Publications for 2009

2009

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.
Mol Oncol Volume 3 (2009) p.9-17

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.
Megy K, Hammond M, Lawson D, Bruggner RV, Birney E, Collins FH.
Infect Genet Evol Volume 9 (2009) p.308-313

Protein promiscuity and its implications for biotechnology.
Nobeli I, Favia AD, Thornton JM.
Nat Biotechnol Volume 27 (2009) p.157-167

Biophysical annotation and representation of CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Crampin EJ, Nielsen PF.
Bioinformatics Volume 25 (2009) p.2263-2270

Towards interoperable reporting standards for omics data: hopes and hurdles.
Sansone SA, Rocca-Serra P, Field D, Taylor CF, Tong W, Brandizi M, Maguire E, Sklyar N.
Summit on Translat Bioinforma Volume 2009 (2009) p.112-115

VectorBase: a data resource for invertebrate vector genomics.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH.
Nucleic Acids Res Volume 37 (2009) p.d583-7

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H.
Bioinformatics Volume 25 (2009) p.279-280

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res Volume 37 (2009) p.d169-74

The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA.
Nucleic Acids Res Volume 37 (2009) p.d310-4

ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr.
Overington J.
J Comput Aided Mol Des Volume 23 (2009) p.195-198

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation.
Tarpey PS, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C, O'Meara S, Latimer C, Dicks E, Menzies A, Stephens P, Blow M, Greenman C, Xue Y, Tyler-Smith C, Thompson D, Gray K, Andrews J, Barthorpe S, Buck G, Cole J, Dunmore R, Jones D, Maddison M, Mironenko T, Turner R, Turrell K, Varian J, West S, Widaa S, Wray P, Teague J, Butler A, Jenkinson A, Jia M, Richardson D, Shepherd R, Wooster R, Tejada MI, Martinez F, Carvill G, Goliath R, de Brouwer AP, van Bokhoven H, Van Esch H, Chelly J, Raynaud M, Ropers HH, Abidi FE, Srivastava AK, Cox J, Luo Y, Mallya U, Moon J, Parnau J, Mohammed S, Tolmie JL, Shoubridge C, Corbett M, Gardner A, Haan E, Rujirabanjerd S, Shaw M, Vandeleur L, Fullston T, Easton DF, Boyle J, Partington M, Hackett A, Field M, Skinner C, Stevenson RE, Bobrow M, Turner G, Schwartz CE, Gecz J, Raymond FL, Futreal PA, Stratton MR.
Nat Genet Volume 41 (2009) p.535-543

DASMI: exchanging, annotating and assessing molecular interaction data.
Blankenburg H, Finn RD, Prlić A, Jenkinson AM, Ramírez F, Emig D, Schelhorn SE, Büch J, Lengauer T, Albrecht M.
Bioinformatics Volume 25 (2009) p.1321-1328

Probing the "dark matter" of protein fold space.
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I.
Structure Volume 17 (2009) p.1244-1252

ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles.
Li W, Gracey AY, Mello LV, Brass A, Cossins AR.
BMC Genomics Volume 10 (2009) p.560

Ensembl 2009.
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P.
Nucleic Acids Res Volume 37 (2009) p.d690-7

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus.
Hu Y, Kaisaki PJ, Argoud K, Wilder SP, Wallace KJ, Woon PY, Blancher C, Tarnow L, Groop PH, Hadjadj S, Marre M, Parving HH, Farrall M, Cox RD, Lathrop M, Vionnet N, Bihoreau MT, Gauguier D.
BMC Med Genomics Volume 2 (2009) p.41

Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM.
J R Soc Interface Volume 6 (2009) p.129-147

Drug target central.
Harland L, Gaulton A.
Expert Opin Drug Discov Volume 4 (2009) p.857-872

Annotations for all by all - the BioSapiens network.
Thornton J, BioSapiens Network.
Genome Biol Volume 10 (2009) p.401

Application of ESTs in microarray analysis.
Li W, Olohan L, Williams D, Hughes M, Gracey A, Cossins A.
Methods Mol Biol Volume 533 (2009) p.289-309

Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, Type 1 Diabetes Genetics Consortium.
Nat Genet Volume 41 (2009) p.703-707

Finding query suggestions for PubMed.
Lu Z, Wilbur WJ, McEntyre JR, Iskhakov A, Szilagyi L.
AMIA Annu Symp Proc Volume 2009 (2009) p.396-400

A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose.
Takeuchi F, McGinnis R, Bourgeois S, Barnes C, Eriksson N, Soranzo N, Whittaker P, Ranganath V, Kumanduri V, McLaren W, Holm L, Lindh J, Rane A, Wadelius M, Deloukas P.
PLoS Genet Volume 5 (2009) p.e1000433

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.
Brazma A.
ScientificWorldJournal Volume 9 (2009) p.420-423

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions.
Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C.
Mol Cell Proteomics Volume 8 (2009) p.696-705

Recent developments in public proteomic MS repositories and pipelines.
Mead JA, Bianco L, Bessant C.
Proteomics Volume 9 (2009) p.861-881

Large scale association analysis of novel genetic loci for coronary artery disease.
Coronary Artery Disease Consortium, Samani NJ, Deloukas P, Erdmann J, Hengstenberg C, Kuulasmaa K, McGinnis R, Schunkert H, Soranzo N, Thompson J, Tiret L, Ziegler A.
Arterioscler Thromb Vasc Biol Volume 29 (2009) p.774-780

ChEBI: an open bioinformatics and cheminformatics resource.
Degtyarenko K, Hastings J, de Matos P, Ennis M.
Curr Protoc Bioinformatics Volume Chapter 14 (2009) p.unit 14.9

Comparison of novel decoy database designs for optimizing protein identification searches using ABRF sPRG2006 standard MS/MS data sets.
Blanco L, Mead JA, Bessant C.
J Proteome Res Volume 8 (2009) p.1782-1791

Network visualization and analysis of gene expression data using BioLayout Express(3D).
Theocharidis A, van Dongen S, Enright AJ, Freeman TC.
Nat Protoc Volume 4 (2009) p.1535-1550

Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization.
Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, Gerstein M, Enright AJ, Giraldez AJ.
Genes Dev Volume 23 (2009) p.619-632

A method for visualizing CellML models.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.
Bioinformatics Volume 25 (2009) p.3012-3019

CellML metadata standards, associated tools and repositories.
Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramanium S, Wimalaratne SM, Yu T.
Philos Trans A Math Phys Eng Sci Volume 367 (2009) p.1845-1867

The Systems Biology Graphical Notation.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.
Nat Biotechnol Volume 27 (2009) p.735-741

Bioclipse 2: a scriptable integration platform for the life sciences.
Spjuth O, Alvarsson J, Berg A, Eklund M, Kuhn S, Mäsak C, Torrance G, Wagener J, Willighagen EL, Steinbeck C, Wikberg JE.
BMC Bioinformatics Volume 10 (2009) p.397

PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins.
Oliva R, Thornton JM, Pellegrini-Calace M.
Bioinformatics Volume 25 (2009) p.3183-3184

Facilitating modularity and reuse: guidelines for structuring CellML 1.1 models by isolating common biophysical concepts.
Wimalaratne SM, Halstead MD, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF.
Exp Physiol Volume 94 (2009) p.472-485

A System for Information Management in BioMedical Studies--SIMBioMS.
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, Lappalainen I, Rung J, Podnieks K, Sarkans U, McCarthy MI, Brazma A.
Bioinformatics Volume 25 (2009) p.2768-2769

New open drug activity data at EBI
Steinbeck C, Al-Lazikani B, Hermjakob H, Overington J, Thornton J.
Chemistry Central Journal Volume 3 (2009) p.o3

Enhanced DNA binding capacity on up-regulated epidermal wild-type p53 in vitiligo by H2O2-mediated oxidation: a possible repair mechanism for DNA damage.
Salem MM, Shalbaf M, Gibbons NC, Chavan B, Thornton JM, Schallreuter KU.
FASEB J Volume 23 (2009) p.3790-3807

Designing and encoding models for synthetic biology.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N.
J R Soc Interface Volume 6 Suppl 4 (2009) p.s405-17

Protein function annotation by homology-based inference.
Loewenstein Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C, Thornton J, Tramontano A.
Genome Biol Volume 10 (2009) p.207

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice.
Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP.
Nat Genet Volume 41 (2009) p.614-618

PoreWalker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three-dimensional structure.
Pellegrini-Calace M, Maiwald T, Thornton JM.
PLoS Comput Biol Volume 5 (2009) p.e1000440

The genome of the blood fluke Schistosoma mansoni.
Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, Coulson R, Day TA, Delcher A, DeMarco R, Djikeng A, Eyre T, Gamble JA, Ghedin E, Gu Y, Hertz-Fowler C, Hirai H, Hirai Y, Houston R, Ivens A, Johnston DA, Lacerda D, Macedo CD, McVeigh P, Ning Z, Oliveira G, Overington JP, Parkhill J, Pertea M, Pierce RJ, Protasio AV, Quail MA, Rajandream MA, Rogers J, Sajid M, Salzberg SL, Stanke M, Tivey AR, White O, Williams DL, Wortman J, Wu W, Zamanian M, Zerlotini A, Fraser-Liggett CM, Barrell BG, El-Sayed NM.
Nature Volume 460 (2009) p.352-358

Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray.
Samolski I, de Luis A, Vizcaíno JA, Monte E, Suárez MB.
BMC Microbiol Volume 9 (2009) p.217

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes.
Wilder SP, Kaisaki PJ, Argoud K, Salhan A, Ragoussis J, Bihoreau MT, Gauguier D.
BMC Genomics Volume 10 (2009) p.63

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation.
Manakov SA, Grant SG, Enright AJ.
BMC Genomics Volume 10 (2009) p.419

PRIDE Converter: making proteomics data-sharing easy.
Barsnes H, Vizcaíno JA, Eidhammer I, Martens L.
Nat Biotechnol Volume 27 (2009) p.598-599

OrChem - An open source chemistry search engine for Oracle(R).
Rijnbeek M, Steinbeck C.
J Cheminform Volume 1 (2009) p.17

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E.
Genome Res Volume 19 (2009) p.327-335

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.
Bruce AW, López-Contreras AJ, Flicek P, Down TA, Dhami P, Dillon SC, Koch CM, Langford CF, Dunham I, Andrews RM, Vetrie D.
Genome Res Volume 19 (2009) p.994-1005

DNA methylation-histone modification relationships across the desmin locus in human primary cells.
Lindahl Allen M, Koch CM, Clelland GK, Dunham I, Antoniou M.
BMC Mol Biol Volume 10 (2009) p.51

Importing ArrayExpress datasets into R/Bioconductor.
Kauffmann A, Rayner TF, Parkinson H, Kapushesky M, Lukk M, Brazma A, Huber W.
Bioinformatics Volume 25 (2009) p.2092-2094

Applying the Gene Ontology in microbial annotation.
Giglio MG, Collmer CW, Lomax J, Ireland A.
Trends Microbiol Volume 17 (2009) p.262-268

Survey-based naming conventions for use in OBO Foundry ontology development.
Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA.
BMC Bioinformatics Volume 10 (2009) p.125

PDBsum new things.
Laskowski RA.
Nucleic Acids Res Volume 37 (2009) p.d355-9

Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.
Pink CJ, Swaminathan SK, Dunham I, Rogers J, Ward A, Hurst LD.
Genome Biol Evol Volume 1 (2009) p.13-22

Applications of high-throughput sequencing to chromatin structure and function in mammals.
Dunham I.
F1000 Biol Rep Volume 1 (2009) p.32

A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJ, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AF, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C.
Nat Genet Volume 41 (2009) p.1182-1190

Integrated Servers for Structure-Informed Function Prediction
Laskowski RA.
Volume (2009) p.251-272

Mapping organelle proteins and protein complexes in Drosophila melanogaster.
Tan DJ, Dvinge H, Christoforou A, Bertone P, Martinez Arias A, Lilley KS.
J Proteome Res Volume 8 (2009) p.2667-2678

HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R.
Dvinge H, Bertone P.
Bioinformatics Volume 25 (2009) p.3325-3326

Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.
Motallebipour M, Enroth S, Punga T, Ameur A, Koch C, Dunham I, Komorowski J, Ericsson J, Wadelius C.
FEBS J Volume 276 (2009) p.1878-1890

AmiGO: online access to ontology and annotation data.
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, AmiGO Hub, Web Presence Working Group.
Bioinformatics Volume 25 (2009) p.288-289

MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M.
Nucleic Acids Res Volume 37 (2009) p.d902-6

Missing in action: enzyme functional annotations in biological databases.
Furnham N, Garavelli JS, Apweiler R, Thornton JM.
Nat Chem Biol Volume 5 (2009) p.521-525

Ribosomal protein S6 kinase 1 signaling regulates mammalian life span.
Selman C, Tullet JM, Wieser D, Irvine E, Lingard SJ, Choudhury AI, Claret M, Al-Qassab H, Carmignac D, Ramadani F, Woods A, Robinson IC, Schuster E, Batterham RL, Kozma SC, Thomas G, Carling D, Okkenhaug K, Thornton JM, Partridge L, Gems D, Withers DJ.
Science Volume 326 (2009) p.140-144

Metal-MACiE: a database of metals involved in biological catalysis.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Bioinformatics Volume 25 (2009) p.2088-2089

Nucleoside diphosphate kinase (NDPK, NM23, AWD): recent regulatory advances in endocytosis, metastasis, psoriasis, insulin release, fetal erythroid lineage and heart failure; translational medicine exemplified.
Mehta A, Orchard S.
Mol Cell Biochem Volume 329 (2009) p.3-15

A protein interaction network for the large conductance Ca(2+)-activated K(+) channel in the mouse cochlea.
Kathiresan T, Harvey M, Orchard S, Sakai Y, Sokolowski B.
Mol Cell Proteomics Volume 8 (2009) p.1972-1987

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U.
Chem Biol Interact Volume 178 (2009) p.94-98

Small Molecule Subgraph Detector (SMSD) toolkit.
Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
J Cheminform Volume 1 (2009) p.12

HUPO World Congress Publication Committee meeting. August 2008, Amsterdam, The Netherlands.
Orchard S, Ping P.
Proteomics Volume 9 (2009) p.502-503

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.
Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA.
Proteomics Volume 9 (2009) p.499-501

Debunking minimum information myths: one hat need not fit all.
Orchard S, Taylor CF.
N Biotechnol Volume 25 (2009) p.171-172

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten B, Herrero J, Beal K, Birney E.
Bioinformatics Volume 25 (2009) p.295-301

Protein Function Prediction from Structure in Structural Genomics and its Contribution to the Study of Health and Disease
Watson JD, Thornton JM.
Volume (2009) p.201-215

Probabilistic retrieval and visualization of biologically relevant microarray experiments.
Caldas J, Gehlenborg N, Faisal A, Brazma A, Kaski S.
Bioinformatics Volume 25 (2009) p.i145-53

Integrating sequence, evolution and functional genomics in regulatory genomics.
Vingron M, Brazma A, Coulson R, van Helden J, Manke T, Palin K, Sand O, Ukkonen E.
Genome Biol Volume 10 (2009) p.202

A guide to the Proteomics Identifications Database proteomics data repository.
Vizcaíno JA, Côté R, Reisinger F, Foster JM, Mueller M, Rameseder J, Hermjakob H, Martens L.
Proteomics Volume 9 (2009) p.4276-4283

Annual spring meeting of the Proteomics Standards Initiative.
Orchard S, Deutsch EW, Binz PA, Jones AR, Creasy D, Montechi-Palazzi L, Corthals G, Hermjakob H.
Proteomics Volume 9 (2009) p.4429-4432

The need for speed.
Flicek P.
Genome Biol Volume 10 (2009) p.212

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.
Carlile M, Swan D, Jackson K, Preston-Fayers K, Ballester B, Flicek P, Werner A.
Nucleic Acids Res Volume 37 (2009) p.2274-2282

The IMGT/HLA database.
Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Res Volume 37 (2009) p.d1013-7

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC.
Proc Natl Acad Sci U S A Volume 106 (2009) p.3829-3834

Second Joint HUPO publication and Proteomics Standards Initiative workshop.
Orchard S, Binz PA, Hermjakob H.
Proteomics Volume 9 (2009) p.4426-4428

Recurated protein interaction datasets.
Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H.
Nat Methods Volume 6 (2009) p.860-861

QuickGO: a user tutorial for the web-based Gene Ontology browser.
Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R.
Database (Oxford) Volume 2009 (2009) p.bap010

Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc.
de Jager SM, Scofield S, Huntley RP, Robinson AS, den Boer BG, Murray JA.
Plant Mol Biol Volume 71 (2009) p.345-365

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.
Bioinformatics Volume 25 (2009) p.3045-3046

The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.
Nucleic Acids Res Volume 37 (2009) p.d396-403

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.
Reference Genome Group of the Gene Ontology Consortium.
PLoS Comput Biol Volume 5 (2009) p.e1000431

Planning the human variome project: the Spain report.
Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, Yoo HS, Contributors to the Human Variome Project Planning Meeting.
Hum Mutat Volume 30 (2009) p.496-510

Charting online OMICS resources: A navigational chart for clinical researchers.
Vizcaíno JA, Mueller M, Hermjakob H, Martens L.
Proteomics Clin Appl Volume 3 (2009) p.18-29

A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ.
BMC Bioinformatics Volume 10 Suppl 6 (2009) p.s13

GLOBAL ANALYSIS OF PROTEIN ACTIVITY USING PROTEOME CHIPS
SNYDER MICHAEL, ZHU HENG, BERTONE PAUL, BIDLINGMAIER SCOTT M, BILGIN METIN, CASAMAYOR ANTONIO J, GERSTEIN MARK, JANSEN RONALD, LAN NING.
Volume (2009) p.

Case-controlled structure validation.
Read RJ, Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 65 (2009) p.140-147

On vital aid: the why, what and how of validation.
Kleywegt GJ.
Acta Crystallogr D Biol Crystallogr Volume 65 (2009) p.134-139

The fission yeast homeodomain protein Yox1p binds to MBF and confines MBF-dependent cell-cycle transcription to G1-S via negative feedback.
Aligianni S, Lackner DH, Klier S, Rustici G, Wilhelm BT, Marguerat S, Codlin S, Brazma A, de Bruin RA, Bähler J.
PLoS Genet Volume 5 (2009) p.e1000626

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.
Nucleic Acids Res Volume 37 (2009) p.d868-72

InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res Volume 37 (2009) p.d211-5

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H.
Proteomics Volume 9 (2009) p.5112-5119

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009.
Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J.
Stand Genomic Sci Volume 1 (2009) p.278-282

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R.
J Proteome Res Volume 8 (2009) p.3689-3692

Web services at the European Bioinformatics Institute-2009.
McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R.
Nucleic Acids Res Volume 37 (2009) p.w6-10

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Galperin MY, Cochrane GR.
Nucleic Acids Res Volume 37 (2009) p.d1-4

Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting.
Orchard S.
J Proteome Res Volume 8 (2009) p.3219

Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion.
Bonaglia MC, Giorda R, Beri S, Bigoni S, Sensi A, Baroncini A, Capucci A, De Agostini C, Gwilliam R, Deloukas P, Dunham I, Zuffardi O.
Eur J Hum Genet Volume 17 (2009) p.426-433

Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P.
Nucleic Acids Res Volume 37 (2009) p.d619-22

Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler.
Zerbino DR, McEwen GK, Margulies EH, Birney E.
PLoS One Volume 4 (2009) p.e8407

Correction: Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome Biol Volume 10 (2009) p.402-402

Structural analysis of metal sites in proteins: non-heme iron sites as a case study.
Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM.
J Mol Biol Volume 388 (2009) p.356-380

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.
Durinck S, Spellman PT, Birney E, Huber W.
Nat Protoc Volume 4 (2009) p.1184-1191

Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E.
Nat Methods Volume 6 (2009) p.s6-s12

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R, Lipman D.
Genome Res Volume 19 (2009) p.1316-1323

Prepublication data sharing.
Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J.
Nature Volume 461 (2009) p.168-170

ENFIN--A European network for integrative systems biology.
Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E.
C R Biol Volume 332 (2009) p.1050-1058

The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.
Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C.
Structure Volume 17 (2009) p.1051-1062

Evolution. Uniting alignments and trees.
Löytynoja A, Goldman N.
Science Volume 324 (2009) p.1528-1529

WSsas: a web service for the annotation of functional residues through structural homologues.
Talavera D, Laskowski RA, Thornton JM.
Bioinformatics Volume 25 (2009) p.1192-1194

Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA.
PLoS Comput Biol Volume 5 (2009) p.e1000585

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochem Soc Trans Volume 37 (2009) p.723-726

Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T.
Genome Biol Volume 10 (2009) p.r108

Understanding the functional roles of amino acid residues in enzyme catalysis.
Holliday GL, Mitchell JB, Thornton JM.
J Mol Biol Volume 390 (2009) p.560-577

The structural basis of allosteric regulation in proteins.
Laskowski RA, Gerick F, Thornton JM.
FEBS Lett Volume 583 (2009) p.1692-1698

Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E.
Nucleic Acids Res Volume 37 (2009) p.d19-25

In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N.
Proc Natl Acad Sci U S A Volume 106 (2009) p.e95; author reply e96

Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I.
J Chem Inf Model Volume 49 (2009) p.2272-2289

Visualising the Epigenome
Flicek P, Birney E.
Volume (2009) p.55-66