Publications for 2010

2010

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),
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
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
Genomic information infrastructure after the deluge
Parkhill, J., Birney E., Kersey P., and others
Genome Biol. Volume 11, (2010), p.402 doi:
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
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
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
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
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 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
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
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
Protein structure databases.
Laskowski, Roman A.
Methods Mol Biol. Volume 609, (2010), p.59–82 doi: 10.1007/978-1-60327-241-4_4
Rfam and Wikipedia: Harnessing people power| SciVee
Bateman, A.
scivee. (2010),
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
Assemblies: the good, the bad, the ugly
Birney, E.
Nature Methods. Volume 8, Number 1, (2010), p.59–60
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Digital archives for molecular microscopy
BEST, C.
Proceedings of the 1st International Digital Preservation Interoperability Framework Symposium. (2010), doi: 10.1145/2039263.2039267
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
SnoPatrol: how many snoRNA genes are there
Gardner, P. P., Bateman A., Poole A. M., and others
J Biol. Volume 9, Number 4, (2010),
The (non)malignancy of cancerous amino acidic substitutions
Talavera, D., Taylor M. S., and Thornton J. M.
Proteins. Volume 78, (2010), p.518-529
An effective model for natural selection in promoters
Hoffman, M. M., and Birney E.
Genome research. Volume 20, Number 5, (2010), p.685–692
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
Archiving next generation sequencing data
Shumway, M., Cochrane G., and Sugawara H.
Nucleic Acids Res. Volume 38, Number Database issue, (2010), p.D870-1
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
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
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
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
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
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
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
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
Genome Biology
Buljan, M., Frankish A., and Bateman A.
Genome Biology. Volume 11, (2010), p.R74
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
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),
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
UniRule–Automatic Annotation In UniProtKB
Bridge, A. J., POGGIOLI D., and O'Donovan C.
(2010), doi:
Research The developmental expression dynamics of Drosophila melanogaster transcription factors
Adryan, B., and Teichmann S. A.
(2010),
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
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 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
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
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
Curators of the world unite: the International Society of Biocuration
Bateman, A.
Bioinformatics. Volume 26, Number 8, (2010), p.991
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
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
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
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
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
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
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
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 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:
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:
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
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
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
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),
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
Design, implementation and updating of knowledge bases
HUNTER, S., Apweiler R., and Martin M. J.
Knowledge-Based Bioinformatics. (2010), p.87
The developmental expression dynamics of Drosophila melanogaster transcription factors
Adryan, B., and Teichmann S. A.
Genome biology. Volume 11, Number 4, (2010), p.R40
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
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
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
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
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
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
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
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
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
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The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative
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Journal of Bacteriology. Volume 192, Number Issue 19, (2010), p.5143-5150 doi: 10.1128/JB.00315-10
Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
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DUFs: families in search of function
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Acta Crystallographica Section F: Structural Biology and Crystallization Communications. Volume 66, Number 10, (2010), p.1148–1152
Sequence and structure analysis of noncoding RNAs
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Evolution of the transcription factor repertoires in the Saccharomycotina
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