Publications for 2009

2009

Systematic comparison of the human saliva and plasma proteomes.
Yan W, Apweiler R, Balgley BM, Boontheung P, Bundy JL, Cargile BJ, Cole S, Fang X, Gonzalez-Begne M, Griffin TJ, Hagen F, Hu S, Wolinsky LE, Lee CS, Malamud D, Melvin JE, Menon R, Mueller M, Qiao R, Rhodus NL, Sevinsky JR, States D, Stephenson JL, Than S, Yates JR, Yu W, Xie H, Xie Y, Omenn GS, Loo JA, Wong DT.
Proteomics. Clinical applications Volume 3 (2009) p.116-134

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 research Volume 37 (2009) p.D211-5

The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patients.
Holden MTG, Seth-Smith HMB, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EPC, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J.
Journal of bacteriology Volume 191 (2009) p.2907-2907

In silico identification of genes in bacteriophage DNA.
Kropinski AM, Borodovsky M, Carver TJ, Cerdeño-Tárraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS.
Methods in molecular biology (Clifton, N.J.) Volume 502 (2009) p.57-89

PDBsum new things.
Laskowski RA.
Nucleic acids research Volume 37 (2009) p.D355-9

Approaching clinical proteomics: current state and future fields of application in fluid proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G.
Clinical chemistry and laboratory medicine Volume 47 (2009) p.724-744

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.
Molecular oncology Volume 3 (2009) p.9-17

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 research Volume 37 (2009) p.D868-72

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 (Oxford, England) Volume 25 (2009) p.2768-2769

Infrastructure for the life sciences: design and implementation of the UniProt website.
Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E.
BMC bioinformatics Volume 10 (2009) p.136

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 research Volume 37 (2009) p.W6-10

Getting a grip on proteomics data - Proteomics Data Collection (ProDaC).
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Häkkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Blüggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C.
Proteomics Volume 9 (2009) p.3928-3933

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

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 biology Volume 10 (2009) p.202

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.
Nature biotechnology Volume 27 (2009) p.735-741

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.
Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J.
Journal of bacteriology Volume 191 (2009) p.261-277

FlyBase: enhancing Drosophila Gene Ontology annotations.
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium.
Nucleic acids research Volume 37 (2009) p.D555-9

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens.
Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR.
Genome biology Volume 10 (2009) p.R51

Genome watch: What a scorcher!
Cerdeño-Tárraga AM.
Nature reviews. Microbiology Volume 7 (2009) p.408-409

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

ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D.
Genomics Volume 93 (2009) p.213-220

The IMGT/HLA database.
Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic acids research Volume 37 (2009) p.D1013-7

Proteomics data collection--4th ProDaC workshop 15 August 2008, Amsterdam, The Netherlands.
Eisenacher M, Kohl M, Martens L, Barsnes H, Hardt T, Levander F, Häkkinen J, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 9 (2009) p.218-222

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 genetics Volume 5 (2009) p.e1000626

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

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

Drug target central.
Harland L, Gaulton A.
Expert opinion on drug discovery Volume 4 (2009) p.857-872

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.
Molecular & cellular proteomics : MCP Volume 8 (2009) p.1972-1987

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 research Volume 19 (2009) p.1316-1323

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase Consortium, Aebersold R, Hafen E.
BMC bioinformatics Volume 10 (2009) p.59

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 research Volume 37 (2009) p.D19-25

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

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 research Volume 37 (2009) p.D690-7

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.
Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Volume 367 (2009) p.1845-1867

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 genetics Volume 5 (2009) p.e1000433

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 (New York, N.Y.) Volume 326 (2009) p.140-144

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 research Volume 37 (2009) p.D619-22

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

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 biology Volume 10 (2009) p.402-402

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.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Volume 9 (2009) p.308-313

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

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

Proteomics Data Collection - 5th ProDaC Workshop: 4 March 2009, Kolympari, Crete, Greece.
Eisenacher M, Martens L, Barsnes H, Hardt T, Kohl M, Häkkinen J, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 9 (2009) p.3626-3629

Haplotype-based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1-DQA1-DQB1 haplotype.
McGinnis R, McLaren W, Ranganath V, Whittaker P, Hunt S, Deloukas P, Type 1 Diabetes Genetics Consortium.
Diabetes, obesity & metabolism Volume 11 Suppl 1 (2009) p.8-16

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.
Arteriosclerosis, thrombosis, and vascular biology Volume 29 (2009) p.774-780

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.
Experimental physiology Volume 94 (2009) p.472-485

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

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

Know your limits: assumptions, constraints and interpretation in systems biology.
Ilsley GR, Luscombe NM, Apweiler R.
Biochimica et biophysica acta Volume 1794 (2009) p.1280-1287

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.
Journal of molecular biology Volume 388 (2009) p.356-380

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

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

Algorithms and databases.
Martens L, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 564 (2009) p.245-259

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

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.
Bioinformatics (Oxford, England) Volume 25 (2009) p.2865-2871

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

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

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.
Chemico-biological interactions Volume 178 (2009) p.94-98

Guidelines for the nomenclature of the human heat shock proteins.
Kampinga HH, Hageman J, Vos MJ, Kubota H, Tanguay RM, Bruford EA, Cheetham ME, Chen B, Hightower LE.
Cell stress & chaperones Volume 14 (2009) p.105-111

Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T.
Genome biology Volume 10 (2009) p.R108

In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N.
Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.E95; author reply E96

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.
Nature genetics Volume 41 (2009) p.703-707

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 research Volume 37 (2009) p.D583-7

Case-controlled structure validation.
Read RJ, Kleywegt GJ.
Acta crystallographica. Section D, Biological crystallography Volume 65 (2009) p.140-147

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

Genes encoding novel secreted and transmembrane proteins are temporally and spatially regulated during Drosophila melanogaster embryogenesis.
Zúñiga A, Hödar C, Hanna P, Ibáñez F, Moreno P, Pulgar R, Pastenes L, González M, Cambiazo V.
BMC biology Volume 7 (2009) p.61

A chemogenomics view on protein-ligand spaces.
Strömbergsson H, Kleywegt GJ.
BMC bioinformatics Volume 10 Suppl 6 (2009) p.S13

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.
Journal of proteome research Volume 8 (2009) p.3689-3692

Designing and encoding models for synthetic biology.
Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C, Le Novère N.
Journal of the Royal Society, Interface Volume 6 Suppl 4 (2009) p.S405-17

Probing the "dark matter" of protein fold space.
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I.
Structure (London, England : 1993) Volume 17 (2009) p.1244-1252

Approaching clinical proteomics: current state and future fields of application in cellular proteomics.
Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G.
Cytometry. Part A : the journal of the International Society for Analytical Cytology Volume 75 (2009) p.816-832

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.
Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.3829-3834

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 (Oxford, England) Volume 25 (2009) p.279-280

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.
Human mutation Volume 30 (2009) p.496-510

Update of the Diatom EST Database: a new tool for digital transcriptomics.
Maheswari U, Mock T, Armbrust EV, Bowler C.
Nucleic acids research Volume 37 (2009) p.D1001-5

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.
Standards in genomic sciences Volume 1 (2009) p.278-282

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 research Volume 37 (2009) p.2274-2282

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Galperin MY, Cochrane GR.
Nucleic acids research Volume 37 (2009) p.D1-4

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

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

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 molecular biology Volume 10 (2009) p.51

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

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

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 biology and evolution Volume 1 (2009) p.13-22

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.
The FEBS journal Volume 276 (2009) p.1878-1890

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 research Volume 19 (2009) p.994-1005

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.
European Journal of Human Genetics Volume 17 (2009) p.426-433

Sense from sequence reads: methods for alignment and assembly.
Flicek P, Birney E.
Nature methods Volume 6 (2009) p.S6-S12

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

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

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.
Nature methods Volume 6 (2009) p.860-861

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

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

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

MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M.
Nucleic acids research Volume 37 (2009) p.D902-6

Finding one's way in proteomics: a protein species nomenclature.
Schlüter H, Apweiler R, Holzhütter HG, Jungblut PR.
Chemistry Central Journal Volume 3 (2009) p.11

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

The fine details of evolution.
Laskowski RA, Thornton JM, Sternberg MJ.
Biochemical Society transactions Volume 37 (2009) p.723-726

Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures.
Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J.
Journal of chemical theory and computation Volume 5 (2009) p.982-992

Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting.
Orchard S.
Journal of proteome research Volume 8 (2009) p.3219

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

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

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

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

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 (London, England : 1993) Volume 17 (2009) p.1051-1062

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 research Volume 37 (2009) p.D396-403

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

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 : the journal of biological databases and curation Volume 2009 (2009) p.bap010

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 computational biology Volume 5 (2009) p.e1000440

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic acids research Volume 37 (2009) p.D169-74

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

Genome and proteome annotation: organization, interpretation and integration.
Reeves GA, Talavera D, Thornton JM.
Journal of the Royal Society, Interface Volume 6 (2009) p.129-147

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

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

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.
Molecular & cellular proteomics : MCP 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

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.
Journal of proteome research Volume 8 (2009) p.1782-1791

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

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 research Volume 37 (2009) p.D310-4

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

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

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.
Molecular and cellular biochemistry Volume 329 (2009) p.3-15

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

A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ, HUPO Test Sample Working Group.
Nature methods Volume 6 (2009) p.423-430

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 microbiology Volume 9 (2009) p.217

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.
Nature genetics Volume 41 (2009) p.614-618

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 & development Volume 23 (2009) p.619-632

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

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 biology Volume 10 (2009) p.207

Mapping human metabolic pathways in the small molecule chemical space.
Macchiarulo A, Thornton JM, Nobeli I.
Journal of chemical information and modeling Volume 49 (2009) p.2272-2289

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

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

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.
Nature genetics Volume 41 (2009) p.1182-1190

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