Publications for 2011

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
Detecting low-complexity unobserved causes
Janzing, D., Sgouritsa E., Stegle O., Peters J., and Schölkopf B.
Uncertainty in Artificial Intelligence. 2011, (2011), doi:
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:
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),
InterPro protein classification
McDowall, J., and HUNTER S.
Methods Mol Biol. Volume 694, (2011), p.37–47
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),
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
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
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
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
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
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
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
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
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
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
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
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:
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
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
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:
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited
Hess, J., and Goldman N.
PLoS ONE. Volume 6, (2011), p.e22783
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
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),
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
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:
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
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
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
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),
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
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
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
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
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
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),
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:
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
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
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),
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),
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
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
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:
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
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
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
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
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
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
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:
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
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
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
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
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
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),
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),
A guide to UniProt for protein scientists
O’DONOVAN, C., and Apweiler R.
Methods Mol. Biol. Volume 694, (2011), p.25–35 doi:
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
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
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
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),
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),
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
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
Asparagine Peptide Lyases
Rawlings, N. D., Barrett A. J., and Bateman A.
Journal of Biological Chemistry. Volume 286, Number 44, (2011), p.38321–38328
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
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:
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
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
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
Parts and wholes, shapes and holes in living beings
HASTINGS, J., Batchelor C., and Schulz S.
Proceedings of the first SHAPES workshop. (2011),
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
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
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
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
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),
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
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),
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
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
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
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),
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
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:
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
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
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
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
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
Chromatin and heritability: how epigenetic studies can complement genetic approaches
Birney, E.
Trends in Genetics. Volume 27, Number 5, (2011), p.172–176
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
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
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 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),
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
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
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
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),
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),
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:
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
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
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
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
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
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
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
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
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
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
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
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
Expression and Genetic Variation Databases for Cancer Research
Rung, J., and BRAZMA A.
Cancer Systems Biology, Bioinformatics and Medicine. (2011), p.153–164
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
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
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
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
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),
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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:
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),
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
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
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
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
Celebrating structural biology.
Thornton, Janet M.
Nat Struct Mol Biol. Dec, Volume 18, Number 12, (2011), p.1304–1316
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
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
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),
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),
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
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
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
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),
Preparing molecular interaction data for publication.
Orchard, S., and Hermjakob H.
Methods in molecular biology (Clifton, NJ). Volume 694, (2011), p.229–236
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:
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
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
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
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
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),
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
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
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),
UniProt Knowledgebase: a hub of integrated protein data
Magrane, M., and others
Database: the journal of biological databases and curation. Volume 2011, (2011),
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
Protein structure databases.
Laskowski, Roman A.
Mol Biotechnol. Jun, Volume 48, Number 2, (2011), p.183–198 doi: 10.1007/s12033-010-9372-4
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
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
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
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
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),
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
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
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
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
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
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
The rise and fall of supervised machine learning techniques
Jensen, L. J., and Bateman A.
Bioinformatics. Volume 27, Number 24, (2011), p.3331–3332
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
Analysis of alignment error and sitewise constraint in mammalian comparative genomics
Jordan, G.
(2011),