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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

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

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

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

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

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

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

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

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

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

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),

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

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

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),

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

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

Potential 2-aminosuccinimide structures in mollusc proteins

GARAVELLI, J., and Hirshberg M.

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

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

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

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

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

Large-scale analysis of microRNA evolution

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

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

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:

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),

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

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

Centroids: Gold Standards with Distributional Variations

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

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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

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.

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

PRIDE: Quality control in a proteomics data repository

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

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

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

ACPYPE - AnteChamber PYthon Parser interfacE

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

The Pfam protein families database

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

Annotating Human P-Glycoprotein Bioassay Data

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

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

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

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),

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),

Metagenomic analysis: the challenge of the data bonanza

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

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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

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

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

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

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

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

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

Molecular interaction databases

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

The HUPO initiative on Model Organism Proteomes, iMOP

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

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:

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

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

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

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

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

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

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

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

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

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

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

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

Systems Biology and Bioinformatics in Aging Research: A Workshop Report

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

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

Fully scalable online-preprocessing algorithm for short oligonucleotide microarray atlases

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Toxicology ontology perspectives.

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

Toward interoperable bioscience data

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

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.

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

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

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

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

ChEMBL: a large-scale bioactivity database for drug discovery

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

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

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.

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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

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

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

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

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

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

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

The 2010 Cryo-EM Modeling Challenge

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

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

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

Accessing and using chemical property databases.

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

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

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

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

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

Protein Structure Validation Using Side-Chain Chemical Shifts

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

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

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

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

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

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

Experimental design in phylogenetics: testing predictions from expected information

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

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The genomic basis of adaptive evolution in threespine sticklebacks

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Metric distances derived from cosine similarity and Pearson and Spearman correlations

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

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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.

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