Publications for 2008

2008

Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
O'Reilly PF, Birney E, Balding DJ.
Genome research Volume 18 (2008) p.1304-1313

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S.
Nature biotechnology Volume 26 (2008) p.889-896

nGASP--the nematode genome annotation assessment project.
Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, Stein LD.
BMC bioinformatics Volume 9 (2008) p.549

The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A.
Nature biotechnology Volume 26 (2008) p.541-547

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD.
Nature biotechnology Volume 26 (2008) p.305-312

Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.
Bioinformatics (Oxford, England) Volume 24 (2008) p.11-17

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.
Braconi Quintaje S, Orchard S.
Molecular & cellular proteomics : MCP Volume 7 (2008) p.1409-1419

Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV.
The Plant cell Volume 20 (2008) p.1426-1436

Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T.
Omics : a journal of integrative biology Volume 12 (2008) p.101-108

GENETICS. The Human Variome Project.
Cotton RG, Auerbach AD, Axton M, Barash CI, Berkovic SF, Brookes AJ, Burn J, Cutting G, den Dunnen JT, Flicek P, Freimer N, Greenblatt MS, Howard HJ, Katz M, Macrae FA, Maglott D, Möslein G, Povey S, Ramesar RS, Richards CS, Seminara D, Smith TD, Sobrido MJ, Solbakk JH, Tanzi RE, Tavtigian SV, Taylor GR, Utsunomiya J, Watson M.
Science (New York, N.Y.) Volume 322 (2008) p.861-862

Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM.
Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry Volume 13 (2008) p.1205-1218

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S.
Genome research Volume 18 (2008) p.1518-1529

The evolution of the DLK1-DIO3 imprinted domain in mammals.
Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium, Dunham I, Renfree MB, Ferguson-Smith AC.
PLoS biology Volume 6 (2008) p.e135

Prediction of protein structure from ideal forms.
Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I.
Proteins Volume 70 (2008) p.1610-1619

Charting plant interactomes: possibilities and challenges.
Morsy M, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC.
Trends in plant science Volume 13 (2008) p.183-191

Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E.
Genome research Volume 18 (2008) p.1829-1843

Minimum reporting guidelines for proteomics released by the Proteomics Standards Initiative.
Jones AR, Orchard S.
Molecular & cellular proteomics : MCP Volume 7 (2008) p.2067-2068

The Gene Ontology - Providing a Functional Role in Proteomic Studies.
Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC.
Practical Proteomics Volume 8 (2008) p.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E.
Genome research Volume 18 (2008) p.821-829

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.
Genome research Volume 18 (2008) p.393-403

The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.
Garrick D, De Gobbi M, Samara V, Rugless M, Holland M, Ayyub H, Lower K, Sloane-Stanley J, Gray N, Koch C, Dunham I, Higgs DR.
Blood Volume 112 (2008) p.3889-3899

Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 8 (2008) p.1326-1330

UniProtJAPI: a remote API for accessing UniProt data.
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1321-1322

SNP and haplotype mapping for genetic analysis in the rat.
STAR Consortium, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N.
Nature genetics Volume 40 (2008) p.560-566

Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S.
BMC genomics Volume 9 (2008) p.564

A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae.
Jones GM, Stalker J, Humphray S, West A, Cox T, Rogers J, Dunham I, Prelich G.
Nature methods Volume 5 (2008) p.239-241

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E.
Genome research Volume 18 (2008) p.1814-1828

Wiley-VCH and HUPO: a global effort to advance proteomic science.
Ping P, Bergeron J, Apweiler R.
Proteomics Volume 8 (2008) p.4-6

Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM.
Nucleic acids research Volume 36 (2008) p.D426-33

Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos JA, Dunham I.
Pharmacogenomics Volume 9 (2008) p.1781-1783

Natural language processing in aid of FlyBase curators.
Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T.
BMC bioinformatics Volume 9 (2008) p.193

Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, Thornton JM, Gems D, Partridge L, Withers DJ.
The FASEB Journal Volume 22 (2008) p.807-818

The OWL of Biomedical Investigations
Courtot M, Bug W, Gibson F, Liste AL, Malone J, Schober D, Brinkman RR, Ruttenberg A.
Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions Volume 432 (2008) p.

Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science.
Ping P, Bergeron J, Apweiler R.
Proteomics. Clinical applications Volume 2 (2008) p.4-6

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E.
Nature reviews. Genetics Volume 9 (2008) p.303-313

What everybody should know about the rat genome and its online resources.
Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ.
Nature genetics Volume 40 (2008) p.523-527

Advanced genomic data mining.
Fernández-Suárez XM, Birney E.
PLoS computational biology Volume 4 (2008) p.e1000121

Altered proteome biology of cardiac mitochondria under stress conditions.
Zhang J, Liem DA, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Korge P, Drews O, Maclellan WR, Honda H, Weiss JN, Apweiler R, Ping P.
Journal of proteome research Volume 7 (2008) p.2204-2214

Fusion and fission of genes define a metric between fungal genomes.
Durrens P, Nikolski M, Sherman D.
PLoS computational biology Volume 4 (2008) p.e1000200

Rapidly evolving human promoter regions.
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA.
Nature genetics Volume 40 (2008) p.1262-3; author reply 1263-4

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S.
Nature biotechnology Volume 26 (2008) p.779-785

Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O.
Omics : a journal of integrative biology Volume 12 (2008) p.137-141

Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells.
Atkinson SP, Koch CM, Clelland GK, Willcox S, Fowler JC, Stewart R, Lako M, Dunham I, Armstrong L.
Stem cells (Dayton, Ohio) Volume 26 (2008) p.1174-1185

Finishing the finished human chromosome 22 sequence.
Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, Dunham I.
Genome biology Volume 9 (2008) p.R78

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic acids research Volume 36 (2008) p.D154-8

Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ.
Molecular biotechnology Volume 38 (2008) p.1-17

Calling on a million minds for community annotation in WikiProteins.
Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A.
Genome biology Volume 9 (2008) p.R89

Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ.
Nature methods Volume 5 (2008) p.1023-1025

Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L, Genomic Standards Consortium.
Omics : a journal of integrative biology Volume 12 (2008) p.109-113

Evolutionary footprints of nucleosome positions in yeast.
Washietl S, Machné R, Goldman N.
Trends in genetics : TIG Volume 24 (2008) p.583-587

Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain.
Eisenacher M, Hardt T, Martens L, Häkkinen J, Apweiler R, Hamacher M, Meyer HE, Stephan C.
Proteomics Volume 8 (2008) p.4163-4167

Functional site prediction selects correct protein models.
Chelliah V, Taylor WR.
BMC bioinformatics Volume 9 Suppl 1 (2008) p.S13

BioJava: an open-source framework for bioinformatics.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2096-2097

Levers and fulcrums: progress in cis-regulatory motif models.
Birney E.
Nature methods Volume 5 (2008) p.297-298

Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.
Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL, McCarrey JR, SAVOIR Consortium, Renfree MB, Reik W, Dunham I.
Nature genetics Volume 40 (2008) p.971-976

The universal protein resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 36 (2008) p.D190-5

Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A.
BMC bioinformatics Volume 9 Suppl 8 (2008) p.S3

The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2767-2772

The Universal Protein Resource (UniProt).
The UniProt Consortium.
Nucl. Acids Res. Volume 36 (2008) p.D190-D195

The Universal Protein Resource. A Growing Online Protein Database.
O'Donovan C, Martin MJ, Apweiler R.
BIOforum Europe Volume 12 (2008) p.32-33

Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM.
Nature reviews. Genetics Volume 9 (2008) p.141-151

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.
Nucleic acids research Volume 36 (2008) p.W372-6

6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H.
Proteomics Volume 8 (2008) p.1331-1333

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T.
Nucleic Acids Research Volume 36 (2008) p.D793-9

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L.
Proteomics Volume 8 (2008) p.1138-1148

Analyzing large-scale proteomics projects with latent semantic indexing.
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H.
Journal of proteome research Volume 7 (2008) p.182-191

A logic-based diagram of signalling pathways central to macrophage activation.
Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC.
BMC systems biology Volume 2 (2008) p.36

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Orchard S, Hermjakob H.
Briefings in bioinformatics Volume 9 (2008) p.166-173

Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A.
Current protocols in bioinformatics Volume Chapter 7 (2008) p.Unit 7.13

PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Nucleic acids research Volume 36 (2008) p.D618-22

Consensus nomenclature for the human ArfGAP domain-containing proteins.
Kahn RA, Bruford E, Inoue H, Logsdon JM, Nie Z, Premont RT, Randazzo PA, Satake M, Theibert AB, Zapp ML, Cassel D.
The Journal of cell biology Volume 182 (2008) p.1039-1044

The HGNC Database in 2008: a resource for the human genome.
Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E.
Nucleic acids research Volume 36 (2008) p.D445-8

PRIDE: new developments and new datasets.
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.
Nucleic Acids Research Volume 36 (2008) p.D878-83

Data standards and controlled vocabularies for proteomics.
Martens L, Palazzi LM, Hermjakob H.
Methods in molecular biology (Clifton, N.J.) Volume 484 (2008) p.279-286

The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S, Members of the RSBI Working Group.
Omics : a journal of integrative biology Volume 12 (2008) p.143-149

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.
Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H.
Proteomics Volume 8 (2008) p.4168-4172

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H.
BMC Bioinformatics Volume 9 (2008) p.437

Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H.
Bioinformatics (Oxford, England) Volume 24 (2008) p.2119-2121

Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.
Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P.
Proteomics Volume 8 (2008) p.1564-1575

InteroPORC: automated inference of highly conserved protein interaction networks.
Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1625-1631

ISPIDER Central: an integrated database web-server for proteomics.
Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ.
Nucleic acids research Volume 36 (2008) p.W485-90

Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?
Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ.
Proteomics Volume 8 (2008) p.1950-1953

Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM.
BMC evolutionary biology Volume 8 (2008) p.247

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.
Genome biology Volume 9 Suppl 2 (2008) p.S5

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W.
Bioinformatics (Oxford, England) Volume 24 (2008) p.1100-1101

Evolution of binding sites for zinc and calcium ions playing structural roles.
Torrance JW, Macarthur MW, Thornton JM.
Proteins Volume 71 (2008) p.813-830

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM.
Journal of molecular biology Volume 375 (2008) p.855-874

Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J.
Bioinformatics (Oxford, England) Volume 24 (2008) p.i105-11

Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project.
Kuhn T, Zielesny A, Steinbeck C.
Chemistry Central Journal Volume 2 (2008) p.P27-P27

The InterPro database and tools for protein domain analysis.
Mulder NJ, Apweiler R.
Current protocols in bioinformatics Volume Chapter 2 (2008) p.Unit 2.7

Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Goldman N, Yang Z.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3889-3892

Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.
Kuhn S, Egert B, Neumann S, Steinbeck C.
BMC bioinformatics Volume 9 (2008) p.400

Data curation + process curation=data integration + science.
Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R.
Briefings in bioinformatics Volume 9 (2008) p.506-517

Biological Data Resources at the EMBL-EBI
Lopez R.
Revista Colombiana de biotecnologia Volume 10 (2008) p.120–128

Performance validation of neural network based (13)c NMR prediction using a publicly available data source.
Blinov KA, Smurnyy YD, Elyashberg ME, Churanova TS, Kvasha M, Steinbeck C, Lefebvre BA, Williams AJ.
Journal of chemical information and modeling Volume 48 (2008) p.550-555

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica C, Labarga A, Gould CM, López R, Gibson TJ.
BMC bioinformatics Volume 9 (2008) p.229

Ensembl 2008.
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S.
Nucleic acids research Volume 36 (2008) p.D707-14

The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M.
Nucleic acids research Volume 36 (2008) p.D1028-33

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Molecular biotechnology Volume 38 (2008) p.165-177

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database.
Cochrane G, Akhtar R, Aldebert P, Althorpe N, Baldwin A, Bates K, Bhattacharyya S, Bonfield J, Bower L, Browne P, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E.
Nucleic acids research Volume 36 (2008) p.D5-12

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Combinatorial chemistry & high throughput screening Volume 11 (2008) p.653-660

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Löytynoja A, Goldman N.
Science (New York, N.Y.) Volume 320 (2008) p.1632-1635

The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M.
Briefings in bioinformatics Volume 9 (2008) p.250-253

A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3913-3919

EBI Proteomics Services
Hermjakob H.
Lecture notes in computer science Volume 5109 (2008) p.207

Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK.
Nature Volume 453 (2008) p.175-183

4DXpress: a database for cross-species expression pattern comparisons.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T.
Nucleic acids research Volume 36 (2008) p.D847-53

The speciation of the proteome.
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H.
Chemistry Central journal Volume 2 (2008) p.16