.0–1

Analysis of the bread wheat genome using whole-genome shotgun sequencing

Brenchley, R., Spannagl M., Pfeifer M., Barker G. L. A., D’Amore R., Allen A. M., McKenzie N., Kramer M., Kerhornou A., Bolser D., et al.

Nature. Volume 491, Number 7426, (2012), p.705–710

Reuse of public genome-wide gene expression data

Rung, J., and BRAZMA A.

Nature Reviews Genetics. Volume 14, Number 2, (2012), p.89–99

Rhea–a manually curated resource of biochemical reactions.

Alcantara, Rafael, Axelsen Kristian B., Morgat Anne, Belda Eugeni, Coudert Elisabeth, Bridge Alan, Cao Hong, De Matos Paula, Ennis Marcus, Turner Steve, et al.

Nucleic Acids Research. jan, Volume 40, Number Database issue, (2012), p.D754–60 doi: 10.1093/nar/gkr1126

The YARHG Domain: An Extracellular Domain in Search of a Function

Coggill, P., and Bateman A.

PloS one. Volume 7, Number 5, (2012), p.e35575

Molecular interaction databases

Orchard, S.

Proteomics. Volume 12, Number 10, (2012), p.1656–1662

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules.

Faure, Andre J., Schmidt Dominic, Watt Stephen, Schwalie Petra C., Wilson Michael D., Xu Huiling, Ramsay Robert G., Odom Duncan T., and Flicek Paul

Genome Res. 10, Volume 22, Number 11, (2012), United States, p.2163-75 doi: 10.1101/gr.136507.111

Analyses of pig genomes provide insight into porcine demography and evolution.

Groenen, Martien A. M., Archibald Alan L., Uenishi Hirohide, Tuggle Christopher K., Takeuchi Yasuhiro, Rothschild Max F., Rogel-Gaillard Claire, Park Chankyu, Milan Denis, Megens Hendrik-Jan J., et al.

Nature. 11, Volume 491, Number 7424, (2012), England, p.393-8 doi: 10.1038/nature11622

Construction of large signaling pathways using an adaptive perturbation approach with phosphoproteomic data

Melas, I. N., Mitsos A., Messinis D. E., Weiss T. S., SAEZ-RODRIGUEZ J., and Alexopoulos L. G.

Molecular bioSystems. Apr 3, Volume 8, Number 5, (2012), p.1571-1584 doi:

MELTING, a flexible platform to predict the melting temperatures of nucleic acids

DUMOUSSEAU, M., Rodriguez N., JUTY N., and NOVERE N. L.

BMC bioinformatics. May 16, Volume 13, (2012), p.101

Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts

Camilloni, C., Simone De A., VRANKEN W. F., and Vendruscolo M.

Biochemistry. Volume 51, Number 11, (2012), p.2224-2231 doi: 10.1021/bi3001825

The future of DNA sequence archiving

Cochrane, G., Cook C. E., and Birney E.

GigaScience. Volume 1, Number 1, (2012), p.2

Automatic recognition of conceptualization zones in scientific articles and two life science applications

Liakata, M., Saha S., Dobnik S., Batchelor C., and REBHOLZ-SCHUHMANN D.

Bioinformatics. Volume 28, Number 7, (2012), p.991–1000

Structure of the signal transduction protein TRAP (target of RNAIII-activating protein)

Henrick, K., and Hirshberg M.

Acta Crystallographica Section F. Volume 68, Number Part 7, (2012), p.744-750 doi: 10.1107/S1744309112020167

Open data for drug discovery: learning from the biological community

HERSEY, A., Senger S., and OVERINGTON J. P.

Future Med. Chem.. Volume 4, Number 15, (2012), p.1865–1867

Implementing an X-ray validation pipeline for the Protein Data Bank

GORE, S., VELANKAR S., and KLEYWEGT G. J.

Acta Crystallographica Section D. Volume 68, Number Pt 4, (2012), p.478-483 doi: 10.1107/S0907444911050359

The effects of alignment error and alignment filtering on the sitewise detection of positive selection

Jordan, G., and Goldman N.

Molecular Biology and Evolution. Volume 29, (2012), p.1125-1139

All your base: a fast and accurate probabilistic approach to base calling

Massingham, T., and Goldman N.

Genome Biology. Volume 13, (2012), p.R13

The HUPO initiative on Model Organism Proteomes, iMOP| Macquarie University ResearchOnline

Jones, A. M. E., Aebersold R., Daube M., Deutsch E.W., Grossniklaus U., Heazlewood J., Hengartner M. O., Hermjakob H., Jovanovic M., Lawless C., et al.

(2012),

MACiE: exploring the diversity of biochemical reactions.

Holliday, Gemma L., Andreini Claudia, Fischer Julia D., Rahman Syed Asad, Almonacid Daniel E., Williams Sophie T., and Pearson William R.

Nucleic Acids Res. Jan, Volume 40, Number Database issue, (2012), p.D783–D789 doi: 10.1093/nar/gkr799

Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome

Albers, C.A., Paul D.S., Schulze H., Freson K., Stephens J.C., Smethurst P.A., Jolley J.D., Cvejic A., Kostadima M., Bertone P., et al.

Nat Genet. Feb, Volume 44, Number 4, (2012), p.435–439

WormBase 2012: more genomes, more data, new website

Yook, K., Harris T. W., Bieri T., Cabunoc A., Chan J., Chen W. J., Davis P., de la Cruz N., Duong A., Fang R., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D735–D741

The NSL Complex Regulates Housekeeping Genes in Drosophila

Lam, Kin Chung, Mühlpfordt Friederike, Vaquerizas Juan M., Raja Sunil Jayaramaiah, Holz Herbert, Luscombe Nicholas M., Manke Thomas, and Akhtar Asifa

PLoS Genetics. Volume 8, Number 6, (2012), p.e1002736

Natural product-likeness score revisited: an open-source, open-data implementation.

Jayaseelan, Kalai Vanii, Moreno Pablo, Truszkowski Andreas, Ertl Peter, and Steinbeck Christoph

BMC Bioinformatics. Volume 13, (2012), p.106 doi: 10.1186/1471-2105-13-106

Metagenomic analysis: the challenge of the data bonanza

Hunter, C. I., Mitchell A., Jones P., MCANULLA C., Pesseat S., Scheremetjew M., and HUNTER S.

Briefings in Bioinformatics. (2012),

Maps for the world of genomic medicine: The 2011 CSHL Personal Genomes Meeting.

Zheng-Bradley, Xiangqun, and Flicek Paul

Hum Mutat. 1, Volume 33, Number 6, (2012), p.1016-1019 doi: 10.1002/humu.22024

Food for thought... A toxicology ontology roadmap.

Hardy, B., Apic G., Carthew P., Clark D., Cook D., DIX I., Escher S., HASTINGS J., Heard D. J., Jeliazkova N., et al.

Altex. Volume 29, Number 2, (2012), p.129

MiR-25 Regulates Wwp2 and Fbxw7 and Promotes Reprogramming of Mouse Fibroblast Cells to iPSCs.

Lu, Dong, Davis Matthew P. A., Abreu-Goodger Cei, Wang Wei, Campos Lia S., Siede Julia, Vigorito Elena, Skarnes William C., Dunham Ian, Enright Anton J., et al.

PLoS One. Volume 7, Number 8, (2012), United States, p.e40938 doi: 10.1371/journal.pone.0040938

Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII

STEFAN, M. I., MARSHALL D. P., and NOVERE LE N.

PloS one. Volume 7, Number 1, (2012), p.e29406

Integrative annotation of chromatin elements from ENCODE data

Hoffman, M. M., Ernst J., Wilder S. P., Kundaje A., Harris R. S., Libbrecht M., Giardine B., Bilmes J. A., Birney E., Hardison R. C., et al.

Genome Res. (2012),

Observ-OM and Observ-TAB: Universal syntax solutions for the integration, search and exchange of phenotype and genotype information

ADAMUSIAK, T., Parkinson H., Muilu J., Roos E., van der Velde K. J., Thorisson1 G. A., Byrne M., Pang C., Gollapudi S., Ferretti V., et al.

Human mutation. Mar 13, Volume 33, (2012), p.873

Data management challenges in three-dimensional EM

PATWARDHAN, A., Carazo J. M., Carragher B., Henderson R., Heymann J. B., Hill E., Jensen G. J., LAGERSTEDT I., Lawson C. L., Ludtke S. J., et al.

Nature Structural & Molecular Biology. Volume 19, Number 12, (2012), p.1203-1207 doi: 10.1038/nsmb.2426

Toward interoperable bioscience data

Sansone, S.A., Rocca-Serra P., Field D., Maguire E., Taylor C., Hofmann O., Fang H., Neumann S., Tong W., Amaral-Zettler L., et al.

Nature genetics. Volume 44, Number 2, (2012), p.121–126

Protein Structure Validation Using Side-Chain Chemical Shifts

Sahakyan, A. B., Cavalli A., VRANKEN W. F., and Vendruscolo M.

The Journal of Physical Chemistry B. Volume 116, Number 16, (2012), p.4754-4759 doi: 10.1021/jp2122054

Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Orchard, S., Kerrien S., Abbani S., Aranda B., Bhate J., Bidwell S., Bridge A., Briganti L., Brinkman F., Cesareni G., et al.

Nature Methods. Volume 9, Number 6, (2012), p.626–626

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

Milacic, M., Haw R., Rothfels K., Wu G., Croft D., Hermjakob H., D'Eustachio P., and Stein L.

Cancers. Volume 4, Number 4, (2012), p.1180–1211

Bioinformatic methods for species-specific metabolome inference

Moreno, Pablo

nov, (2012), Cambridge,

2011

Retroactivity as a Criterion to Define Modules in Signaling Networks

SAEZ-RODRIGUEZ, J., Conzelmann H., Ederer M., and Gilles E. D.

Design and Analysis of Biomolecular Circuits. (2011), p.139-159

Efficient inference in matrix-variate Gaussian models with iid observation noise

Stegle, O., Lippert C., Mooij J., Lawrence N., and Borgwardt K.

Advances in Neural Information processing Systems. 2011, (2011), doi:

Detecting low-complexity unobserved causes

Janzing, D., Sgouritsa E., Stegle O., Peters J., and Schölkopf B.

Uncertainty in Artificial Intelligence. 2011, (2011), doi:

Celebrating structural biology.

Thornton, Janet M.

Nat Struct Mol Biol. Dec, Volume 18, Number 12, (2011), p.1304–1316

Ensembl BioMarts: a hub for data retrieval across taxonomic space

Kinsella, R. J., Kähäri A., Haider S., Zamora J., Proctor G., Spudich G., Almeida-King J., Staines D., Derwent P., Kerhornou A., et al.

Database: the journal of biological databases and curation. Volume 2011, (2011),

Minimum information about a bioactive entity (MIABE)

Orchard, Sandra, Al-Lazikani Bissan, Bryant Steve, Clark Dominic, Calder Elizabeth, Dix Ian, Engkvist Ola, Forster Mark, Gaulton Anna, Gilson Michael, et al.

Nature Reviews Drug Discovery. Volume 10, Number 9, (2011), p.661–669 doi: 10.1038/nrd3503

Deciphering the colon cancer genes–report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010.

Kohonen-Corish, Maija R. J., Macrae Finlay, Genuardi Maurizio, Aretz Stefan, Bapat Bharati, Bernstein Inge T., Burn John, Cotton Richard G. H., den Dunnen Johan T., Frebourg Thierry, et al.

Hum Mutat. 4, Volume 32, Number 4, (2011), United States, p.491-4 doi: 10.1002/humu.21450

A guide to UniProt for protein scientists

O’DONOVAN, C., and Apweiler R.

Methods Mol. Biol. Volume 694, (2011), p.25–35 doi:

Setting the standards for signal transduction research

SAEZ-RODRIGUEZ, J., Alexopoulos L. G., and Stolovitzky G.

Science signaling. Feb 15, Volume 4, Number 160, (2011), p.pe10

A genome-wide metabolic QTL analysis in europeans implicates two Loci shaped by recent positive selection

Nicholson, G., Rantalainen M., Li J. V., Maher A. D., Malmodin D., Ahmadi K. R., Faber J. H., Barrett A., Min J. L., Rayner N. W., et al.

PLoS Genetics. Volume 7, Number 9, (2011),

A high-resolution map of human evolutionary constraint using 29 mammals

Lindblad-Toh, K., Garber M., Zuk O., Lin M. F., Parker B. J., Washietl S., Kheradpour P., Ernst J., Jordan G., Mauceli E., et al.

Nature. Volume 478, Number 7370, (2011), p.476–482

mzML—a community standard for mass spectrometry data

Martens, L., Chambers M., Sturm M., Kessner D., Levander F., Shofstahl J., Tang W. H., Römpp A., Neumann S., Pizarro A. D., et al.

Molecular & Cellular Proteomics. Volume 10, Number 1, (2011),

Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum’s relatives infecting great apes

Blanquart, S., and Gascuel O.

BMC Evolutionary Biology. Volume 11, (2011), p.70

Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data

Hu, M., Ayub Q., GUERRA-ASSUNÇÃO J. A., Long Q., Ning Z., Huang N., Romero I. G., Mamanova L., Akan P., Liu X., et al.

Human Genetics. (2011), p.1–10

Towards BioDBcore: a community-defined information specification for biological databases

Gaudet, P., Bairoch A., Field D., Sansone S. A., TAYLOR C., Attwood T. K., Bateman A., Blake J. A., Bult C. J., Cherry J. M., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D7

Parts and wholes, shapes and holes in living beings

HASTINGS, J., Batchelor C., and Schulz S.

Proceedings of the first SHAPES workshop. (2011),

The Genomic Standards Consortium

Field, D., Amaral-Zettler L., Cochrane G., Cole J. R., Dawyndt P., Garrity G. M., Gilbert J., Glockner F. O., Hirschman L., KARSCH-MIZRACHI I., et al.

PLoS Biol. Volume 9, Number 6, (2011), p.e1001088

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet, Pascale, Bairoch Amos, Field Dawn, Sansone Susanna-Assunta A., Taylor Chris, Attwood Teresa K., Bateman Alex, Blake Judith A., Bult Carol J., Cherry Michael J., et al.

Database (Oxford). Volume 2011, (2011), England, p.baq027 doi: 10.1093/database/baq027

Mapping copy number variation by population-scale genome sequencing.

Mills, Ryan E., Walter Klaudia, Stewart Chip, Handsaker Robert E., Chen Ken, Alkan Can, Abyzov Alexej, Yoon Seungtai Chris, Ye Kai, Cheetham Keira R., et al.

Nature. 2, Volume 470, Number 7332, (2011), England, p.59-65 doi: 10.1038/nature09708

The Protein Data Bank in Europe (PDBe): bringing structure to biology

VELANKAR, S., and KLEYWEGT G. J.

Acta Crystallographica Section D. Volume 67, (2011), p.324-330 doi: 10.1107/S090744491004117X

DAS Writeback: a collaborative annotation system

Salazar, G. A., Jimenez R.C., Garcia A., Hermjakob H., Mulder N., and Blake E.

BMC bioinformatics. Volume 12, Number 1, (2011), p.143

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

Parkinson, H., Sarkans U., KOLESNIKOV N., ABEYGUNAWARDENA N., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., HOLLOWAY E., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D1002–D1004

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Schneider, M. V., Walter P., Blatter M. C., Watson J., Brazas M. D., Rother K., Budd A., Via A., van Gelder C. W. G., Jacob J., et al.

Briefings in Bioinformatics. (2011),

Analysis and simulation of gene expression profiles in pure and mixed cell populations

Hebenstreit, D., and Teichmann S. A.

Physical biology. Volume 8, Number 3, (2011), p.035013

A pipeline for RNA-seq data processing and quality assessment

GONCALVES, A., TIKHONOV A., BRAZMA A., and KAPUSHESKY M.

Bioinformatics. Volume 27, Number 6, (2011), p.867–869

Exome sequencing identifies a missense mutation in Isl1 associated with low penetrance otitis media in dearisch mice.

Hilton, Jennifer M., Lewis Morag A., Grati M'hamed, Ingham Neil, Pearson Selina, Laskowski Roman A., Adams David J., and Steel Karen P.

Genome Biol. Volume 12, Number 9, (2011), p.R90 doi: 10.1186/gb-2011-12-9-r90

Ten simple rules for developing a short bioinformatics training course

Via, A., De Las Rivas J., Attwood T. K., Landsman D., Brazas M. D., Leunissen J. A., Tramontano A., and Schneider M. V.

PLoS Computational Biology. Volume 7, Number 10, (2011), p.e1002245

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.

O'Boyle, Noel M., Guha Rajarshi, Willighagen Egon L., Adams Samuel E., Alvarsson Jonathan, Bradley Jean-Claude, Filippov Igor V., Hanson Robert M., Hanwell Marcus D., Hutchison Geoffrey R., et al.

Journal of cheminformatics. Volume 3, Number 1, (2011), p.37 doi: 10.1186/1758-2946-3-37

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions

Woodwark, C., and Bateman A.

PloS one. Volume 6, Number 5, (2011), p.e14814

The European Nucleotide Archive

Leinonen, R., Akhtar R., Birney E., Bower L., CERDENO-TARRAGA A., Cheng Y., Cleland I., Faruque N., Goodgame N., Gibson R., et al.

Nucleic Acids Res. Volume 39, Number Database issue, (2011), p.D28-31 doi:

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses.

Vilella, Albert J., Birney Ewan, Flicek Paul, and Herrero Javier

Genome Biol. 2, Volume 12, Number 2, (2011), p.401 doi: 10.1186/gb-2011-12-2-401

A User's Guide to the Encyclopedia of DNA Elements (ENCODE).

Consortium, ENCODE Project

PLoS Biol. 4, Volume 9, Number 4, (2011), United States, p.e1001046 doi: 10.1371/journal.pbio.1001046

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

ARANDA, B., Blankenburg H., KERRIEN S., Brinkman F. S. L., Ceol A., Chautard E., DANA J. M., De Las Rivas J., DUMOUSSEAU M., Galeota E., et al.

Nature methods. Volume 8, Number 7, (2011), p.528–529

Macromolecular complexes in crystals and solutions

Krissinel, E.

Acta Crystallographica Section D. Volume 67, Number Part 4, (2011), p.376-385 doi: 10.1107/S0907444911007232

SAIL—a software system for sample and phenotype availability across biobanks and cohorts

GOSTEV, M., FERNANDEZ-BANET J., Rung J., Dietrich J., Prokopenko I., Ripatti S., McCarthy M. I., BRAZMA A., and KRESTYANINOVA M.

Bioinformatics. Volume 27, Number 4, (2011), p.589–591

The new science of ageing.

Partridge, Linda, Thornton Janet M., and Bates Gillian

Philos Trans R Soc Lond B Biol Sci. Jan, Volume 366, Number 1561, (2011), p.6–8 doi: 10.1098/rstb.2010.0298

Phenotypic landscape of a bacterial cell

Nichols, R. J., SEN S., Choo Y. J., Beltrao P., Zietek M., Chaba R., Lee S., Kazmierczak K. M., Lee K. J., Wong A., et al.

Cell. Volume 144, Number 1, (2011), p.143–156

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Gan, X., Stegle O., Behr J., Steffen J. G., Drewe P., Hildebrand K. L., Lyngsoe R., Schultheiss S. J., Osborne E. J., Sreedharan V. T., et al.

Nature. Volume 477, Number 7365, (2011), p.419–423

Every Spider Web has a Simple Flat Twist Tessellation

Lang, R. J., and Bateman A.

Origami 5: Fifth International Meeting of Origami Science, Mathematics, and Education. (2011), p.455

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song, Lingyun, Zhang Zhancheng, Grasfeder Linda L., Boyle Alan P., Giresi Paul G., Lee Bum-Kyu K., Sheffield Nathan C., Gräf Stefan, Huss Mikael, Keefe Damian, et al.

Genome Res. 7, Volume 21, Number 10, (2011), United States, p.1757-67 doi: 10.1101/gr.121541.111

Efficient branch-and-bound techniques for two-locus association mapping

Klotzbücher, K., Kobayashi Y., Shervashidze N., Stegle O., Müller-Myhsok B., Weigel D., and Borgwardt K.

BMC Bioinformatics. Volume 12, Number Suppl 11, (2011), p.A3

Human metabolic profiles are stably controlled by genetic and environmental variation

Nicholson, G., Rantalainen M., Maher A. D., Li J. V., Malmodin D., Ahmadi K. R., Faber J. H., Hallgrímsdóttir I. B., Barrett A., Toft H., et al.

Molecular Systems Biology. Volume 7, (2011),

SAIL-a software system for sample and phenotype availability across biobanks and cohorts

GOSTEV, M., FERNANDEZ-BANET J., Rung J., Dietrich J., Prokopenko I., Ripatti S., McCarthy M. I., BRAZMA A., and KRESTYANINOVA M.

Bioinformatics. Volume 27, Number 4, (2011), p.589-591

A novel strategy for NMR resonance assignment and protein structure determination

Lemak, A., GUTMANAS A., Chitayat S., Karra M., Farès C., Sunnerhagen M., and Arrowsmith C. H.

Journal of Biomolecular NMR. Volume 49, Number Issue 1, (2011), p.27-38 doi: 10.1007/s10858-010-9458-0

The Impact of Focused Gene Ontology Curation of Specific Mammalian Systems

Alam-Faruque, Y., Huntley R.P., Khodiyar V.K., Camon E.B., Dimmer E.C., Sawford T., Martin M. J., O'Donovan C., Talmud P.J., Scambler P., et al.

PloS one. Volume 6, Number 12, (2011), p.e27541 doi:

1,000 structures and more from the MCSG.

Lee, David, de Beer Tjaart A. P., Laskowski Roman A., Thornton Janet M., and Orengo Christine A.

BMC Struct Biol. Volume 11, (2011), p.2 doi: 10.1186/1472-6807-11-2

Computational biology for ageing.

Wieser, Daniela, Papatheodorou Irene, Ziehm Matthias, and Thornton Janet M.

Philos Trans R Soc Lond B Biol Sci. Jan, Volume 366, Number 1561, (2011), p.51–63 doi: 10.1098/rstb.2010.0286

A Metadata description of the data in

Griffin, J. L., Atherton H. J., Steinbeck C., and Salek R. M.

BMC Research Notes. Volume 4, Number 1, (2011), p.272

The International Nucleotide Sequence Database Collaboration

Cochrane, G., KARSCH-MIZRACHI I., NAKAMURA Y., and International Nucleotide Sequence Database Collaboration

Nucleic Acids Res. Volume 39, Number Database issue, (2011), p.D15-8

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Sievers, Fabian, Wilm Andreas, Dineen David, Gibson Toby J., Karplus Kevin, Li Weizhong, Lopez Rodrigo, McWilliam Hamish, Remmert Michael, Söding Johannes, et al.

Molecular systems biology. Volume 7, Number 1, (2011),

InterPro protein classification

McDowall, J., and HUNTER S.

Methods Mol Biol. Volume 694, (2011), p.37–47

Disease and phenotype data at ensembl.

Spudich, Giulietta M., and Fernández-Suárez Xosé M.

Curr Protoc Hum Genet. 2, Volume Chapter 6, (2011), United States, p.Unit6.11 doi: 10.1002/0471142905.hg0611s69

The European nucleotide archive

Leinonen, R., Akhtar R., Birney E., Bower L., Cerdeno-Tárraga A., Cheng Y., Cleland I., Faruque N., Goodgame N., Gibson R., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D28–D31

Comparative and demographic analysis of orang-utan genomes.

Locke, Devin P., Hillier LaDeana W., Warren Wesley C., Worley Kim C., Nazareth Lynne V., Muzny Donna M., Yang Shiaw-Pyng P., Wang Zhengyuan, Chinwalla Asif T., Minx Pat, et al.

Nature. 1, Volume 469, Number 7331, (2011), England, p.529-33 doi: 10.1038/nature09687

Reactome: a database of reactions, pathways and biological processes

Croft, D., O’Kelly G., Wu G., Haw R., Gillespie M., Matthews L., Caudy M., Garapati P., Gopinath G., Jassal B., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D691–D697

Chromatin and heritability: how epigenetic studies can complement genetic approaches

Birney, E.

Trends in Genetics. Volume 27, Number 5, (2011), p.172–176

Structural bioinformatics: current status and future directions

GORE, S. P., VELANKAR S., and KLEYWEGT G. J.

Proceedings of the 29th Leeds Annual Statistical Research Workshop. (2011), p.65-69 doi:

Structures of sequential open states in a symmetrical opening transition of the TolC exit duct

Pei, X-Y, Hinchliffe P., SYMMONS M. F., Koronakis E., Benz R., Hughes C., and Koronakis V.

Proceedings of the National Academy of Sciences. Volume 108, Issue 5, (2011), p.2112-2117 doi: 10.1073/pnas.1012588108

The Reactome BioMart

Haw, R. A., Croft D., Yung C. K., Ndegwa N., D'Eustachio P., Hermjakob H., and Stein L. D.

Database: the journal of biological databases and curation. Volume 2011, (2011),

easyDAS: Automatic creation of DAS servers

Moreno, B. G., Jenkinson A.M., Jimenez R.C., Peypoch X. M., and Hermjakob H.

BMC bioinformatics. Volume 12, Number 1, (2011), p.23

EpiChIP: gene-by-gene quantification of epigenetic modification levels

Hebenstreit, D., Gu M., Haider S., Turner D. J., Liò P., and Teichmann S. A.

Nucleic acids research. Volume 39, Number 5, (2011), p.e27–e27

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Sievers, F., Wilm A., Dineen D., Gibson T. J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., et al.

Molecular systems biology. Volume 7, Number 1, (2011),

A Model for Collaborative Curation, The IEDB and ChEBI Curation of Non-peptidic Epitopes.

Vita, Randi, Peters Bjoern, Josephs Zara, De Matos Paula, Ennis Marcus, Turner Steve, Steinbeck Christoph, Seymour Emily, Zarebski Laura, and Sette Alessandro

Immunome research. Volume 7, Number 1, (2011), p.1–8

Ensembl 2011

Flicek, P., Amode M. R., Barrell D., Beal K., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D800

Asparagine Peptide Lyases

Rawlings, N. D., Barrett A. J., and Bateman A.

Journal of Biological Chemistry. Volume 286, Number 44, (2011), p.38321–38328

Efficient storage of high throughput DNA sequencing data using reference-based compression

Hsi-Yang Fritz, M., Leinonen R., Cochrane G., and Birney E.

Genome Res. Volume 21, Number 5, (2011), p.734-40

Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts.

Malone, Caroline M. P., Domaschenz Renae, Amagase Yoko, Dunham Ian, Murai Kasumi, and Jones Philip H.

Exp Cell Res. 7, Volume 317, Number 11, (2011), United States, p.1590-602 doi: 10.1016/j.yexcr.2011.03.023

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.

Ringwald, Martin, Iyer Vivek, Mason Jeremy C., Stone Kevin R., Tadepally Hamsa D., Kadin James A., Bult Carol J., Eppig Janan T., Oakley Darren J., Briois Sebastien, et al.

Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D849-55 doi: 10.1093/nar/gkq879

ChEMBL: a large-scale bioactivity database for drug discovery

GAULTON, A., BELLIS L. J., BENTO A. P., CHAMBERS J., DAVIES M., HERSEY A., LIGHT Y., MCGLINCHEY S., Michalovich D., Al-Lazikani B., et al.

Nucleic Acids Research. (2011),

Enabling BioSharing–a report on the Annual Spring Workshop of the HUPO-PSI April 11–13, 2011, EMBL-Heidelberg, Germany

Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Vizcaino J.A., and Hermjakob H.

Proteomics. Volume 11, Number 22, (2011), p.4284–4290

Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": significance for the validation of scoring functions.

Ballester, Pedro J., and Mitchell John B. O.

J Chem Inf Model. Aug, Volume 51, Number 8, (2011), p.1739–1741 doi: 10.1021/ci200057e

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

Griss, J., Mart{\'ın M., O'Donovan C., Apweiler R., Hermjakob H., and Vizca{\'ıno J. A.

Proteomics. (2011), doi:

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Earl, D. A., Bradnam K., John J. S., Darling A., Lin D., Faas J., Yu H. O. K., Vince B., Zerbino D. R., Diekhans M., et al.

Genome Research. (2011),

RNIE: genome-wide prediction of bacterial intrinsic terminators

Gardner, P. P., Barquist L., Bateman A., Nawrocki E. P., and Weinberg Z.

Nucleic acids research. Volume 39, Number 14, (2011), p.5845–5852

The rise and fall of supervised machine learning techniques

Jensen, L. J., and Bateman A.

Bioinformatics. Volume 27, Number 24, (2011), p.3331–3332

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Boyle, Alan P., Song Lingyun, Lee Bum-Kyu K., London Darin, Keefe Damian, Birney Ewan, Iyer Vishwanath R., Crawford Gregory E., and Furey Terrence S.

Genome Res. 3, Volume 21, Number 3, (2011), United States, p.456-64 doi: 10.1101/gr.112656.110

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker, C., Hagmann J., Müller J., Koenig D., Stegle O., Borgwardt K., and Weigel D.

Nature. (2011),

RNAcentral: A vision for an international database of RNA sequences.

Bateman, Alex, Agrawal Shipra, Birney Ewan, Bruford Elspeth A., Bujnicki Janusz M., Cochrane Guy, Cole James R., Dinger Marcel E., Enright Anton J., Gardner Paul P., et al.

RNA. 11, Volume 17, Number 11, (2011), United States, p.1941-6 doi: 10.1261/rna.2750811

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

ARANDA, B., Blankenburg H., KERRIEN S., Brinkman F. S. L., Ceol A., Chautard E., DANA J. M., Rivas De Las J., DUMOUSSEAU M., Galeota E., et al.

Nature Methods. Volume 8, Number Issue 7, (2011), p.528-529 doi: 10.1038/nmeth.1637

EMDataBank.org: unified data resource for CryoEM

Lawson, C. L., Baker M. L., BEST C., Bi C., Dougherty M., Feng P., GINKEL VAN G., Devkota B., LAGERSTEDT I., Newman R. H., et al.

Nucleic Acids Research. Volume 39, Number Database issue, (2011), p.D456-D464 doi: 10.1093/nar/gkq880

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

Ndegwa, N., Côté R.G., Ovelleiro D., D'Eustachio P., Hermjakob H., Vizcaino J.A., and Croft D.

Database: the journal of biological databases and curation. Volume 2011, (2011),

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models

Kosiol, C., and Goldman N.

Journal of Molecular Biology. Volume 411, (2011), p.910-923

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

Griss, J., Mart{\'ın M., O'Donovan C., Apweiler R., Hermjakob H., and Vizcaino J.A.

Proteomics. (2011),

Messenger RNA and microRNA profiling during early mouse EB formation

Tripathi, R., Saini H. K., Rad R., ABREU-GOODGER C., Van Dongen S., and Enright A. J.

Gene Expression Patterns. (2011),

Unintended consequences of existential quantifications in biomedical ontologies.

Boeker, Martin, Tudose Ilinca, Hastings Janna, Schober Daniel, and Schulz Stefan

BMC Bioinformatics. Volume 12, (2011), p.456 doi: 10.1186/1471-2105-12-456

RNAcentral: A vision for an international database of RNA sequences

Bateman, A., Agrawal S., Birney E., Bruford E. A., Bujnicki J. M., Cochrane G., Cole J. R., Dinger M. E., Enright A. J., Gardner P. P., et al.

Rna-a Publication of the Rna Society. Volume 17, Number 11, (2011), p.1941-1946

SORGOdb: Superoxide Reductase Gene Ontology curated DataBase.

Lucchetti-Miganeh, Céline, Goudenège David, Thybert David, Salbert Gilles, and Barloy-Hubler Frédérique

BMC Microbiol. Volume 11, (2011), England, p.105 doi: 10.1186/1471-2180-11-105

Variation in genome-wide mutation rates within and between human families.

Conrad, Donald F., Keebler Jonathan E. M., Depristo Mark A., Lindsay Sarah J., Zhang Yujun, Casals Ferran, Idaghdour Youssef, Hartl Chris L., Torroja Carlos, Garimella Kiran V., et al.

Nat Genet. 7, Volume 43, Number 7, (2011), United States, p.712-4 doi: 10.1038/ng.862

Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures

Bernard, A., VRANKEN W. F., Bardiaux B., Nilges M., and Malliavin T. E.

Proteins. Volume 79, (2011), p.1525-1537 doi: 10.1002/prot.22980

The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

Morris, C., Pajon A., Griffiths S. L., Daniel E., Savitsky M., Lin B., Diprose J. M., A. da Silva Wilter, Pilicheva K., Troshin P., et al.

Acta Crystallographica Section D. Volume 67, (2011), p.249-260 doi: 10.1107/S0907444911007943

A high-resolution map of human evolutionary constraint using 29 mammals

Lindblad-Toh, Kerstin, Garber Manuel, Zuk Or, Lin Michael F., Parker Brian J., Washietl Stefan, Kheradpour Pouya, Ernst Jason, Jordan Gregory, Mauceli Evan, et al.

Nature. Volume 478, (2011), p.476-482

Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion

Puri, V., Goyal A., Sankaranarayanan R., Enright A. J., and Vaidya T.

BMC evolutionary biology. Volume 11, Number 1, (2011), p.334

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data

Washietl, S., Findeiß S., Müller S. A., Kalkhof S., von Bergen M., Hofacker I. L., Stadler P. F., and Goldman N.

RNA. Volume 17, (2011), p.578-594

The metastasis-promoting phosphatase PRL-3 shows activity toward phosphoinositides.

McParland, Victoria, Varsano Giulia, Li Xun, Thornton Janet M., Baby Jancy, Aravind Ajay, Meyer Christoph, Pavic Karolina, Rios Pablo, and Köhn Maja

Biochemistry. Sep, Volume 50, Number 35, (2011), p.7579–7590 doi: 10.1021/bi201095z

What's in an `is about'link? Chemical diagrams and the IAO

HASTINGS, J., Batchelor C., Neuhaus F., and Steinbeck C.

Proceedings of the International Conference on Biomedical Ontology (ICBO2011), Buffalo, USA. (2011),

RNAcentral: A vision for an international database of RNA sequences

Bateman, A., Agrawal S., Birney E., Bruford E. A., Bujnicki J. M., Cochrane G., Cole J. R., Dinger M. E., Enright A. J., Gardner P. P., et al.

RNA. Volume 17, Number 11, (2011), p.1941–1946 doi:

Towards BioDBcore: a community-defined information specification for biological databases

Gaudet, P., Bairoch A., Field D., Sansone S. A., TAYLOR C., Attwood T. K., Bateman A., Blake J. A., Bult C. J., Cherry J. M., et al.

Nucleic Acids Research. Volume 39, (2011), p.D7-D10

BioMart Central Portal: an open database network for the biological community.

Guberman, Jonathan M., Ai J., Arnaiz O., Baran Joachim, Blake Andrew, Baldock Richard, Chelala Claude, Croft David, Cros Anthony, Cutts Rosalind J., et al.

Database (Oxford). Volume 2011, (2011), England, p.bar041 doi: 10.1093/database/bar041

Ensembl 2011.

Flicek, Paul, Amode Ridwan M., Barrell Daniel, Beal Kathryn, Brent Simon, Chen Yuan, Clapham Peter, Coates Guy, Fairley Susan, Fitzgerald Stephen, et al.

Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D800-6 doi: 10.1093/nar/gkq1064

UKPMC: a full text article resource for the life sciences

McEntyre, J. R., Ananiadou S., Andrews S., Black W. J., Boulderstone R., Buttery P., Chaplin D., Chevuru S., Cobley N., Coleman L. A., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D58–D65

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

Kutter, C., Brown G. D., Gonçalves Â., Wilson M. D., Watt S., BRAZMA A., White R. J., and Odom D. T.

Nature Genetics. Volume 43, Number 10, (2011), p.948–955

Preparing molecular interaction data for publication.

Orchard, S., and Hermjakob H.

Methods in molecular biology (Clifton, NJ). Volume 694, (2011), p.229–236

Minimum information about a bioactive entity (MIABE).

Orchard, Sandra, Al-Lazikani Bissan, Bryant Steve, Clark Dominic, Calder Elizabeth, Dix Ian, Engkvist Ola, Forster Mark, Gaulton Anna, Gilson Michael, et al.

Nat Rev Drug Discov. Sep, Volume 10, Number 9, (2011), p.661–669 doi: 10.1038/nrd3503

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

Albers, C.A., Cvejic A., Favier R., Bouwmans E. E., Alessi M. C., Bertone P., Jordan G., Kettleborough R. N. W., Kiddle G., Kostadima M., et al.

Nat Genet. Jul, Volume 43, Number 8, (2011), p.735–737

PomBase: a comprehensive online resource for fission yeast

Wood, V., Harris M. A., McDowall M. D., Rutherford K., Vaughan B. W., Staines D. M., Aslett M., Lock A., Bähler J., Kersey P. J., et al.

Nucleic acids research. (2011),

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, P., Kottmann R., Field D., Knight R., Cole J. R., Amaral-Zettler L., Gilbert J. A., KARSCH-MIZRACHI I., Johnston A., Cochrane G., et al.

Nat Biotechnol. Volume 29, Number 5, (2011), p.415-20 doi:

The functional spectrum of low-frequency coding variation.

Marth, Gabor T., Yu Fuli, Indap Amit R., Garimella Kiran, Gravel Simon, Leong Wen Fung, Tyler-Smith Chris, Bainbridge Matthew, Blackwell Thomas, Zheng-Bradley Xiangqun, et al.

Genome Biol. 9, Volume 12, Number 9, (2011), p.R84 doi: 10.1186/gb-2011-12-9-r84

Demographic history and rare allele sharing among human populations.

Gravel, Simon, Henn Brenna M., Gutenkunst Ryan N., Indap Amit R., Marth Gabor T., Clark Andrew G., Yu Fuli, Gibbs Richard A., and Bustamante Carlos D.

Proc Natl Acad Sci U S A. 7, Volume 108, Number 29, (2011), United States, p.11983-8 doi: 10.1073/pnas.1019276108

Efficient storage of high throughput DNA sequencing data using reference-based compression

Fritz, M. H. Y., Leinonen R., Cochrane G., and Birney E.

Genome research. Volume 21, Number 5, (2011), p.734–740

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

PRILL, R. J., SAEZ-RODRIGUEZ J., Alexopoulos L. G., Sorger P. K., and Stolovitzky G.

Science signaling. Sep 6, Volume 4, Number 189, (2011), p.mr7

Mouse genomic variation and its effect on phenotypes and gene regulation

Keane, T. M., Goodstadt L., Danecek P., White M. A., Wong K., Yalcin B., Heger A., Agam A., Slater G., Goodson M., et al.

Nature. Volume 477, Number 7364, (2011), p.289–294

Reactome pathway analysis to enrich biological discovery in proteomics data sets

Haw, R., Hermjakob H., D'Eustachio P., and Stein L.

Proteomics. Volume 11, Number 18, (2011), p.3598–3613

Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures

Sahakyan, A. B., VRANKEN W. F., Cavalli A., and Vendruscolo M.

Angewandte Chemie International Edition. Volume 50, (2011), p.9620-9623 doi: 10.1002/anie.201101641

Protein structure databases.

Laskowski, Roman A.

Mol Biotechnol. Jun, Volume 48, Number 2, (2011), p.183–198 doi: 10.1007/s12033-010-9372-4

Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress

Charles, G. M., Chen C., Shih S. C., Collins S. R., Beltrao P., Zhang X., Sharma T., Tan S., Burlingame A. L., Krogan N. J., et al.

Proceedings of the National Academy of Sciences. Volume 108, Number 26, (2011), p.10620–10625

Controlled vocabularies and semantics in systems biology.

Courtot, Mélanie, Juty Nick, Knüpfer Christian, Waltemath Dagmar, Zhukova Anna, Dräger Andreas, Dumontier Michel, Finney Andrew, Golebiewski Martin, Hastings Janna, et al.

Molecular Systems Biology. Volume 7, (2011), p.543 doi: 10.1038/msb.2011.77

Investigating the effect of paralogs on microarray gene-set analysis.

Faure, Andre J., Seoighe Cathal, and Mulder Nicola J.

BMC Bioinformatics. 1, Volume 12, Number 1, (2011), p.29 doi: 10.1186/1471-2105-12-29

Cre recombinase resources for conditional mouse mutagenesis.

Smedley, Damian, Salimova Ekaterina, and Rosenthal Nadia

Methods. 4, Volume 53, Number 4, (2011), United States, p.411-6 doi: 10.1016/j.ymeth.2010.12.027

PDBe: Protein Data Bank in Europe

VELANKAR, S., ALHROUB Y., Alili A., BEST C., Boutselakis H. C., CABOCHE S., CONROY M. J., DANA J. M., GINKEL VAN G., Golovin A., et al.

Nucleic Acids Research. Volume 39, Number Database issue, (2011), p.D402-D410 doi: 10.1093/nar/gkq985

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited

Hess, J., and Goldman N.

PLoS ONE. Volume 6, (2011), p.e22783

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles)

Kinsinger, C. R., Apffel J., Baker M., Bian X., Borchers C.H., Bradshaw R., Brusniak M.Y., Chan D. W., Deutsch E.W., Domon B., et al.

PROTEOMICS-Clinical Applications. Volume 5, Number 11-12, (2011), p.580–589

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

Lakner, C., Holder M. T., Goldman N., and Naylor G. J. P.

Systematic Biology. Volume 60, (2011), p.161-174

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

De Fazio, S., BARTONICEK N., Di Giacomo M., ABREU-GOODGER C., Sankar A., Funaya C., Antony C., Moreira P. N., Enright A. J., and O’Carroll D.

Nature. (2011),

Structural annotation of Mycobacterium tuberculosis proteome.

Anand, Praveen, Sankaran Sandhya, Mukherjee Sumanta, Yeturu Kalidas, Laskowski Roman A., Bhardwaj Anshu, Bhagavat Raghu, Consortium O. S. D. D., Brahmachari Samir K., and Chandra Nagasuma

PLoS One. Volume 6, Number 10, (2011), p.e27044 doi: 10.1371/journal.pone.0027044

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.

Laskowski, Roman A., and Swindells Mark B.

J Chem Inf Model. Oct, Volume 51, Number 10, (2011), p.2778–2786 doi: 10.1021/ci200227u

New developments on the cheminformatics open workflow environment CDK-Taverna.

Truszkowski, Andreas, Jayaseelan Kalai Vanii, Neumann Stefan, Willighagen Egon L., Zielesny Achim, and Steinbeck Christoph

Journal of cheminformatics. Volume 3, (2011), p.54 doi: 10.1186/1758-2946-3-54

Towards BioDBcore: a community-defined information specification for biological databases

Gaudet, P., Bairoch A., Field D., Sansone S. A., TAYLOR C., Attwood T. K., Bateman A., Blake J. A., Bult C. J., Cherry J. M., et al.

Database-the Journal of Biological Databases and Curation. (2011),

The InterPro BioMart: federated query and web service access to the InterPro Resource

Jones, P., Binns D., McMenamin C., MCANULLA C., and HUNTER S.

Database: the journal of biological databases and curation. Volume 2011, (2011),

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

Kinsella, Rhoda J., Kähäri Andreas, Haider Syed, Zamora Jorge, Proctor Glenn, Spudich Giulietta, Almeida-King Jeff, Staines Daniel, Derwent Paul, Kerhornou Arnaud, et al.

Database (Oxford). Volume 2011, (2011), England, p.bar030 doi: 10.1093/database/bar030

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Boyle, A. P., Song L., Lee B. K., London D., Keefe D., Birney E., Iyer V. R., Crawford G. E., and Furey TS

Genome research. Volume 21, Number 3, (2011), p.456–464

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet, Pascale, Bairoch Amos, Field Dawn, Sansone Susanna-Assunta A., Taylor Chris, Attwood Teresa K., Bateman Alex, Blake Judith A., Bult Carol J., Cherry Michael J., et al.

Nucleic Acids Res. 1, Volume 39, Number Database issue, (2011), England, p.D7-10 doi: 10.1093/nar/gkq1173

Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

Kahlem, P., DiCara A., Durot M., Hancock J. M., Klipp E., Schächter V., Segal E., Xenarios I., Birney E., and Mendoza L.

(2011),

Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments

KAPUSHESKY, M., ADAMUSIAK T., BURDETT T., CULHANE A., FARNE A., FILIPPOV A., HOLLOWAY E., KLEBANOV A., KRYVYCH N., KURBATOVA N., et al.

Nucleic Acids Research. (2011),

Dasty3, a WEB Framework for DAS

Villaveces, J. M., Jimenez R.C., Garcia L. J., Salazar G. A., Gel B., Mulder N., Martin M., Garcia A., and Hermjakob H.

Bioinformatics. Volume 27, Number 18, (2011), p.2616–2617

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

Hebenstreit, D., Fang M., Gu M., Charoensawan V., van Oudenaarden A., and Teichmann S. A.

Molecular systems biology. Volume 7, Number 1, (2011),

PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment

Sipos, B., Massingham T., Jordan G. E., and Goldman N.

BMC Bioinformatics. Volume 12, (2011), p.104

Extending CATH: increasing coverage of the protein structure universe and linking structure with function.

Cuff, Alison L., Sillitoe Ian, Lewis Tony, Clegg Andrew B., Rentzsch Robert, Furnham Nicholas, Pellegrini-Calace Marialuisa, Jones David, Thornton Janet M., and Orengo Christine A.

Nucleic Acids Res. Jan, Volume 39, Number Database issue, (2011), p.D420–D426 doi: 10.1093/nar/gkq1001

Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis.

Holliday, Gemma L., Fischer Julia D., Mitchell John B. O., and Thornton Janet M.

FEBS J. Oct, Volume 278, Number 20, (2011), p.3835–3845 doi: 10.1111/j.1742-4658.2011.08190.x

NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression

Reynolds, N., Salmon-Divon M., Dvinge H., Hynes-Allen A., Balasooriya G., Leaford D., Behrens A., Bertone P., and Hendrich B.

EMBO J. Dec, Volume 31, Number 3, (2011), p.593–605

Rfam: Wikipedia, clans and the “decimal” release

Gardner, P. P., Daub J., Tate J., Moore B. L., Osuch I. H., Griffiths-Jones S., Finn R. D., Nawrocki E. P., Kolbe D. L., Eddy S. R., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D141

The genomic standards consortium: bringing standards to life for microbial ecology

Yilmaz, P., Gilbert J. A., Knight R., Amaral-Zettler L., KARSCH-MIZRACHI I., Cochrane G., NAKAMURA Y., Sansone S. A., Glockner F. O., and Field D.

ISME J. Volume 5, Number 10, (2011), p.1565-7 doi:

The EBI Metagenomics Archive, Integration and Analysis Resource

Hunter, C., Cochrane G., Apweiler R., and HUNTER S.

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. (2011), p.333–340

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

Renfree, Marilyn B., Papenfuss Anthony T., Deakin Janine E., Lindsay James, Heider Thomas, Belov Katherine, Rens Willem, Waters Paul D., Pharo Elizabeth A., Shaw Geoff, et al.

Genome Biol. 8, Volume 12, Number 8, (2011), p.R81 doi: 10.1186/gb-2011-12-8-r81

Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.

Pignatelli, Miguel, and Moya Andrés

PLoS One. Volume 6, Number 5, (2011), United States, p.e19984 doi: 10.1371/journal.pone.0019984

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

Song, L., Zhang Z., Grasfeder L. L., Boyle A. P., Giresi P. G., Lee B. K., Sheffield N. C., Gräf S., Huss M., Keefe D., et al.

Genome research. Volume 21, Number 10, (2011), p.1757–1767

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

Doreleijers, J. F., VRANKEN W. F., Schulte C., Markley J. L., Ulrich E. L., Vriend G., and Vuister G. W.

Nucleic Acids Research. Volume 40, Number Database issue, (2011), p.D519-D524 doi: 10.1093/nar/gkr1134

Rapid Analysis of Pharmacology for Infectious Diseases

Hopkins, A. L., Richard Bickerton G., Carruthers I. M., K Boyer S., Rubin H., and OVERINGTON J. P.

Current Topics in Medicinal Chemistry. Volume 11, Number 10, (2011), p.1292–1300

Structure-based prediction of methyl chemical shifts in proteins

Sahakyan, A. B., VRANKEN W. F., Cavalli A., and Vendruscolo M.

Journal of Biomolecular NMR. Volume 50, Number (Issue 4), (2011), p.331-346 doi: 10.1007/s10858-011-9524-2

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data

Griss, J., Côté R.G., Gerner C., Hermjakob H., and Vizcaino J.A.

Molecular & Cellular Proteomics. Volume 10, Number 9, (2011),

Relative solvent accessible surface area predicts protein conformational changes upon binding

Marsh, J. A., and Teichmann S. A.

Structure. Volume 19, Number 6, (2011), p.859–867

Quality metrics

Beisv{\aa}g, V., KAUFFMANN A., MALONE J., Foy C., Salit M., Schimmel H., Bongcam-Rudloff E., Landegren U., Parkinson H., Huber W., et al.

BioTechniques. Volume 50, Number 1, (2011), p.27–31

Gramene database in 2010: updates and extensions

Youens-Clark, K., Buckler E., Casstevens T., Chen C., DeClerck G., Derwent P., Dharmawardhana P., Jaiswal P., Kersey P., Karthikeyan AS, et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D1085

BioMed Central | Full text | A Metadata description of the data in "A metabolomic comparison of urinary changes in type 2 diabetes in mouse, rat, and human."

Griffin, Julian, Atherton Helen, Steinbeck Christoph, and Salek Reza

BMC Research Notes. jul, Volume 4, Number 1, (2011), p.272 doi: 10.1186/1756-0500-4-272

Towards BioDBcore: a community-defined information specification for biological databases| Macquarie University ResearchOnline

Gaudet, P., Bairoch A., Chisholm R. L., Cochrane G., Cook C. E., Eppig J. T., Galperin M. Y., Gentleman R., Goble C. A., Gojobori T., et al.

(2011),

The Variant Call Format and VCFtools.

Danecek, Petr, Auton Adam, Abecasis Goncalo, Albers Cornelis A., Banks Eric, Depristo Mark A., Handsaker Robert, Lunter Gerton, Marth Gabor, Sherry Stephen T., et al.

Bioinformatics. 6, Volume 27, Number 15, (2011), p.2156-8 doi: 10.1093/bioinformatics/btr330

Genome sequence of Lactococcus garvieae UNIUD074, isolated in Italy from a lactococcosis outbreak.

Reimundo, Pilar, Pignatelli Miguel, Alcaraz Luis David, D'Auria Giuseppe, Moya Andrés, and Guijarro José A.

J Bacteriol. 7, Volume 193, Number 14, (2011), United States, p.3684-5 doi: 10.1128/JB.05210-11

Probing the links between in vitro potency, ADMET and physicochemical parameters

Gleeson, M. P., HERSEY A., Montanari D., and OVERINGTON J.

Nature Reviews Drug Discovery. Volume 10, Number 3, (2011), p.197–208

Solving the Problem: Genome Annotation Standards before the data deluge

Klimke, W., O'Donovan C., White O., Brister J. R., Clark K., Fedorov B., Mizrachi I., Pruitt K. D., and Tatusova T.

Standards in Genomic Sciences. Volume 5, Number 1, (2011), p.168 doi:

Arrayexpress update-An archive of microarray and high-throughput sequencing-based functional genomics experiments

Parkinson, H., Sarkans U., KOLESNIKOV N., ABEYGUNAWARDENA N., BURDETT T., DYLAG M., EMAM I., FARNE A., HASTINGS E., HOLLOWAY E., et al.

Nucleic Acids Research. Volume 39, Number SUPPL. 1, (2011), p.D1002-D1004

Collation and data-mining of literature bioactivity data for drug discovery

BELLIS, L. J., Akhtar R., AlLazikani B., ATKINSON F., BENTO A. P., CHAMBERS J., DAVIES M., GAULTON A., HERSEY A., IKEDA K., et al.

Biochemical Society Transactions. Volume 39, Number 5, (2011), p.1365

Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines - Workshop Introduction

Ludtke, S. J., Lawson C. L., KLEYWEGT G. J., Berman H. M., and Chiu W.

Pacific Symposium on Biocomputing. Volume 16, (2011), p.369-373 doi: 10.1142/9789814335058_0039

Assymetric synthesis and conformational analysis by NMR spectroscopy and MD of Aba- and α-MeAba-containing demorphin analogues

Vandormael, B., De Wachter R., Martins J. C., Hendrickx P. M. S., Keresztes A., Ballet S., Mallareddy J. R., Tóth F., Tóth G., and Tourwé D.

ChemMedChem. Volume 6, Number Issue 11, (2011), p.2035-2047 doi: 10.1002/cmdc.201100314

MiR-221 Influences Effector Functions and Actin Cytoskeleton in Mast Cells

Mayoral, R. J., Deho L., Rusca N., BARTONICEK N., Saini H. K., Enright A. J., and Monticelli S.

PloS one. Volume 6, Number 10, (2011), p.e26133

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling.

Alic, Nazif, T. Andrews Daniel, Giannakou Maria E., Papatheodorou Irene, Slack Cathy, Hoddinott Matthew P., Cochemé Helena M., Schuster Eugene F., Thornton Janet M., and Partridge Linda

Mol Syst Biol. Volume 7, (2011), p.502 doi: 10.1038/msb.2011.36

Ongoing and future developments at the Universal Protein Resource

Apweiler, R., Martin MJ, O’Donovan C., Magrane M., Alam-Faruque Y., Antunes R., Barrell D., Bely B., Bingley M., Binns D., et al.

Nucleic Acids Res. Volume 39, (2011), p.D214–D219 doi:

Recent developments in the ChEBI ontology

HASTINGS, J., De Matos P., DEKKER A., ENNIS M., HAUG K., Josephs Z., OWEN G., TURNER S., and Steinbeck C.

Proceedings of the International Conference on Biomedical Ontology (ICBO), CEUR-WS. Volume 833, (2011),

The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

Galperin, M. Y., and COCHRANE G. R.

Nucleic Acids Res. Volume 39, Number Database issue, (2011), p.D1-6

BioMart as an integration solution for the International Knockout Mouse Consortium.

Oakley, Darren J., Iyer Vivek, Skarnes William C., and Smedley Damian

Database (Oxford). Volume 2011, (2011), England, p.bar028 doi: 10.1093/database/bar028

Whole-genome sequencing of multiple Arabidopsis thaliana populations

Cao, J., Schneeberger K., Ossowski S., Günther T., Bender S., Fitz J., Koenig D., Lanz C., Stegle O., Lippert C., et al.

Nature Genetics. Volume 43, Number 10, (2011), p.956–963

A high-resolution map of human evolutionary constraint using 29 mammals.

Lindblad-Toh, Kerstin, Garber Manuel, Zuk Or, Lin Michael F., Parker Brian J., Washietl Stefan, Kheradpour Pouya, Ernst Jason, Jordan Gregory, Mauceli Evan, et al.

Nature. 10, Volume 478, Number 7370, (2011), England, p.476-82 doi: 10.1038/nature10530

A new generation of crystallographic validation tools for the Protein Data Bank

Read, R. J., Adams P. D., Arendall W. B., Brunger A. T., Emsley P., Joosten R. P., KLEYWEGT G. J., Krissinel E. B., Lüttel T., Otwinowski Z., et al.

Structure. Volume 19, Number Issue 10, (2011), p.1395-1412 doi: 10.1016/j.str.2011.08.006

Expression and Genetic Variation Databases for Cancer Research

Rung, J., and BRAZMA A.

Cancer Systems Biology, Bioinformatics and Medicine. (2011), p.153–164

EUROCarbDB: An open-access platform for glycoinformatics

von der Lieth, C-W, A. Freire Ardá, Blank D., Campbell M. P., Fogh R. H., Damerell D. A., Dell A., Dwek R. A., Ernst B., Fogh R., et al.

Glycobiology. Volume 21, Number Issue 4, (2011), p.493-502 doi: 10.1093/glycob/cwq188

Ultrafast shape recognition: method and applications.

Ballester, Pedro J.

Future Med Chem. Jan, Volume 3, Number 1, (2011), p.65–78 doi: 10.4155/fmc.10.280

UniProt Knowledgebase: a hub of integrated protein data

Magrane, M., and others

Database: the journal of biological databases and curation. Volume 2011, (2011),

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Gan, Xiangchao, Stegle Oliver, Behr Jonas, Steffen Joshua G., Drewe Philipp, Hildebrand Katie L., Lyngsoe Rune, Schultheiss Sebastian J., Osborne Edward J., Sreedharan Vipin T., et al.

Nature. Volume 477, Number 7365, (2011), p.419–423

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Hastings, Janna, Chepelev Leonid, Willighagen Egon, Adams Nico, Steinbeck Christoph, and Dumontier Michel

PLoS ONE. Volume 6, Number 10, (2011), p.e25513 doi: 10.1371/journal.pone.0025513

The Sequence Read Archive

Leinonen, R., Sugawara H., Shumway M., and C Int Nucleotide Sequence Database

Nucleic Acids Research. Volume 39, (2011), p.D19-D21 doi:

Reactome: a database of reactions, pathways and biological processes

Croft, D., O’Kelly G., Wu G., Haw R., Gillespie M., Matthews L., Caudy M., Garapati P., Gopinath G., Jassal B., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D691

Closure of the NCBI SRA and implications for the long-term future of genomics data storage.

Lipman, David, Flicek Paul, Salzberg Steven, Gerstein Mark, and Knight Rob

Genome Biol. Volume 12, Number 3, (2011), England, p.402 doi: 10.1186/gb-2011-12-3-402

Joint genetic analysis of gene expression data with inferred cellular phenotypes

Parts, L., Stegle O., Winn J., and Durbin R.

PLoS genetics. Volume 7, Number 1, (2011), p.e1001276

A user's guide to the encyclopedia of DNA elements (ENCODE)

Consortium, ENCODE Project, and others

PLoS Biol. Volume 9, Number 4, (2011), p.e1001046

Modernizing reference genome assemblies.

Church, Deanna M., Schneider Valerie A., Graves Tina, Auger Katherine, Cunningham Fiona, Bouk Nathan, Chen Hsiu-Chuan C., Agarwala Richa, McLaren William M., Ritchie Graham R. S., et al.

PLoS Biol. 7, Volume 9, Number 7, (2011), United States, p.e1001091 doi: 10.1371/journal.pbio.1001091

Training signaling pathway maps to biochemical data with constrained fuzzy logic: Quantitative analysis of liver cell responses to inflammatory stimuli

Morris, M. K., SAEZ-RODRIGUEZ J., Clarke D. C., Sorger P. K., and Lauffenburger D. A.

PLoS Computational Biology. Volume 7, Number 3, (2011), p.Art. No.: e1001099

Minimum information about a bioactive entity (MIABE)

Orchard, S., Al-Lazikani B., Bryant S., Clark D., Calder E., DIX I., Engkvist O., Forster M., GAULTON A., Gilson M., et al.

Nature Reviews Drug Discovery. Volume 10, Number 9, (2011), p.661–669 doi:

Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space

van der Horst, E., E Peironcely J., JP van Westen G., O van den Hoven O., RJD Galloway W., R Spring D., Wegner J. K., WT van Vlijmen H., P IJzerman A., OVERINGTON J. P., et al.

Current Topics in Medicinal Chemistry. Volume 11, Number 15, (2011), p.1964–1977

Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome

Albers, C. A., Cvejic A., Favier R., Bouwmans E. E., Alessi M. - C., Bertone P., Jordan G., Kettleborough R. N. W., Kiddle G., KOSTADIMA M., et al.

Nature Genetics. Volume 43, (2011), p.735-737

Data standardization by the HUPO-PSI: how has the community benefitted

Orchard, S., and Hermjakob H.

Methods in molecular biology (Clifton, NJ). Volume 696, (2011), p.149–160

Analysis of alignment error and sitewise constraint in mammalian comparative genomics

Jordan, G.

(2011),

2010

Graph representations and algorithms in computational biology of RNA secondary structure

Washietl, S., and Gesell T.

Structural Analysis of Complex Networks. (2010), p.421-438

Unified data resource for Cryo-EM

Lawson, C.L.

Methods in Enzymology . Volume 483, (2010), p.73-90 doi: 10.1016/S0076-6879(10)83004-6

Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure

Cochrane, G., Martin M. J., and Apweiler R.

Metagenomics: Theory, Methods and Applications. (2010),

An information retrieval perspective on visualization of gene expression data with ontological annotation

Peltonen, J., Aidos H., GEHLENBORG N., BRAZMA A., and Kaski S.

Acoustics Speech and Signal Processing (ICASSP), 2010 IEEE International Conference on. (2010), p.2178–2181

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

Lefebvre, C., Rajbhandari P., Alvarez M. J., Bandaru P., Lim W. K., Sato M., Wang K., Sumazin P., Kustagi M., Bisikirska B. C., et al.

Molecular systems biology. Volume 6, Number 1, (2010),

A draft sequence of the Neandertal genome

Green, R. E., Krause J., Briggs A. W., Maricic T., Stenzel U., Kircher M., Patterson N., Li H., Zhai W., Fritz M. H. Y., et al.

science. Volume 328, Number 5979, (2010), p.710

Ensembl’s 10th year

Flicek, P., Aken BL, Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D557–D562

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

Daelemans, Caroline, Ritchie Matthew E., Smits Guillaume, Abu-Amero Sayeda, Sudbery Ian M., Forrest Matthew S., Campino Susana, Clark Taane G., Stanier Philip, Kwiatkowski Dominic, et al.

BMC Genet. 4, Volume 11, Number 1, (2010), p.25 doi: 10.1186/1471-2156-11-25

Ontological dependence, dispositions and institutional reality in chemistry

Batchelor, C., HASTINGS J., and Steinbeck C.

Proceeding of the 2010 conference on Formal Ontology in Information Systems. (2010), p.271–284

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8

Kyrpides, N., Field D., Sterk P., Kottmann R., Glockner F. O., Hirschman L., Garrity G. M., Cochrane G., and Wooley J.

Stand Genomic Sci. Volume 3, Number 1, (2010), p.93-6

Heritable individual-specific and allele-specific chromatin signatures in humans

McDaniell, R., Lee B. K., Song L., Liu Z., Boyle A. P., Erdos M. R., Scott L. J., Morken M. A., Kucera K. S., Battenhouse A., et al.

Science. Volume 328, Number 5975, (2010), p.235

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.

Peric-Hupkes, Daan, Meuleman Wouter, Pagie Ludo, Bruggeman Sophia W. M., Solovei Irina, Brugman Wim, Gräf Stefan, Flicek Paul, Kerkhoven Ron M., van Lohuizen Maarten, et al.

Mol Cell. 5, Volume 38, Number 4, (2010), United States, p.603-13 doi: 10.1016/j.molcel.2010.03.016

Diversity of human copy number variation and multicopy genes.

Sudmant, Peter H., Kitzman Jacob O., Antonacci Francesca, Alkan Can, Malig Maika, Tsalenko Anya, Sampas Nick, Bruhn Laurakay, Shendure Jay, Project Genomes 1000, et al.

Science. 10, Volume 330, Number 6004, (2010), United States, p.641-6 doi: 10.1126/science.1197005

Improvements to services at the European Nucleotide Archive

Leinonen, Rasko, Akhtar Ruth, Birney Ewan, Bonfield James, Bower Lawrence, Corbett Matt, Cheng Ying, Demiralp Fehmi, Faruque Nadeem, Goodgame Neil, et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D39–D45

Improvements to services at the European Nucleotide Archive

Leinonen, R., Akhtar R., Birney E., Bonfield J., Bower L., Corbett M., Cheng Y., Demiralp F., Faruque N., Goodgame N., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D39–D45

EMMA—mouse mutant resources for the international scientific community

Wilkinson, P., Sengerova J., Matteoni R., Chen C. K., Soulat G., Ureta-Vidal A., Fessele S., Hagn M., Massimi M., Pickford K., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D570–D576

Genomic information infrastructure after the deluge

Parkhill, J., Birney E., Kersey P., and others

Genome Biol. Volume 11, (2010), p.402 doi:

Towards proteome–wide interaction models using the proteochemometrics approach

Strömbergsson, H., Lapins M., KLEYWEGT G. J., and Wikberg J. E.

Molecular Informatics. Volume 29, Number Issue 6-7, (2010), p.499-508 doi: 10.1002/minf.201000052

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative

Gibson, F., Hoogland C., Martinez-Bartolomé S., Medina-Aunon J. A., Albar J.P., Babnigg G., Wipat A., Hermjakob H., Almeida J. S., Stanislaus R., et al.

Proteomics. Volume 10, Number 17, (2010), p.3073–3081

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids

Fabani, M. M., ABREU-GOODGER C., Williams D., Lyons P. A., Torres A. G., Smith K. G. C., Enright A. J., Gait M. J., and Vigorito E.

Nucleic acids research. Volume 38, Number 13, (2010), p.4466–4475

High-throughput proteomics and bioinformatics: joined at the hip

Martens, L., and Hermjakob H.

Proteomics. (2010),

Robustness of phylogenetic inference based on minimum evolution

Pardi, F., Guillemot S., and Gascuel O.

Bulletin of Mathematical Biology. Volume 72, (2010), p.1820-1839

Fast and efficient searching of biological data resources—using EB-eye

Valentin, F., Squizzato S., GOUJON M., McWilliam H., Paern J., and Lopez R.

Briefings in bioinformatics. Volume 11, Number 4, (2010), p.375–384

Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.

Gruenberger, Michael, Alberts Rudi, Smedley Damian, Swertz Morris, Schofield Paul, consortium The CASIMIR, and Schughart Klaus

BMC Res Notes. Volume 3, Number 1, (2010), p.16 doi: 10.1186/1756-0500-3-16

A map of human genome variation from population-scale sequencing.

Consortium, Genomes Project 1000

Nature. 10, Volume 467, Number 7319, (2010), England, p.1061-73 doi: 10.1038/nature09534

Fast and efficient searching of biological data resources—using EB-eye

Valentin, Franck, Squizzato Silvano, Goujon Mickael, McWilliam Hamish, Paern Juri, and Lopez Rodrigo

Briefings in bioinformatics. Volume 11, Number 4, (2010), p.375–384

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

Stegle, O., Denby K. J., Cooke E. J., Wild D. L., Ghahramani Z., and Borgwardt K. M.

Journal of Computational Biology. Volume 17, Number 3, (2010), p.355–367

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation

ABAD-ZAPATERO, C., Perisic O., Wass J., BENTO A. P., OVERINGTON J., Al-Lazikani B., and Johnson M. E.

Drug discovery today. Volume 15, Number 19-20, (2010), p.804–811

The proteomics identifications database: 2010 update

Vizcaino, J.A., Côté R., Reisinger F., Barsnes H., Foster J.M., Rameseder J., Hermjakob H., and Martens L.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D736–D742

Diversity of monomers in non-ribosomal peptides

CABOCHE, S., Leclère V., Pupin M., Kucherov G., and Jacques P.

Journal of Bacteriology. Volume 192, Number Issue 19, (2010), p.5143-5150 doi: 10.1128/JB.00315-10

The Ontology Lookup Service: bigger and better

Côté, R., Reisinger F., Martens L., Barsnes H., Vizcaino J.A., and Hermjakob H.

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W155–W160

Straightforward and complete deposition of NMR data to the PDBe

PENKETT, C. J., GINKEL VAN G., VELANKAR S., Swaminathan J., Ulrich E. L., Mading S., Stevens T. J., Fogh R. H., GUTMANAS A., KLEYWEGT G. J., et al.

Journal of Biomolecular NMR. Volume 48, Number Issue 2, (2010), p.85-92 doi: 10.1007/s10858-010-9439-3

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis

Sudbery, I., Enright A., Fraser A., and Dunham I.

BMC genomics. Volume 11, Number 1, (2010), p.175

The developmental expression dynamics of Drosophila melanogaster transcription factors

Adryan, B., and Teichmann S. A.

Genome biology. Volume 11, Number 4, (2010), p.R40

Nucleic acid sequence and structure databases

Washietl, S., and Hofacker I. L.

Methods in Molecular Biology. Volume 609, (2010), p.3-15

Visualization of macromolecular structures.

O'Donoghue, Seán I., Goodsell David S., Frangakis Achilleas S., Jossinet Fabrice, Laskowski Roman A., Nilges Michael, Saibil Helen R., Schafferhans Andrea, Wade Rebecca C., Westhof Eric, et al.

Nat Methods. Mar, Volume 7, Number 3 Suppl, (2010), p.S42–S55 doi: 10.1038/nmeth.1427

The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission

Tewari, R., Straschil U., Bateman A., Böhme U., Cherevach I., Gong P., Pain A., and Billker O.

Cell host & microbe. Volume 8, Number 4, (2010), p.377–387

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Xu, Q., Bateman A., Finn R. D., Abdubek P., Astakhova T., Axelrod H. L., Bakolitsa C., Carlton D., Chen C., Chiu H. J., et al.

Journal of molecular biology. Volume 396, Number 1, (2010), p.31–46

A standard variation file format for human genome sequences.

Reese, Martin G., Moore Barry, Batchelor Colin, Salas Fidel, Cunningham Fiona, Marth Gabor, Stein Lincoln, Flicek Paul, Yandell Mark, and Eilbeck Karen

Genome Biol. 8, Volume 11, Number 8, (2010), p.R88 doi: 10.1186/gb-2010-11-8-r88

A new bioinformatics analysis tools framework at EMBL–EBI

Goujon, Mickael, McWilliam Hamish, Li Weizhong, Valentin Franck, Squizzato Silvano, Paern Juri, and Lopez Rodrigo

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W695–W699

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis.

Dalloul, Rami A., Long Julie A., Zimin Aleksey V., Aslam Luqman, Beal Kathryn, Ann Blomberg Le, Bouffard Pascal, Burt David W., Crasta Oswald, Crooijmans Richard P. M. A., et al.

PLoS Biol. 9, Volume 8, Number 9, (2010), United States, p.e1000475 doi: 10.1371/journal.pbio.1000475

Non-redundant patent sequence databases with value-added annotations at two levels

Li, Weizhong, McWilliam Hamish, de la Torre Ana Richart, Grodowski Adam, Benediktovich Irina, Goujon Mickael, Nauche Stephane, and Lopez Rodrigo

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D52–D56

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Smedley, D., Schofield P., Chen C. K., Aidinis V., Ainali C., Bard J., Balling R., Birney E., Blake A., Bongcam-Rudloff E., et al.

Database: the journal of biological databases and curation. Volume 2010, (2010),

A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking.

Ballester, Pedro J., and Mitchell John B. O.

Bioinformatics. May, Volume 26, Number 9, (2010), p.1169–1175 doi: 10.1093/bioinformatics/btq112

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.

Kahraman, Abdullah, Morris Richard J., Laskowski Roman A., Favia Angelo D., and Thornton Janet M.

Proteins. Apr, Volume 78, Number 5, (2010), p.1120–1136 doi: 10.1002/prot.22633

Research The developmental expression dynamics of Drosophila melanogaster transcription factors

Adryan, B., and Teichmann S. A.

(2010),

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression

Git, A., Dvinge H., Salmon-Divon M., Osborne M., Kutter C., Hadfield J., Bertone P., and Caldas C.

RNA. May, Volume 16, Number 5, (2010), p.991–1006

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.

Tamuri, Asif U., and Laskowski Roman A.

Bioinformatics. May, Volume 26, Number 9, (2010), p.1260–1261 doi: 10.1093/bioinformatics/btq119

Dosage sensitivity shapes the evolution of copy-number varied regions

Schuster-Böckler, B., Conrad D., and Bateman A.

PloS one. Volume 5, Number 3, (2010), p.e9474

DUFs: families in search of function

Bateman, A., Coggill P., and Finn R. D.

Acta Crystallographica Section F: Structural Biology and Crystallization Communications. Volume 66, Number 10, (2010), p.1148–1152

eHive: An Artificial Intelligence workflow system for genomic analysis.

Severin, Jessica, Beal Kathryn, Vilella Albert J., Fitzgerald Stephen, Schuster Michael, Gordon Leo, Ureta-Vidal Abel, Flicek Paul, and Herrero Javier

BMC Bioinformatics. 5, Volume 11, Number 1, (2010), p.240 doi: 10.1186/1471-2105-11-240

A large-scale protein-function database

Apweiler, R., Armstrong R., Bairoch A., Cornish-Bowden A., Halling P. J., Hofmeyr J. H. S., Kettner C., Leyh T. S., Rohwer J., Schomburg D., et al.

Nature Chemical Biology. Volume 6, Number 11, (2010), p.785–785 doi: doi:10.1038/nchembio.460

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010

Hirschman, L., Sterk P., Field D., Wooley J., Cochrane G., Gilbert J., Kolker E., Kyrpides N., Meyer F., Mizrachi I., et al.

Stand Genomic Sci. Volume 2, Number 3, (2010), p.357-60

Mining Unique-m Substrings from Genomes

Ye, Kai, Jia Zhenyu, Wang Yipeng, Flicek Paul, and Apweiler Rolf

J Proteomics Bioinform. 3, Volume 3, (2010), p.099-100 doi: 10.4172/jpb.1000127

The BioPAX community standard for pathway data sharing

Demir, E., Cary M. P., Paley S., Fukuda K., Lemer C., Vastrik I., Wu G., D'Eustachio P., Schaefer C., Luciano J., et al.

Nature biotechnology. Volume 28, Number 9, (2010), p.935–942

Research funding. Sustaining the data and bioresource commons.

Schofield, Paul N., Eppig Janan, Huala Eva, Hrabe de Angelis Martin, Harvey Mark, Davidson Duncan, Weaver Tom, Brown Steve, Smedley Damian, Rosenthal Nadia, et al.

Science. 10, Volume 330, Number 6004, (2010), United States, p.592-3 doi: 10.1126/science.1191506

The renal gene ontology annotation initiative

ALAM-FARUQUE, Y., DIMMER E. C., HUNTLEY R. P., O’DONOVAN C., Scambler P., and Apweiler R.

Organogenesis. Volume 6, Number 2, (2010), p.71–75 doi:

MEMOPS: data modelling and automatic code generation

Fogh, R. H., Boucher W., Ionides J. M., VRANKEN W. F., Stevens T. J., and Laue E. D.

Journal of Integrative Bioinformatics. Volume 7, Number Issue 3, (2010), p.123 doi: 10.2390/biecoll-jib-2010-123

A community standard format for the representation of protein affinity reagents

Gloriam, D.E., Orchard S., Bertinetti D., Björling E., Bongcam-Rudloff E., Borrebaeck C. A. K., Bourbeillon J., Bradbury A. R. M., De Daruvar A., Dübel S., et al.

Molecular & Cellular Proteomics. Volume 9, Number 1, (2010), p.1–10

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets

Palmer, R. D., Murray M. J., Saini H. K., Van Dongen S., ABREU-GOODGER C., Muralidhar B., Pett M. R., Thornton C. M., Nicholson J. C., Enright A. J., et al.

Cancer research. Volume 70, Number 7, (2010), p.2911

The Pfam protein families database

Finn, R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G., Forslund K., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D211–D222

Non-redundant patent sequence databases with value-added annotations at two levels

Li, W., McWilliam H., de la Torre A. R., Grodowski A., Benediktovich I., GOUJON M., Nauche S., and Lopez R.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D52–D56

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.

Schuster, Eugene, McElwee Joshua J., Tullet Jennifer M. A., Doonan Ryan, Matthijssens Filip, Reece-Hoyes John S., Hope Ian A., Vanfleteren Jacques R., Thornton Janet M., and Gems David

Mol Syst Biol. Aug, Volume 6, (2010), p.399 doi: 10.1038/msb.2010.54

Consistent annotation of gene expression arrays.

Ballester, Benoit, Johnson Nathan, Proctor Glenn, and Flicek Paul

BMC Genomics. 5, Volume 11, Number 1, (2010), p.294 doi: 10.1186/1471-2164-11-294

International network of cancer genome projects.

Consortium, International Cancer Genome

Nature. 4, Volume 464, Number 7291, (2010), England, p.993-8 doi: 10.1038/nature08987

Allele-specific and heritable chromatin signatures in humans

Birney, E., Lieb J. D., Furey TS, Crawford G. E., and Iyer V. R.

Human molecular genetics. Volume 19, Number R2, (2010), p.R204–R209

Role of open chemical data in aiding drug discovery and design

GAULTON, A., and OVERINGTON J. P.

Future Med Chem. Volume 2, Number 6, (2010), p.903–907

Digital archives for molecular microscopy

BEST, C.

Proceedings of the 1st International Digital Preservation Interoperability Framework Symposium. (2010), doi: 10.1145/2039263.2039267

A domain level interaction network of amyloid precursor protein and A$\beta$ of Alzheimer's disease

Perreau, V. M., Orchard S., Adlard P. A., Bellingham S. A., Cappai R., Ciccotosto G. D., Cowie T. F., Crouch P. J., Duce J. A., Evin G., et al.

Proteomics. Volume 10, Number 12, (2010), p.2377–2395

Combined agonist–antagonist genome-wide functional screening identifies broadly active antiviral microRNAs

Santhakumar, D., Forster T., Laqtom N. N., Fragkoudis R., Dickinson P., ABREU-GOODGER C., MANAKOV S. A., Choudhury N. R., Griffiths S. J., Vermeulen A., et al.

Proceedings of the National Academy of Sciences. Volume 107, Number 31, (2010), p.13830–13835

A global map of human gene expression

Lukk, M., KAPUSHESKY M., Nikkilä J., Parkinson H., GONCALVES A., Huber W., Ukkonen E., and BRAZMA A.

Nature biotechnology. Volume 28, Number 4, (2010), p.322–324

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.

Chan, A. W. Edith, Laskowski Roman A., and Selwood David L.

J Med Chem. Apr, Volume 53, Number 8, (2010), p.3086–3094 doi: 10.1021/jm901696w

The universal protein resource (UniProt) in 2010

Apweiler, R., Martin MJ, O'Donovan C., Magrane M., Alam-Faruque Y., Antunes R., Barrell D., Bely B., Bingley M., Binns D., et al.

Nucleic Acids Res. Volume 38, (2010), p.D142–D148 doi:

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Swertz, Morris A., van der Velde Joeri K., Tesson Bruno M., Scheltema Richard A., Arends Danny, Vera Gonzalo, Alberts Rudi, Dijkstra Martijn, Schofield Paul, Schughart Klaus, et al.

Genome Biol. 3, Volume 11, Number 3, (2010), p.R27 doi: 10.1186/gb-2010-11-3-r27

EMMA–mouse mutant resources for the international scientific community.

Wilkinson, Phil, Sengerova Jitka, Matteoni Raffaele, Chen Chao-Kung K., Soulat Gaetan, Ureta-Vidal Abel, Fessele Sabine, Hagn Michael, Massimi Marzia, Pickford Karen, et al.

Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D570-6 doi: 10.1093/nar/gkp799

IPD—the immuno polymorphism database

Robinson, James, Mistry Kavita, McWilliam Hamish, Lopez Rodrigo, and Marsh Steven G. E.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D863–D869

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

Field, D., SANSONE S., DeLong E. F., Sterk P., Friedberg I., Kottmann R., Hirschman L., Garrity G., Cochrane G., Wooley J., et al.

Standards in genomic sciences. Volume 3, Number 3, (2010), p.232

A toolbox for predicting G-quadruplex formation and stability

Wong, H. M., Stegle O., Rodgers S., Huppert J. L., and others

J. Nucleic Acids. (2010),

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria

Gnad, F., Forner F., Zielinska D. F., Birney E., Gunawardena J., and Mann M.

Molecular & Cellular Proteomics. Volume 9, Number 12, (2010), p.2642–2653

Mapping plant interactomes using literature curated and predicted protein–protein interaction data sets

Lee, K. Y., Thorneycroft D., Achuthan P., Hermjakob H., and Ideker T.

The Plant Cell Online. Volume 22, Number 4, (2010), p.997–1005

Ensembl's 10th year

Flicek, P., Aken BL, Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., et al.

Nucleic Acids Research. Volume 38, (2010), p.D557-D562

Large scale comparison of global gene expression patterns in human and mouse

ZHENG-BRADLEY, X., Rung J., Parkinson H., and BRAZMA A.

Genome Biol. Volume 11, Number 12, (2010), p.R124

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci

Salmon-Divon, M., Dvinge H., Tammoja K., and Bertone P.

BMC Bioinformatics. Aug, Volume 11, Number 1, (2010), p.415

The (non)malignancy of cancerous amino acidic substitutions.

Talavera, David, Taylor Martin S., and Thornton Janet M.

Proteins. Feb, Volume 78, Number 3, (2010), p.518–529 doi: 10.1002/prot.22574

SnoPatrol: how many snoRNA genes are there

Gardner, P. P., Bateman A., Poole A. M., and others

J Biol. Volume 9, Number 4, (2010),

A database and API for variation, dense genotyping and resequencing data.

Rios, Daniel, McLaren William M., Chen Yuan, Birney Ewan, Stabenau Arne, Flicek Paul, and Cunningham Fiona

BMC Bioinformatics. 5, Volume 11, Number 1, (2010), p.238 doi: 10.1186/1471-2105-11-238

What are chemical structures and their relations?

HASTINGS, J., Batchelor C., Steinbeck C., and Schulz S.

Proceeding of the 2010 conference on Formal Ontology in Information Systems. (2010), p.257–270

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010

Field, D., SANSONE S., DeLong E. F., Sterk P., Friedberg I., Kottmann R., Hirschman L., Garrity G., Cochrane G., Wooley J., et al.

Stand Genomic Sci. Volume 3, Number 3, (2010), p.232-4

How to catch all those mutations–the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.

Kohonen-Corish, Maija R. J., Al-Aama Jumana Y., Auerbach Arleen D., Axton Myles, Barash Carol Isaacson, Bernstein Inge, Béroud Christophe, Burn John, Cunningham Fiona, Cutting Garry R., et al.

Hum Mutat. 12, Volume 31, Number 12, (2010), United States, p.1374-81 doi: 10.1002/humu.21379

Ensembl Genomes: extending Ensembl across the taxonomic space

Kersey, P. J., Lawson D., Birney E., Derwent PS, Haimel M., Herrero J., Keenan S., Kerhornou A., Koscielny G., Kähäri A., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D563–D569 doi:

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Arensburger, Peter, Megy Karine, Waterhouse Robert M., Abrudan Jenica, Amedeo Paolo, Antelo Beatriz, Bartholomay Lyric, Bidwell Shelby, Caler Elisabet, Camara Francisco, et al.

Science. 10, Volume 330, Number 6000, (2010), United States, p.86-8 doi: 10.1126/science.1191864

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

Atanur, S. S., Birol İ., Guryev V., Hirst M., Hummel O., Morrissey C., Behmoaras J., Fernandez-Suarez X. M., Johnson M. D., McLaren W. M., et al.

Genome research. Volume 20, Number 6, (2010), p.791–803

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases

Antonov, A.V., Schmidt E. E., Dietmann S., Krestyaninova M., and Hermjakob H.

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W78–W83

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

Löytynoja, A., and Goldman N.

BMC Bioinformatics. Volume 11, (2010), p.579

Modeling sample variables with an Experimental Factor Ontology

MALONE, J., HOLLOWAY E., ADAMUSIAK T., KAPUSHESKY M., Zheng J., KOLESNIKOV N., ZHUKOVA A., BRAZMA A., and Parkinson H.

Bioinformatics. Volume 26, Number 8, (2010), p.1112–1118

How do proteins gain new domains

Marsh, J. A., Teichmann S. A., and others

Genome Biol. Volume 11, Number 7, (2010), p.126

Sequences and topology: evolution of proteins and evolution of computational approaches

Teichmann, S. A., and Grishin N.

Current opinion in structural biology. Volume 20, Number 3, (2010), p.333–334

Protein structure databases.

Laskowski, Roman A.

Methods Mol Biol. Volume 609, (2010), p.59–82 doi: 10.1007/978-1-60327-241-4_4

Quantifying the mechanisms of domain gain in animal proteins

Buljan, M., Frankish A., Bateman A., and others

Genome Biol. Volume 11, (2010), p.R74

Time to underpin Wikipedia wisdom

Bateman, A., and Logan D. W.

Nature. Volume 468, Number 7325, (2010), p.765–765

Ensembl Variation Resources.

Chen, Yuan, Cunningham Fiona, Rios Daniel, McLaren William M., Smith James, Pritchard Bethan, Spudich Giulietta M., Brent Simon, Kulesha Eugene, Marin-Garcia Pablo, et al.

BMC Genomics. 5, Volume 11, Number 1, (2010), p.293 doi: 10.1186/1471-2164-11-293

CDK-Taverna: an open workflow environment for cheminformatics.

Kuhn, Thomas, Willighagen Egon L., Zielesny Achim, and Steinbeck Christoph

BMC Bioinformatics. Volume 11, Number 1, (2010), p.159 doi: 10.1186/1471-2105-11-159

The genome of a songbird.

Warren, Wesley C., Clayton David F., Ellegren Hans, Arnold Arthur P., Hillier LaDeana W., Künstner Axel, Searle Steve, White Simon, Vilella Albert J., Fairley Susan, et al.

Nature. 4, Volume 464, Number 7289, (2010), England, p.757-62 doi: 10.1038/nature08819

A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies

Stegle, O., Parts L., Durbin R., and Winn J.

PLoS computational biology. Volume 6, Number 5, (2010), p.e1000770

A new strategy for genome assembly using short sequence reads and reduced representation libraries

Young, A. L., Abaan H. O., Zerbino D., Mullikin J. C., Birney E., and Margulies E. H.

Genome research. Volume 20, Number 2, (2010), p.249–256

The consequence of natural selection on genetic variation in the mouse

Reuveni, E., Birney E., and Gross C. T.

Genomics. Volume 95, Number 4, (2010), p.196–202

Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens

Magariños, M. P., OVERINGTON J., Carmona S., Shanmugam D., Doyle M., Ralph S., Crowther G., Hertz-Fowler C., Nwaka S., Berriman M., et al.

BMC Bioinformatics. Volume 11, Number Suppl 10, (2010), p.O10

Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Gorbalenya, A. E., Lieutaud P., Harris M. R., Coutard B., Canard B., KLEYWEGT G. J., Kravchenko A. A., Samborskiy D. V., Sidorov I. A., Lentovich A. M., et al.

Antiviral Research. Volume 87, Number Issue 2, (2010), p.95-110 doi: 10.1016/j.antiviral.2010.02.005

Tackling Quantitation: A Report on the Annual Spring Workshop of the HUPO-PSI 28–30 March 2010, Seoul, South Korea

Orchard, S., Jones A., Albar J.P., Cho S.Y., Kwon K. H., Lee C., and Hermjakob H.

Proteomics. Volume 10, Number 17, (2010), p.3062–3066

Organelle proteomics experimental designs and analysis

Gatto, L., Vizcaino J.A., Hermjakob H., Huber W., and Lilley K. S.

Proteomics. Volume 10, Number 22, (2010), p.3957–3969

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression

Murray, M. J., Saini H. K., Van Dongen S., Palmer R. D., Muralidhar B., Pett M. R., Piipari M., Thornton C. M., Nicholson J. C., Enright A. J., et al.

Molecular cancer. Volume 9, Number 1, (2010), p.290

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease

McKinney, E. F., Lyons P. A., Carr E. J., Hollis J. L., Jayne D. R. W., Willcocks L. C., Koukoulaki M., BRAZMA A., Jovanovic V., Kemeny D. M., et al.

Nature medicine. Volume 16, Number 5, (2010), p.586–591

Molecular evolution and functional characterization of Drosophila insulin-like peptides.

Grönke, Sebastian, Clarke David-Francis, Broughton Susan, T. Andrews Daniel, and Partridge Linda

PLoS Genet. Feb, Volume 6, Number 2, (2010), p.e1000857 doi: 10.1371/journal.pgen.1000857

Heme proteins–diversity in structural characteristics, function, and folding.

Smith, Lorna J., Kahraman Abdullah, and Thornton Janet M.

Proteins. Aug, Volume 78, Number 10, (2010), p.2349–2368 doi: 10.1002/prot.22747

International network of cancer genome projects

Hudson, T. J., Anderson W., Aretz A., Barker A. D., Bell C., Bernabé R. R., Bhan MK, Calvo F., Eerola I., Gerhard D. S., et al.

Nature. Volume 464, Number 7291, (2010), p.993–998

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.

Smedley, Damian, Schofield Paul, Chen Chao-Kung K., Aidinis Vassilis, Ainali Chrysanthi, Bard Jonathan, Balling Rudi, Birney Ewan, Blake Andrew, Bongcam-Rudloff Erik, et al.

Database (Oxford). Volume 2010, (2010), England, p.baq014 doi: 10.1093/database/baq014

Ensembl Genomes: extending Ensembl across the taxonomic space.

Kersey, P. J., Lawson D., Birney E., Derwent PS, Haimel M., Herrero J., Keenan S., Kerhornou A., Koscielny G., Kähäri A., et al.

Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D563-9 doi: 10.1093/nar/gkp871

Tissue-specific rewiring of signalling pathways through alternatively spliced disordered segments

Buljan, M., Bateman A., and Babu M. M.

New Biotechnology. Volume 27, (2010), p.S31

Meeting report from the genomic standards consortium (GSC) workshop 10

Glass, E., Meyer F., Gilbert J. A., Field D., HUNTER S., Kottmann R., Kyrpides N., SANSONE S., Schriml L., Sterk P., et al.

Standards in genomic sciences. Volume 3, Number 3, (2010), p.225

Probabilistic latent variable models for distinguishing between cause and effect

Mooij, J., Stegle O., Janzing D., Zhang K., and Schölkopf B.

(2010),

An international bioinformatics infrastructure to underpin the Arabidopsis community

Bastow, R., Beynon J., Estelle M., Friesner J., Grotewold E., Lavagi I., Lindsey K., Meyers B., Provart N., Benfey P., et al.

(2010),

Validation of archived chemical shifts through atomic coordinates

Rieping, W., and VRANKEN W. F.

Proteins. Volume 78, Number Issue 3, (2010), p.2482-2489 doi: 10.1002/prot.22756

Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations”(MIBBI) workshop

Kettner, C., Field D., Sansone S.A., Taylor C., Aerts J., Binns N., Blake A., Britten C. M., de Marco A., Fostel J., et al.

Standards in genomic sciences. Volume 3, Number 3, (2010), p.259

The miR-144/451 locus is required for erythroid homeostasis

Rasmussen, K. D., Simmini S., ABREU-GOODGER C., BARTONICEK N., Di Giacomo M., Bilbao-Cortes D., Horos R., Von Lindern M., Enright A. J., and O’Carroll D.

The Journal of experimental medicine. Volume 207, Number 7, (2010), p.1351

SylArray: a web server for automated detection of miRNA effects from expression data

BARTONICEK, N., and Enright A. J.

Bioinformatics. Volume 26, Number 22, (2010), p.2900

Assessing computational methods of cis-regulatory module prediction

Su, J., Teichmann S. A., and Down T. A.

PLoS computational biology. Volume 6, Number 12, (2010), p.e1001020

The European Bioinformatics Institute's data resources

Brooksbank, C., Cameron G., and Thornton J.

Nucleic acids research. Volume 38, Number Database issue, (2010), p.D17-D25

Curators of the world unite: the International Society of Biocuration

Bateman, A.

Bioinformatics. Volume 26, Number 8, (2010), p.991

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

McLaren, William, Pritchard Bethan, Rios Daniel, Chen Yuan, Flicek Paul, and Cunningham Fiona

Bioinformatics. 6, Volume 26, Number 16, (2010), p.2069-70 doi: 10.1093/bioinformatics/btq330

So what have data standards ever done for us? The view from metabolomics.

Griffin, Julian L., and Steinbeck Christoph

Genome medicine. Volume 2, Number 6, (2010), p.38 doi: 10.1186/gm159

Rfam and Wikipedia: Harnessing people power| SciVee

Bateman, A.

scivee. (2010),

Meeting Report: BioSharing at ISMB 2010

Field, D., SANSONE S., DeLong E. F., Sterk P., Friedberg I., Gaudet P., Lewis S., Kottmann R., Hirschman L., Garrity G., et al.

Stand Genomic Sci. Volume 3, Number 3, (2010), p.254-8

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.

Atanur, Santosh S., Birol Inanç, Guryev Victor, Hirst Martin, Hummel Oliver, Morrissey Catherine, Behmoaras Jacques, Fernandez-Suarez Xose M., Johnson Michelle D., McLaren William M., et al.

Genome Res. 4, Volume 20, Number 6, (2010), p.791-803 doi: 10.1101/gr.103499.109

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding.

Schmidt, Dominic, Wilson Michael D., Ballester Benoit, Schwalie Petra C., Brown Gordon D., Marshall Aileen, Kutter Claudia, Watt Stephen, Martinez-Jimenez Celia P., Mackay Sarah, et al.

Science. 4, Volume 328, Number 5981, (2010), p.1036-40 doi: 10.1126/science.1186176

Design, implementation and updating of knowledge bases

HUNTER, S., Apweiler R., and Martin M. J.

Knowledge-Based Bioinformatics. (2010), p.87

Ensembl variation resources

Chen, Y., Cunningham F., Rios D., McLaren W. M., Smith J., Pritchard B., Spudich G. M., Brent S., Kulesha E., Marin-Garcia P., et al.

BMC genomics. Volume 11, Number 1, (2010), p.293

An atlas of combinatorial transcriptional regulation in mouse and man

Ravasi, T., Suzuki H., Cannistraci C. V., Katayama S., Bajic V. B., Tan K., Akalin A., Schmeier S., Kanamori-Katayama M., Bertin N., et al.

Cell. Volume 140, Number 5, (2010), p.744–752

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database

Pfreundt, U., James D. P., Tweedie S., WILSON D., Teichmann S. A., and Adryan B.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D443–D447

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins

Berka, Karel, Laskowski Roman A., Hobza Pavel, and Vondrášek Jiří

Journal of Chemical Theory and Computation. Volume 6, Number 7, (2010), p.2191-2203 doi: 10.1021/ct100007y

The impact of gene expression regulation on evolution of extracellular signaling pathways

Charoensawan, V., Adryan B., Martin S., Söllner C., Thisse B., Thisse C., Wright G. J., and Teichmann S. A.

Molecular & Cellular Proteomics. Volume 9, Number 12, (2010), p.2666–2677

MEROPS: the peptidase database

Rawlings, N. D., Barrett A. J., and Bateman A.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D227–D233

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

Vainshtein, Y., Sanchez M., BRAZMA A., Hentze M. W., Dandekar T., and Muckenthaler M. U.

BMC bioinformatics. Volume 11, Number 1, (2010), p.112

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

Shankar, R., Parkinson H., BURDETT T., HASTINGS E., Liu J., Miller M., Srinivasa R., White J., BRAZMA A., Sherlock G., et al.

Bioinformatics. Volume 26, Number 19, (2010), p.2470–2471

An international bioinformatics infrastructure to underpin the Arabidopsis community

Bastow, R., Beynon J., Estelle M., Friesner J., Grotewold E., Lavagi I., Lindsey K., Meyers B., Provart N., Benfey P., et al.

Plant Cell. Volume 22, Number 8, (2010), p.2530

Ten simple rules for editing Wikipedia

Logan, D. W., Sandal M., Gardner P. P., Manske M., and Bateman A.

PLoS computational biology. Volume 6, Number 9, (2010), p.e1000941

Touring Ensembl: a practical guide to genome browsing.

Spudich, Giulietta M., and Fernández-Suárez Xosé M.

BMC Genomics. Volume 11, (2010), England, p.295 doi: 10.1186/1471-2164-11-295

Substance concentrations as conditions for the realization of dispositions

HASTINGS, J., Steinbeck C., Jansen L., and Schulz S.

Semantic Applications in Life Sciences: Proceedings of the 4th International Workshop on Formal Biomedical Knowledge Representation, KR-MED. (2010), p.9–10

Archiving next generation sequencing data

Shumway, M., Cochrane G., and Sugawara H.

Nucleic Acids Res. Volume 38, Number Database issue, (2010), p.D870-1

Journal club. A computational geneticist looks at mechanisms of chromosomal evolution.

Flicek, Paul

Nature. 2, Volume 463, Number 7282, (2010), England, p.713 doi: 10.1038/463713e

The IntAct molecular interaction database in 2010

Aranda, B., Achuthan P., Alam-Faruque Y., Armean I., Bridge A., Derow C., Feuermann M., Ghanbarian AT, Kerrien S., Khadake J., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D525–D531

A database and API for variation, dense genotyping and resequencing data

Rios, D., McLaren W. M., Chen Y., Birney E., Stabenau A., Flicek P., and Cunningham F.

BMC bioinformatics. Volume 11, Number 1, (2010), p.238

Safeguarding the integrity of protein archive

Berman, H. M., KLEYWEGT G. J., Nakamura H., Markley J. L., and Burley S. K.

Nature. Volume 463, Number Issue 7280, (2010), p.425 doi: 10.1038/463425c

Minimum information about a protein affinity reagent (MIAPAR)

Bourbeillon, J., Orchard S., Benhar I., Borrebaeck C., De Daruvar A., Dübel S., Frank R., Gibson F., Gloriam D., Haslam N., et al.

Nature biotechnology. Volume 28, Number 7, (2010), p.650–653

Lineage-specific expansion of DNA-binding transcription factor families

Charoensawan, V., WILSON D., and Teichmann S. A.

Trends in Genetics. Volume 26, Number 9, (2010), p.388–393

Locus Reference Genomic sequences: an improved basis for describing human DNA variants

Dalgleish, R., Flicek P., Cunningham F., Astashyn A., Tully R. E., Proctor G., Chen Y., McLaren W. M., Larsson P., Vaughan B. W., et al.

Genome Med. Volume 2, Number 4, (2010), p.24

Mutations at key pore-lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates.

Calvanese, Luisa, Pellegrini-Calace Marialuisa, and Oliva Romina

FEBS Lett. Dec, Volume 584, Number 23, (2010), p.4797–4801 doi: 10.1016/j.febslet.2010.10.058

Sequence and structure analysis of noncoding RNAs

Washietl, S.

Methods in Molecular Biology. Volume 609, (2010), p.285-306

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.

Slack, Cathy, Werz Christian, Wieser Daniela, Alic Nazif, Foley Andrea, Stocker Hugo, Withers Dominic J., Thornton Janet M., Hafen Ernst, and Partridge Linda

PLoS Genet. Mar, Volume 6, Number 3, (2010), p.e1000881 doi: 10.1371/journal.pgen.1000881

Mouse Resource Browser–a database of mouse databases.

Zouberakis, Michael, Chandras Christina, Swertz Morris, Smedley Damian, Gruenberger Michael, Bard Jonathan, Schughart Klaus, Rosenthal Nadia, Hancock John M., Schofield Paul N., et al.

Database (Oxford). Volume 2010, (2010), England, p.baq010 doi: 10.1093/database/baq010

Ensembl's 10th year.

Flicek, Paul, Aken Bronwen L., Ballester Benoit, Beal Kathryn, Bragin Eugene, Brent Simon, Chen Yuan, Clapham Peter, Coates Guy, Fairley Susan, et al.

Nucleic Acids Res. 1, Volume 38, Number Database issue, (2010), England, p.D557-62 doi: 10.1093/nar/gkp972

Bioinformatics training: selecting an appropriate learning content management system—an example from the European Bioinformatics Institute

Wright, Victoria Ann, Vaughan Brendan W., Laurent Thomas, Lopez Rodrigo, Brooksbank Cath, and Schneider Maria Victoria

Briefings in bioinformatics. Volume 11, Number 6, (2010), p.552–562

The systematic annotation of the three main GPCR families in Reactome

Jassal, B., Jupe S., Caudy M., Birney E., Stein L., Hermjakob H., and D’Eustachio P.

Database: the journal of biological databases and curation. Volume 2010, (2010),

ISA software suite: Supporting standards-compliant experimental annotation and enabling curation at the community level

Rocca-Serra, P., BRANDIZI M., Maguire E., Sklyar N., TAYLOR C., Begley K., Field D., Harris S., Hide W., Hofmann O., et al.

Bioinformatics. Volume 26, Number 18, (2010), p.2354-2356

YhgC protects Bacillus anthracis from oxidative stress

Kiran, M. D., Bala S., Hirshberg M., and Balaban N.

International Journal of Artificial Organs. Volume 33, Number Issue 9, (2010), p.590-607 doi:

iMotifs: an integrated sequence motif visualization and analysis environment

Piipari, M., Down T. A., Saini H., Enright A., and Hubbard T. J. P.

Bioinformatics. Volume 26, Number 6, (2010), p.843–844

Integration of chemical information with protein sequences and 3D structures

Golovin, A., Henrick K., and Kleywegt G.

Journal of Cheminformatics. Volume 2, Issue Suppl. 1, (2010), doi: 10.1186/1758-2946-2-S1-O17

IPD—the immuno polymorphism database

Robinson, J., Mistry K., McWilliam H., Lopez R., and Marsh S. G. E.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D863–D869

Bioinformatics training: A review of challenges, actions and support requirements

Schneider, M. V., Watson J., Attwood T., Rother K., Budd A., McDowall J., Via A., Fernandes P., Nyronen T., Blicher T., et al.

Briefings in Bioinformatics. Volume 11, Number 6, (2010), p.544-551

Systemizing the structures and structuring the system

Levy, E. D., and Teichmann S. A.

Expert Review of Proteomics. Volume 7, Number 3, (2010), p.319–322

Chemical Entities of Biological Interest: an update.

De Matos, Paula, Alcantara Rafael, Dekker Adriano, Ennis Marcus, Hastings Janna, Haug Kenneth, Spiteri Inmaculada, Turner Steve, and Steinbeck Christoph

Nucleic Acids Research. jan, Volume 38, Number Database issue, (2010), p.D249–D254 doi: 10.1093/nar/gkp886

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources

COCHRANE, G. R., and Galperin M. Y.

Nucleic Acids Res. Volume 38, Number Database issue, (2010), p.D1-4

A CTCF-independent role for cohesin in tissue-specific transcription.

Schmidt, Dominic, Schwalie Petra C., Ross-Innes Caryn S., Hurtado Antoni, Brown Gordon D., Carroll Jason S., Flicek Paul, and Odom Duncan T.

Genome Res. 4, Volume 20, Number 5, (2010), p.578-88 doi: 10.1101/gr.100479.109

Heritable individual-specific and allele-specific chromatin signatures in humans.

McDaniell, Ryan, Lee Bum-Kyu K., Song Lingyun, Liu Zheng, Boyle Alan P., Erdos Michael R., Scott Laura J., Morken Mario A., Kucera Katerina S., Battenhouse Anna, et al.

Science. 4, Volume 328, Number 5975, (2010), United States, p.235-9 doi: 10.1126/science.1184655

Public data archives for genomic structural variation

Church, D. M., LAPPALAINEN I., Sneddon T. P., HINTON J., MAGUIRE M., Lopez J., Garner J., Paschall J., Dicuccio M., Yaschenko E., et al.

Nature Genetics. Volume 42, Number 10, (2010), p.813-814

Approximate maximum parsimony and ancestral maximum likelihood

Alon, N., Chor B., Pardi F., and Rapoport A.

IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 7, (2010), p.183-187

Gene expression atlas at the European bioinformatics institute

KAPUSHESKY, M., EMAM I., HOLLOWAY E., KURNOSOV P., ZORIN A., MALONE J., RUSTICI G., WILLIAMS E., Parkinson H., and BRAZMA A.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D690–D698

Genomic repertoires of DNA-binding transcription factors across the tree of life

Charoensawan, V., WILSON D., and Teichmann S. A.

Nucleic acids research. Volume 38, Number 21, (2010), p.7364–7377

Domain-ligand mapping for enzymes.

Bashton, Matthew, and Thornton Janet M.

J Mol Recognit. Volume 23, Number 2, (2010), p.194–208 doi: 10.1002/jmr.992

The CoFactor database: organic cofactors in enzyme catalysis.

Fischer, Julia D., Holliday Gemma L., and Thornton Janet M.

Bioinformatics. Oct, Volume 26, Number 19, (2010), p.2496–2497 doi: 10.1093/bioinformatics/btq442

Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action

Kapitzky, L., Beltrao P., Berens T. J., Gassner N., Zhou C., Wüster A., Wu J., Babu M. M., Elledge S. J., Toczyski D., et al.

Molecular Systems Biology. Volume 6, Number 1, (2010),

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.

Sudbery, Ian, Enright Anton J., Fraser Andrew G., and Dunham Ian

BMC Genomics. Volume 11, (2010), England, p.175 doi: 10.1186/1471-2164-11-175

Representing chemicals using OWL, description graphs and rules

HASTINGS, J., Dumontier M., Hull D., Horridge M., Steinbeck C., Sattler U., Stevens R., Horne T., and Britz K.

CEUR Workshop Proceedings. Volume 614, (2010),

Improvements to services at the European Nucleotide Archive

Leinonen, R., Akhtar R., Birney E., Bonfield J., Bower L., Corbett M., Cheng Y., Demiralp F., Faruque N., Goodgame N., et al.

Nucleic Acids Res. Volume 38, Number Database issue, (2010), p.D39-45

Public data archives for genomic structural variation.

Church, Deanna M., Lappalainen Ilkka, Sneddon Tam P., Hinton Jonathan, Maguire Michael, Lopez John, Garner John, Paschall Justin, Dicuccio Michael, Yaschenko Eugene, et al.

Nat Genet. 10, Volume 42, Number 10, (2010), United States, p.813-4 doi: 10.1038/ng1010-813

BioCatalogue: a universal catalogue of web services for the life sciences

Bhagat, Jiten, Tanoh Franck, Nzuobontane Eric, Laurent Thomas, Orlowski Jerzy, Roos Marco, Wolstencroft Katy, Aleksejevs Sergejs, Stevens Robert, Pettifer Steve, et al.

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W689–W694

implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

Orchard, S., Albar J.P., Deutsch E.W., Eisenacher M., Binz P.A., and Hermjakob H.

Proteomics. Volume 10, Number 10, (2010), p.1895–1898

Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling

Martin, S., Söllner C., Charoensawan V., Adryan B., Thisse B., Thisse C., Teichmann S., and Wright G. J.

Molecular & Cellular Proteomics. Volume 9, Number 12, (2010), p.2654–2665

The European Bioinformatics Institute's data resources.

Brooksbank, Catherine, Cameron Graham, and Thornton Janet M.

Nucleic Acids Res. Jan, Volume 38, Number Database issue, (2010), p.D17–D25 doi: 10.1093/nar/gkp986

BioCatalogue: a universal catalogue of web services for the life sciences

Bhagat, J., Tanoh F., NZUOBONTANE E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S., et al.

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W689–W694

Public data resources as a foundation for a worldwide metagenomics data infrastructure

Cochrane, G., Martin M. J., and Apweiler R.

Metagenomics: Theory, Methods and Applications. (2010), p.79

ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner.

Law, Martin J., Lower Karen M., Voon Hsiao P. J., Hughes Jim R., Garrick David, Viprakasit Vip, Mitson Matthew, De Gobbi Marco, Marra Marco, Morris Andrew, et al.

Cell. 10, Volume 143, Number 3, (2010), United States, p.367-78 doi: 10.1016/j.cell.2010.09.023

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.

Gheldof, Nele, Smith Emily M., Tabuchi Tomoko M., Koch Christoph M., Dunham Ian, Stamatoyannopoulos John A., and Dekker Job

Nucleic Acids Res. 7, Volume 38, Number 13, (2010), England, p.4325-36 doi: 10.1093/nar/gkq175

Meeting report: BioSharing at ISMB 2010

Field, D., SANSONE S., DeLong E. F., Sterk P., Friedberg I., Gaudet P., Lewis S., Kottmann R., Hirschman L., Garrity G., et al.

Standards in genomic sciences. Volume 3, Number 3, (2010), p.254

UniRule–Automatic Annotation In UniProtKB

Bridge, A. J., POGGIOLI D., and O'Donovan C.

(2010), doi:

Bioinformatics training: selecting an appropriate learning content management system—an example from the European Bioinformatics Institute

Wright, V. A., Vaughan B. W., Laurent T., Lopez R., Brooksbank C., and Schneider M. V.

Briefings in bioinformatics. Volume 11, Number 6, (2010), p.552–562

Bioinformatics training: Selecting an appropriate learning content management systemc-an example from the European Bioinformatics Institute

Wright, V. A., Vaughan B. W., Laurent T., Lopez R., Brooksbank C., and Schneider M. V.

Briefings in Bioinformatics. Volume 11, Number 6, (2010), p.552-562

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.

Oliva, Romina, Calamita Giuseppe, Thornton Janet M., and Pellegrini-Calace Marialuisa

Proc Natl Acad Sci U S A. Mar, Volume 107, Number 9, (2010), p.4135–4140 doi: 10.1073/pnas.0910632107

Quantitative genetic interactions reveal biological modularity

Beltrao, P., Cagney G., and Krogan N. J.

Cell. Volume 141, Number 5, (2010), p.739–745 doi:

Genome Biology

Buljan, M., Frankish A., and Bateman A.

Genome Biology. Volume 11, (2010), p.R74

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

Dalgleish, Raymond, Flicek Paul, Cunningham Fiona, Astashyn Alex, Tully Raymond E., Proctor Glenn, Chen Yuan, McLaren William M., Larsson Pontus, Vaughan Brendan W., et al.

Genome Med. 4, Volume 2, Number 4, (2010), p.24 doi: 10.1186/gm145

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

Schnetz, Michael P., Handoko Lusy, Akhtar-Zaidi Batool, Bartels Cynthia F., Pereira Filipe C., Fisher Amanda G., Adams David J., Flicek Paul, Crawford Gregory E., Laframboise Thomas, et al.

PLoS Genet. Volume 6, Number 7, (2010), United States, p.e1001023 doi: 10.1371/journal.pgen.1001023

An effective model for natural selection in promoters

Hoffman, M. M., and Birney E.

Genome research. Volume 20, Number 5, (2010), p.685–692

Assemblies: the good, the bad, the ugly

Birney, E.

Nature Methods. Volume 8, Number 1, (2010), p.59–60

A small cell lung cancer genome reports complex tobacco exposure signatures

Pleasance, E. D., Stephens P. J., O'Meara S., McBride D. J., Meynert A., Jones D., Lin M. L., Beare D., Lau K. W., Greenman C., et al.

Nature. Volume 463, Number 7278, (2010), p.184

Modeling sample variables with an Experimental Factor Ontology

MALONE, J., HOLLOWAY E., ADAMUSIAK T., KAPUSHESKY M., Zheng J., KOLESNIKOV N., ZHUKOVA A., BRAZMA A., and Parkinson H.

Bioinformatics. Volume 26, Number 8, (2010), p.1112-1118

Crystal contacts as nature’s docking solutions

Krissinel, E. B.

Journal of Computational Chemistry. Volume 31, Number Issue 1, (2010), p.133-143 doi: 10.1002/jcc.21303

The publication and database deposition of molecular interaction data

Orchard, S., Aranda B., and Hermjakob H.

Current Protocols in Protein Science. (2010), p.25–3

MapMi: automated mapping of microRNA loci

Guerra-Assunção, J., and Enright A.

BMC bioinformatics. Volume 11, Number 1, (2010), p.133

Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases.

Ballester, Pedro J., Westwood Isaac, Laurieri Nicola, Sim Edith, and W. Richards Graham

J R Soc Interface. Feb, Volume 7, Number 43, (2010), p.335–342 doi: 10.1098/rsif.2009.0170

The (non)malignancy of cancerous amino acidic substitutions

Talavera, D., Taylor M. S., and Thornton J. M.

Proteins. Volume 78, (2010), p.518-529

Homomeric protein complexes: evolution and assembly

Venkatakrishnan, AJ, Levy E. D., Teichmann S. A., and others

Biochemical Society Transactions. Volume 38, Number 4, (2010), p.879

The structures and physicochemical properties of organic cofactors in biocatalysis.

Fischer, Julia D., Holliday Gemma L., Rahman Syed A., and Thornton Janet M.

J Mol Biol. Nov, Volume 403, Number 5, (2010), p.803–824 doi: 10.1016/j.jmb.2010.09.018

A new bioinformatics analysis tools framework at EMBL–EBI

GOUJON, M., McWilliam H., Li W., Valentin F., Squizzato S., Paern J., and Lopez R.

Nucleic acids research. Volume 38, Number suppl 2, (2010), p.W695–W699

Evolution of the transcription factor repertoires in the Saccharomycotina

Hess, J.

(2010),

2009

Visualising the Epigenome

Flicek, Paul, and Birney Ewan

Epigenomics. (2009), p.55-66

Applications of Graph Theory in Chemo- and Bioinformatics

Dimitropoulos, D., Golovin A., John M., and Krissinel E.

Analysis of Complex Networks. (2009), p.chapter 9, 221-244 doi: 10.1002.1002/9/9783527981.ch9

Comparative genomics and mammalian promoter evolution

Taylor, M. S., Jordan G. E., and Semple C. A. M.

Cap-Analysis Gene Expression (CAGE). (2009), Singapore, p.209-222

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease

Watson, James D., and Thornton Janet M.

From Molecules to Medicines. (2009), p.201-215 doi: 10.1007/978-90-481-2339-1_13

Integrated Servers for Structure-Informed Function Prediction

Laskowski, Roman A.

From Protein Structure to Function with Bioinformatics. (2009), p.251-272

The Worldwide Protein Data Bank

Berman, H. M., Henrick K., Nakamura H., and Markley J. L.

Structural Bioinformatics. (2009), p.chapter 11, 293-303. doi:

Structure Quality Assurance

Laskowski, Roman A.

Structural Bioinformatics. (2009), p.341-375

Discovering temporal patterns of differential gene expression in microarray time series

Stegle, O., Denby K., McHattie S., Meade S., Wild D. L., Ghahramani Z., and Borgwardt K.

German Conference on Bioinformatics. (2009), doi:

Visualization of large microarray experiments with space maps

GEHLENBORG, N., and BRAZMA A.

BMC Bioinformatics. Volume 10, Number Suppl 13, (2009), p.O7

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.

Pellegrini-Calace, Marialuisa, Maiwald Tim, and Thornton Janet M.

PLoS Comput Biol. Jul, Volume 5, Number 7, (2009), p.e1000440 doi: 10.1371/journal.pcbi.1000440

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R

Dvinge, H., and Bertone P.

Bioinformatics. Dec, Volume 25, Number 24, (2009), p.3325–3326

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

Bateman, A., Finn R. D., Sims P. J., Wiedmer T., Biegert A., and Söding J.

Bioinformatics. Volume 25, Number 2, (2009), p.159–162

Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion.

Bonaglia, Maria Clara, Giorda Roberto, Beri Silvana, Bigoni Stefania, Sensi Alberto, Baroncini Anna, Capucci Antonella, De Agostini Cristina, Gwilliam Rhian, Deloukas Panos, et al.

Eur J Hum Genet. 4, Volume 17, Number 4, (2009), England, p.426-33 doi: 10.1038/ejhg.2008.195

The structure of Jann\_2411 (DUF1470) from Jannaschia sp. at 1.45 A resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

Bakolitsa, C., Bateman A., Jin K. K., McMullan D., Krishna S. S., Miller M. D., Abdubek P., Acosta C., Astakhova T., Axelrod H. L., et al.

Acta Crystallographica Section F: Structural Biology and Crystallization Communications. Volume 66, Number 10, (2009), p.1198–1204

Highlights from the Fifth International Society for Computational Biology (ISCB) Student Council Symposium

Abeel, T., de Ridder J., Schultheiss S. J., Busch W., Chikhi R., Lavenier D., Van Du Tran P. C., Koeva M., Forsberg C., Lee P. H., et al.

(2009),

New open drug activity data at EBI

Steinbeck, C., Al-Lazikani B., Hermjakob H., Overington J., and Thornton J.

Chemistry Central Journal. Volume 3, (2009), p.1–1

11beta-Hydroxysteroid dehydrogenase type 1 inhibitors with oleanan and ursan scaffolds.

Blum, Andreas, Favia Angelo D., and Maser Edmund

Mol Cell Endocrinol. Mar, Volume 301, Number 1-2, (2009), p.132–136 doi: 10.1016/j.mce.2008.08.028

Importing arrayexpress datasets into r/bioconductor

KAUFFMANN, A., Rayner T. F., Parkinson H., KAPUSHESKY M., Lukk M., BRAZMA A., and Huber W.

Bioinformatics. Volume 25, Number 16, (2009), p.2092–2094

Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.

Selman, Colin, Tullet Jennifer M. A., Wieser Daniela, Irvine Elaine, Lingard Steven J., Choudhury Agharul I., Claret Marc, Al-Qassab Hind, Carmignac Danielle, Ramadani Faruk, et al.

Science. Oct, Volume 326, Number 5949, (2009), p.140–144 doi: 10.1126/science.1177221

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Pruitt, Kim D., Harrow Jennifer, Harte Rachel A., Wallin Craig, Diekhans Mark, Maglott Donna R., Searle Steve, Farrell Catherine M., Loveland Jane E., Ruef Barbara J., et al.

Genome Res. 7, Volume 19, Number 7, (2009), United States, p.1316-23 doi: 10.1101/gr.080531.108

OrChem - An open source chemistry search engine for Oracle(R).

Rijnbeek, Mark, and Steinbeck Christoph

Journal of cheminformatics. Volume 1, Number 1, (2009), p.17 doi: 10.1186/1758-2946-1-17

DATABASE Editorial Board 2009

Landsman, D., Gentleman R., Kelso J., Ouellette F., Altman R., Attwood T., Bader G., Bairoch A., Bateman A., Baxevanis A. D., et al.

DATABASE. (2009),

Present and future of proteomics data curation at the PRIDE database

Vizcaino, J.A., Hermjakob H., and Martens L.

(2009),

New open drug activity data at EBI

Steinbeck, Christoph, Al-Lazikani B, Hermjakob Henning, Overington John, and Thornton Janet M.

Chemistry Central Journal. Volume 3, Number Suppl 1, (2009), p.O3 doi: 10.1186/1752-153X-3-S1-O3

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

Paten, Benedict, Herrero Javier, Beal Kathryn, and Birney Ewan

Bioinformatics. 2, Volume 25, Number 3, (2009), England, p.295-301 doi: 10.1093/bioinformatics/btn630

Ensembl 2009.

Hubbard, T. J. P., Aken BL, Ayling S., Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Clarke L., et al.

Nucleic Acids Res. 1, Volume 37, Number Database issue, (2009), England, p.D690-7 doi: 10.1093/nar/gkn828

InterPro: the integrative protein signature database

Hunter, Sarah, Apweiler Rolf, Attwood Teresa K., Bairoch Amos, Bateman Alex, Binns David, Bork Peer, Das Ujjwal, Daugherty Louise, Duquenne Lauranne, et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D211–D215

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009

Galperin, M. Y., and COCHRANE G. R.

Nucleic Acids Res. Volume 37, Number Database issue, (2009), p.D1-4

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Pruitt, K. D., Harrow J., Harte R. A., Wallin C., Diekhans M., Maglott D. R., Searle S., Farrell C. M., Loveland J. E., Ruef B. J., et al.

Genome research. Volume 19, Number 7, (2009), p.1316–1323

Inference algorithms and learning theory for Bayesian sparse factor analysis

Rattray, M., Stegle O., Sharp K., and Winn J.

Journal of Physics: Conference Series. Volume 197, (2009), p.012002

Gene expression Atlas at the European Bioinformatics Institute

KAPUSHESKY, M., EMAM I., HOLLOWAY E., KURNOSOV P., ZORIN A., MALONE J., RUSTICI G., WILLIAMS E., Parkinson H., and BRAZMA A.

Nucleic Acids Research. Volume 38, Number SUPPL.1, (2009), p.D690-D698

CASD-NMR: critical assessment of automated structure determination by NMR

Rosato, A., Bagaria A., Baker D., Bardiaux B., Cavalli A., Doreleijers J. F., Giachetti A., Guerry P., Güntert P., Herrmann T., et al.

Nature Methods. Volume 6, Number Issue 9, (2009), p.625-626 doi: 10.1038/nmeth0909-625

Second Joint HUPO Publication and Proteomics Standards Initiative Workshop

Orchard, S., Binz P.A., and Hermjakob H.

Proteomics. Volume 9, Number 19, (2009), p.4426–4428

The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development

Wilson, N. K., Miranda-Saavedra D., Kinston S., Bonadies N., Foster S. D., Calero-Nieto F., Dawson M. A., Donaldson I. J., Dumon S., Frampton J., et al.

Blood. Volume 113, Number 22, (2009), p.5456–5465

BloodExpress: a database of gene expression in mouse haematopoiesis

Miranda-Saavedra, D., De S., Trotter M. W., Teichmann S. A., and Göttgens B.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D873–D879

MEROPS: the peptidase database

Rawlings, N. D., Barrett A. J., and Bateman A.

Nucleic Acids Res. Volume 38, (2009), p.D227–233

New open drug activity data at EBI

Steinbeck, C., Al-Lazikani B., Hermjakob H., OVERINGTON J., and Thornton J.

Chemistry Central Journal. Volume 3, (2009), p.1–1

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy-The Amsterdam Principles

Rodriguez, H., Snyder M., Uhlén M., Andrews P., Beavis R., Borchers C., Chalkley R. J., Cho S.Y., Cottingham K., Dunn M., et al.

Journal of proteome research. Volume 8, Number 7, (2009), p.3689

Assigning strains to bacterial species via the internet

Bishop, C. J., Aanensen D. M., Jordan G. E., Kilian M., Hanage W. P., and Spratt B. G.

BMC Biology. Volume 7, (2009), p.3

A chemogenomics view on protein-ligand spaces

Strömbergsson, H., and KLEYWEGT G. J.

BMC Bioinformatics. Volume 10, Number Supplement 6, (2009), p.S13 doi: 10.1186/1471-2105-10-S6-S13

Prepublication data sharing.

Birney, Ewan, Hudson Thomas J., Green Eric D., Gunter Chris, Eddy Sean, Rogers Jane, Harris Jennifer R., S. Ehrlich Dusko, Apweiler Rolf, Austin Christopher P., et al.

Nature. Sep, Volume 461, Number 7261, (2009), p.168–170 doi: 10.1038/461168a

PDBsum new things.

Laskowski, Roman A.

Nucleic Acids Res. Jan, Volume 37, Number Database issue, (2009), p.D355–D359 doi: 10.1093/nar/gkn860

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Bruce, Alexander W., López-Contreras Andrés J., Flicek Paul, Down Thomas A., Dhami Pawandeep, Dillon Shane C., Koch Christoph M., Langford Cordelia F., Dunham Ian, Andrews Robert M., et al.

Genome Res. 4, Volume 19, Number 6, (2009), p.994-1005 doi: 10.1101/gr.089086.108

Bioclipse 2: a scriptable integration platform for the life sciences.

Spjuth, Ola, Alvarsson Jonathan, Berg Arvid, Eklund Martin, Kuhn Stefan, Masak Carl, Torrance Gilleain, Wagener Johannes, Willighagen Egon L., Steinbeck Christoph, et al.

BMC Bioinformatics. Volume 10, Number 1, (2009), p.397 doi: 10.1186/1471-2105-10-397

Benefits and Best Practices of Rapid Pre-Publication Data Release

Birney, E., Hudson T. J., Green E. D., Gunter C., Eddy S., Rogers J., Harris J. R., Ehrlich S. D., Apweiler R., Austin C. P., et al.

Nature. Volume 461, Number 7261, (2009), p.168

MAPU 2.0: high-accuracy proteomes mapped to genomes

Gnad, F., Oroshi M., Birney E., and Mann M.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D902–D906

Recurated protein interaction datasets

Salwinski, L., Licata L., Winter A., Thorneycroft D., Khadake J., Ceol A., Aryamontri A. C., Oughtred R., Livstone M., Boucher L., et al.

Nature methods. Volume 6, Number 12, (2009), p.860–861

Finding query suggestions for PubMed

Lu, Z., Wilbur W. J., McEntyre J. R., Iskhakov A., and Szilagyi L.

AMIA Annual Symposium Proceedings. Volume 2009, (2009), p.396

Genomic DNA $k$-mer spectra: models and modalities

Chor, B., Horn D., Levy Y., Goldman N., and Massingham T.

Genome Biology. Volume 10, (2009), p.R108

A census of human transcription factors: function, expression and evolution

VAQUERIZAS, J. M., Kummerfeld S. K., Teichmann S. A., and Luscombe N. M.

Nature Reviews Genetics. Volume 10, Number 4, (2009), p.252–263

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

Parkinson, H., KAPUSHESKY M., KOLESNIKOV N., RUSTICI G., Shojatalab M., ABEYGUNAWARDENA N., Berube H., DYLAG M., EMAM I., FARNE A., et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D868–D872

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.

Andreini, Claudia, Bertini Ivano, Cavallaro Gabriele, Najmanovich Rafael J., and Thornton Janet M.

J Mol Biol. May, Volume 388, Number 2, (2009), p.356–380 doi: 10.1016/j.jmb.2009.02.052

Toll-like receptor stimulation differentially regulates vasoactive intestinal peptide type 2 receptor in macrophages.

Herrera, Juan Luis, Gonzalez-Rey Elena, Fernandez-Montesinos Rafael, Quintana Francisco J., Najmanovich Rafael, and Pozo David

J Cell Mol Med. Sep, Volume 13, Number 9B, (2009), p.3209–3217 doi: 10.1111/j.1582-4934.2009.00662.x

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.

Soranzo, Nicole, Spector Tim D., Mangino Massimo, Kühnel Brigitte, Rendon Augusto, Teumer Alexander, Willenborg Christina, Wright Benjamin, Chen Li, Li Mingyao, et al.

Nat Genet. Nov, Volume 41, Number 11, (2009), p.1182–1190 doi: 10.1038/ng.467

Bioinformatics for next generation sequencing

Bateman, A., and QUACKENBUSH J.

Bioinformatics. (2009),

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.

Carlile, Mark, Swan Daniel, Jackson Kelly, Preston-Fayers Keziah, Ballester Benoit, Flicek Paul, and Werner Andreas

Nucleic Acids Res. 2, Volume 37, Number 7, (2009), p.2274-82 doi: 10.1093/nar/gkp088

Ten Simple Rules for Chairing a Scientific Session

Bateman, A., and Bourne P. E.

PLoS Computational Biology. Volume 5, Number 9, (2009), p.e1000517

Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7

Field, D., Sterk P., Kyrpides N., Kottmann R., Glockner F. O., Hirschman L., Garrity G. M., Wooley J., and Gilna P.

Stand Genomic Sci. Volume 1, Number 1, (2009), p.68-71

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler

Zerbino, D. R., McEwen G. K., Margulies E. H., and Birney E.

PloS one. Volume 4, Number 12, (2009), p.e8407

The genome of the blood fluke Schistosoma mansoni

Berriman, M., Haas B. J., LoVerde P. T., Wilson R. A., Dillon G. P., Cerqueira G. C., Mashiyama S. T., Al-Lazikani B., Andrade L. F., Ashton P. D., et al.

Nature. Volume 460, Number 7253, (2009), p.352–358

On vital aid: the why, what and how of validation

KLEYWEGT, G. J.

Acta Crystallographica Section D. Volume 65, Number Part 2, (2009), p.134-139 doi: 10.1107/S090744490900081X

Protein-protein interactions: analysis and prediction

Frishman, D., Albrecht M., Blankenburg H., Bork P., Harrington E. D., Hermjakob H., Jensen L.J., Juan D. A., Lengauer T., Pagel P., et al.

Modern genome annotation: The biosapiens network. (2009), p.353–410

A HaemAtlas: characterizing gene expression in differentiated human blood cells

Watkins, N. A., Gusnanto A., de Bono B., De S., Miranda-Saavedra D., Hardie D. L., Angenent W. G. J., Attwood A. P., Ellis P. D., Erber W., et al.

Blood. Volume 113, Number 19, (2009), p.e1–e9

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization

Mishima, Y., ABREU-GOODGER C., Staton A. A., Stahlhut C., Shou C., Cheng C., Gerstein M., Enright A. J., and Giraldez A. J.

Genes & development. Volume 23, Number 5, (2009), p.619

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation

Manakov, S., Grant S., and Enright A.

BMC genomics. Volume 10, Number 1, (2009), p.419

Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis.

El-Hawari, Yasser, Favia Angelo D., Pilka Ewa S., Kisiela Michael, Oppermann Udo, Martin Hans-Jörg, and Maser Edmund

Chem Biol Interact. Mar, Volume 178, Number 1-3, (2009), p.234–241 doi: 10.1016/j.cbi.2008.11.004

Rfam: updates to the RNA families database

Gardner, P. P., Daub J., Tate J. G., Nawrocki E. P., Kolbe D. L., Lindgreen S., Wilkinson A. C., Finn R. D., Griffiths-Jones S., Eddy S. R., et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D136–D140

The European Bioinformatics Institute's data resources

Brooksbank, C., Cameron G., and Thornton J.

Nucleic Acids Research. Volume 38, Number SUPPL.1, (2009), p.D17-D25

18-P009 Regulation and evolution of an extracellular glycoprotein interaction network

Martin, S., Charoensawan V., Soellner C., Adryan B., Thisse B., Thisse C., Teichmann S., and Wright G.

Mechanisms of Development. Volume 126, (2009), p.S287

ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs

Encinar, JA, Fernandez-Ballester G., Sánchez I. E., Hurtado-Gomez E., Stricher F., Beltrao P., and Serrano L.

Bioinformatics. Volume 25, Number 18, (2009), p.2418–2424

The evolution of protein domain families

Buljan, M., Bateman A., and others

Biochem Soc Trans. Volume 37, Number Pt 4, (2009), p.751–755

Models for financial sustainability of biological databases and resources.

Chandras, Christina, Weaver Thomas, Zouberakis Michael, Smedley Damian, Schughart Klaus, Rosenthal Nadia, Hancock John M., Kollias George, Schofield Paul N., and Aidinis Vassilis

Database (Oxford). Volume 2009, (2009), p.bap017 doi: 10.1093/database/bap017

QuickGO: a user tutorial for the web-based Gene Ontology browser

HUNTLEY, R. P., Binns D., DIMMER E., Barrell D., O’DONOVAN C., and Apweiler R.

Database: the journal of biological databases and curation. Volume 2009, (2009), doi:

Data Deposition and Annotation at the Worldwide Protein Data Bank

Dutta, S., Burkhardt K., Young J., SWAMINATHAN G. J., Matsuura T., Henrick K., Nakamura H., and Berman H. M.

Molecular Biotechnology. Volume 42, Number Issue 1, (2009), p.1-13 doi: 10.1007/s12033-008-9127-7

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures

Berka, Karel, Laskowski Roman A., Riley Kevin E., Hobza Pavel, and Vondrášek Jiří

Journal of Chemical Theory and Computation. Volume 5, Number 4, (2009), p.982-992 doi: 10.1021/ct800508v

Missing in action: enzyme functional annotations in biological databases.

Furnham, Nicholas, Garavelli John S., Apweiler Rolf, and Thornton Janet M.

Nat Chem Biol. Aug, Volume 5, Number 8, (2009), p.521–525 doi: 10.1038/nchembio0809-521

In defense of statistical methods for detecting positive selection

Yang, Z., Nielsen R., and Goldman N.

Proceedings of the National Academy of Sciences U.S.A.. Volume 106, (2009), p.E95

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback

Aligianni, S., Lackner D. H., Klier S., RUSTICI G., Wilhelm B. T., Marguerat S., Codlin S., BRAZMA A., de Bruin R. A. M., and Bähler J.

PLoS genetics. Volume 5, Number 8, (2009), p.e1000626

BioCatalogue: a curated Web Service registry for the Life Science community

Goble, C. A., Belhajjame K., Tanoh F., Bhagat J., Wolstencroft K., Stevens R., NZUOBONTANE E., McWilliam H., Laurent T., and Lopez R.

(2009),

Genome and proteome annotation: organization, interpretation and integration.

Reeves, Gabrielle A., Talavera David, and Thornton Janet M.

J R Soc Interface. Feb, Volume 6, Number 31, (2009), p.129–147 doi: 10.1098/rsif.2008.0341

Remote homology detection using a kernel method that combines sequence and secondary-structure similarity scores.

Wieser, Daniela, and Niranjan Mahesan

In Silico Biol. Volume 9, Number 3, (2009), p.89–103

Reactome knowledgebase of human biological pathways and processes

Matthews, L., Gopinath G., Gillespie M., Caudy M., Croft D., de Bono B., Garapati P., Hemish J., Hermjakob H., Jassal B., et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D619–D622

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Vilella, Albert J., Severin Jessica, Ureta-Vidal Abel, Heng Li, Durbin Richard, and Birney Ewan

Genome Res. 1, Volume 19, Number 2, (2009), p.327-35 doi: 10.1101/gr.073585.107

Broadening Pfam Protein Sequence Annotations

Mistry, J., Cogghill P., Eddy S., Finn R., Tate J., and Bateman A.

(2009),

VectorBase: a data resource for invertebrate vector genomics

Lawson, D., Arensburger P., Atkinson P., Besansky N. J., Bruggner R. V., Butler R., Campbell K. S., Christophides G. K., Christley S., Dialynas E., et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D583–D587

BioCatalogue: a curated Web Service registry for the Life Science community

Goble, Carole A., Belhajjame Khalid, Tanoh Franck, Bhagat Jiten, Wolstencroft Katy, Stevens Robert, Nzuobontane Eric, McWilliam Hamish, Laurent Thomas, and Lopez Rodrigo

(2009),

ArrayExpress update - From an archive of functional genomics experiments to the atlas of gene expression

Parkinson, H., KAPUSHESKY M., KOLESNIKOV N., RUSTICI G., Shojatalab M., ABEYGUNAWARDENA N., Berube H., DYLAG M., EMAM I., FARNE A., et al.

Nucleic Acids Research. Volume 37, Number SUPPL. 1, (2009), p.D868-D872

PDBe: Protein Data Bank in Europe

VELANKAR, S., BEST C., Beuth B., Boutselakis C. H., Cobley N., SILVA SOUSA DA A. W., Dimitropoulos D., Golovin A., Hirshberg M., John M., et al.

Nucleic Acids Research. Volume 38, Number Database issue, (2009), p.D308-D317 doi: 10.1093/nar/gkp916

High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues

Huang, G. J., Shifman S., Valdar W., Johannesson M., Yalcin B., Taylor M. S., Taylor J. M., Mott R., and Flint J.

Genome Research. Volume 19, (2009), p.1133-1140

Metal-MACiE: a database of metals involved in biological catalysis.

Andreini, Claudia, Bertini Ivano, Cavallaro Gabriele, Holliday Gemma L., and Thornton Janet M.

Bioinformatics. Aug, Volume 25, Number 16, (2009), p.2088–2089 doi: 10.1093/bioinformatics/btp256

Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1

San Mauro, D., Gower D. J., Massingham T., Wilkinson M., Zardoya R., and Cotton J. A.

Systematic Biology. Volume 58, (2009), p.425-438

Protein domain organisation: adding order

Kummerfeld, S., and Teichmann S.

BMC bioinformatics. Volume 10, Number 1, (2009), p.39

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.

Capra, John A., Laskowski Roman A., Thornton Janet M., Singh Mona, and Funkhouser Thomas A.

PLoS Comput Biol. Dec, Volume 5, Number 12, (2009), p.e1000585 doi: 10.1371/journal.pcbi.1000585

The imgt/hla database

Robinson, J., Waller M. J., Fail S. C., McWilliam H., Lopez R., Parham P., and Marsh S. G. E.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D1013–D1017

The fine details of evolution.

Laskowski, Roman A., Thornton Janet M., and Sternberg Michael J. E.

Biochem Soc Trans. Aug, Volume 37, Number Pt 4, (2009), p.723–726 doi: 10.1042/BST0370723

Post-publication sharing of data and tools.

Schofield, Paul N., Bubela Tania, Weaver Thomas, Portilla Lili, Brown Stephen D., Hancock John M., Einhorn David, Tocchini-Valentini Glauco, Hrabe de Angelis Martin, Rosenthal Nadia, et al.

Nature. 9, Volume 461, Number 7261, (2009), England, p.171-3 doi: 10.1038/461171a

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009

Field, D., Friedberg I., Sterk P., Kottmann R., Glockner F. O., Hirschman L., Garrity G. M., Cochrane G., Wooley J., and Gilbert J.

Stand Genomic Sci. Volume 1, Number 3, (2009), p.278-82

Web services at the european bioinformatics institute-2009

McWilliam, Hamish, Valentin Franck, Goujon Mickael, Li Weizhong, Narayanasamy Menaka, Martin Jenny, Miyar Teresa, and Lopez Rodrigo

Nucleic acids research. Volume 37, Number suppl 2, (2009), p.W6–W10

The GOA database in 2009—an integrated Gene Ontology Annotation resource

Barrell, D., DIMMER E., HUNTLEY R. P., Binns D., O’DONOVAN C., and Apweiler R.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D396–D403 doi:

Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins

Simone, De A., Cavalli A., Hsu S. T., VRANKEN W. F., and Vendruscolo M.

Journal of the American Chemical Society. Volume 131, Number Issue 45, (2009), p.16332-16333 doi: 10.1021/ja904937a

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

consortium, FANTOM, and the Riken Omics Science Center The

Nature Genetics. Volume 41, (2009), p.553-562

Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)

Aebersold, R., Auffray C., Baney E., Barillot E., BRAZMA A., Brett C., Brunak S., Butte A., Califano A., Celis J., et al.

Molecular oncology. Volume 3, Number 1, (2009), p.9

The CATH classification revisited–architectures reviewed and new ways to characterize structural divergence in superfamilies.

Cuff, Alison L., Sillitoe Ian, Lewis Tony, Redfern Oliver C., Garratt Richard, Thornton Janet M., and Orengo Christine A.

Nucleic Acids Res. Jan, Volume 37, Number Database issue, (2009), p.D310–D314 doi: 10.1093/nar/gkn877

Understanding the functional roles of amino acid residues in enzyme catalysis.

Holliday, Gemma L., Mitchell John B. O., and Thornton Janet M.

J Mol Biol. Jul, Volume 390, Number 3, (2009), p.560–577 doi: 10.1016/j.jmb.2009.05.015

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.

Fernandez-Ballester, G., Beltrao P., Gonzalez J. M., Song Y. H., Wilmanns M., Valencia A., Serrano L., and others

Journal of molecular biology. Volume 388, Number 4, (2009), p.902

Alternative splicing of transcription factors' genes: beyond the increase of proteome diversity.

Talavera, David, Orozco Modesto, and de la Cruz Xavier

Comp Funct Genomics. (2009), p.905894 doi: 10.1155/2009/905894

DNA methylation-histone modification relationships across the desmin locus in human primary cells.

Allen, Marianne Lindahl, Koch Christoph M., Clelland Gayle K., Dunham Ian, and Antoniou Michael

BMC Mol Biol. Volume 10, (2009), England, p.51 doi: 10.1186/1471-2199-10-51

Unifying biological image formats with HDF5

Dougherty, M. T., Folk M. J., Zadok E., Bernstein H. J., Bernstein F. C., Eliceiri K. W.,