Publications for 2006

2006

The Universal Protein Resource (UniProt): an expanding universe of protein information.
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.
Nucleic Acids Res Volume 34 (2006) p.d187-91

Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation.
Tarpey PS, Stevens C, Teague J, Edkins S, O'Meara S, Avis T, Barthorpe S, Buck G, Butler A, Cole J, Dicks E, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, West S, Widaa S, Yates A, Catford R, Butler J, Mallya U, Moon J, Luo Y, Dorkins H, Thompson D, Easton DF, Wooster R, Bobrow M, Carpenter N, Simensen RJ, Schwartz CE, Stevenson RE, Turner G, Partington M, Gecz J, Stratton MR, Futreal PA, Raymond FL.
Am J Hum Genet Volume 79 (2006) p.1119-1124

Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence.
Hum Mol Genet Volume 15 Spec No 1 (2006) p.r81-7

Overview of gene structure.
Spieth J, Lawson D.
WormBook Volume (2006) p.1-10

Picking pyknons out of the human genome.
Meynert A, Birney E.
Cell Volume 125 (2006) p.836-838

Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans.
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mech Ageing Dev Volume 127 (2006) p.458-472

A method for localizing ligand binding pockets in protein structures.
Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM.
Proteins Volume 62 (2006) p.479-488

Curator driven protein sequence analysis and annotation
Magrane M, O'Donovan C.
Volume (2006) p.55-70

Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults.
Bignell G, Smith R, Hunter C, Stephens P, Davies H, Greenman C, Teague J, Butler A, Edkins S, Stevens C, O'Meara S, Parker A, Avis T, Barthorpe S, Brackenbury L, Buck G, Clements J, Cole J, Dicks E, Edwards K, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Shepherd R, Small A, Solomon H, Stephens Y, Tofts C, Varian J, Webb A, West S, Widaa S, Yates A, Gillis AJ, Stoop HJ, van Gurp RJ, Oosterhuis JW, Looijenga LH, Futreal PA, Wooster R, Stratton MR.
Genes Chromosomes Cancer Volume 45 (2006) p.42-46

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Flicek P, Brent MR.
Genome Biol Volume 7 Suppl 1 (2006) p.s8.1-9

Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A.
Philos Trans R Soc Lond B Biol Sci Volume 361 (2006) p.483-494

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ Jr, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A.
BMC Bioinformatics Volume 7 (2006) p.489

HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.
Orchard S, Ping P.
Proteomics Volume 6 (2006) p.4436-4438

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies.
Hamacher M, Stephan C, Blüggel M, Chamrad D, Körting G, Martens L, Müller M, Hermjakob H, Parkinson D, Dowsey A, Reidegeld KA, Marcus K, Dunn MJ, Meyer HE, Apweiler R.
Proteomics Volume 6 (2006) p.1719-1721

A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report.
Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M.
Mol Cell Proteomics Volume 5 (2006) p.1996-2007

WormBase: better software, richer content.
Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW.
Nucleic Acids Res Volume 34 (2006) p.d475-8

EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG.
Genome Biol Volume 7 Suppl 1 (2006) p.s2.1-31

Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM.
Philos Trans R Soc Lond B Biol Sci Volume 361 (2006) p.389-391

Sequence clustering as a method of protein functional annotation
Petryszak R, Kersey P.
Volume (2006) p.11-23

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nat Rev Genet Volume 7 (2006) p.593-605

Guilt by association: using protein interactions and expression patterns to predict protein function
Orchard S, Hermjakob H.
Volume (2006) p.79-88

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Taylor CF, Hermjakob H, Julian RK Jr, Garavelli JS, Aebersold R, Apweiler R.
OMICS Volume 10 (2006) p.145-151

Integr8: Navigating Genome Reviews and the Proteome Analysis Database
Kersey P, Kulikova T, Pruess M.
Volume (2006) p.201-217

Proteomic Data Standardization, Deposition and Exchange
Orchard S, Hermjakob H, Pruess M, Apweiler R.
Volume (2006) p.19–30

Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M.
Methods Enzymol Volume 411 (2006) p.370-386

Wrestling with SUMO and bio-ontologies.
Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, White J.
Nat Biotechnol Volume 24 (2006) p.21-2; author reply 23

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
Côté RG, Jones P, Apweiler R, Hermjakob H.
BMC Bioinformatics Volume 7 (2006) p.97

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.
Orchard S, Hermjakob H, Taylor C, Binz PA, Hoogland C, Julian R, Garavelli JS, Aebersold R, Apweiler R.
Proteomics Volume 6 (2006) p.738-741

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R.
Expert Rev Proteomics Volume 3 (2006) p.1-3

Ensembl 2006.
Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Gräf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kähäri A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ.
Nucleic Acids Res Volume 34 (2006) p.d556-61

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
J Mol Biol Volume 364 (2006) p.836-852

PRIDE: a public repository of protein and peptide identifications for the proteomics community.
Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.
Nucleic Acids Res Volume 34 (2006) p.d659-63

A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM.
Bioessays Volume 28 (2006) p.534-545

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ, Goo YA, Grimmond S, Henrich T, Johnson MH, Korb M, Mills JC, Oudes A, Parkinson HE, Pascal LE, Quackenbush J, Ramialison M, Ringwald M, Sansone SA, Sherlock G, Stoeckert CJ Jr, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD.
OMICS Volume 10 (2006) p.205-208

Erratum to "Diapause-associated metabolic traits reiterated in long-lived daf-2 mutants in the nematode Caenorhabditis elegans" [Mech. Ageing Dev. 127 (5) (2006) 458-472].
McElwee JJ, Schuster E, Blanc E, Thornton J, Gems D.
Mech Ageing Dev Volume 127 (2006) p.922-936

SPINE bioinformatics and data-management aspects of high-throughput structural biology.
Albeck S, Alzari P, Andreini C, Banci L, Berry IM, Bertini I, Cambillau C, Canard B, Carter L, Cohen SX, Diprose JM, Dym O, Esnouf RM, Felder C, Ferron F, Guillemot F, Hamer R, Ben Jelloul M, Laskowski RA, Laurent T, Longhi S, Lopez R, Luchinat C, Malet H, Mochel T, Morris RJ, Moulinier L, Oinn T, Pajon A, Peleg Y, Perrakis A, Poch O, Prilusky J, Rachedi A, Ripp R, Rosato A, Silman I, Stuart DI, Sussman JL, Thierry JC, Thompson JD, Thornton JM, Unger T, Vaughan B, Vranken W, Watson JD, Whamond G, Henrick K.
Acta Crystallogr D Biol Crystallogr Volume 62 (2006) p.1184-1195

TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E, Adams DJ.
Nat Genet Volume 38 (2006) p.853

Ensembl’s annotation pipeline and its use in eukaryotic genomes
Fernandez XM, Searle S, Birney E.
Volume (2006) p.109-203

Data standards: a call to action.
Brooksbank C, Quackenbush J.
OMICS Volume 10 (2006) p.94-99

UniSave: the UniProtKB sequence/annotation version database.
Leinonen R, Nardone F, Zhu W, Apweiler R.
Bioinformatics Volume 22 (2006) p.1284-1285

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.
Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H.
Proteomics Volume 6 (2006) p.4439-4443

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nat Cell Biol Volume 8 (2006) p.1183-1189

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
OMICS Volume 10 (2006) p.114-118

Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R.
Methods Biochem Anal Volume 49 (2006) p.397-414

MGED standards: work in progress.
Ball CA, Brazma A.
OMICS Volume 10 (2006) p.138-144

XRate: a fast prototyping, training and annotation tool for phylo-grammars.
Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.
BMC Bioinformatics Volume 7 (2006) p.428

Transcriptional regulatory networks in bacteria: from input signals to output responses.
Seshasayee AS, Bertone P, Fraser GM, Luscombe NM.
Curr Opin Microbiol Volume 9 (2006) p.511-519

Observing local and global properties of metabolic pathways: 'load points' and 'choke points' in the metabolic networks.
Rahman SA, Schomburg D.
Bioinformatics Volume 22 (2006) p.1767-1774

Evidence standards in experimental and inferential INSDC Third Party Annotation data.
Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M.
OMICS Volume 10 (2006) p.105-113

Detection of peptaibols and partial cloning of a putative peptaibol synthetase gene from T. harzianum CECT 2413.
Vizcaíno JA, Cardoza RE, Dubost L, Bodo B, Gutiérrez S, Monte E.
Folia Microbiol (Praha) Volume 51 (2006) p.114-120

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.
Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S, Santarius T, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Hunter C, Jenkinson A, Jones D, Kosmidou V, Lugg R, Menzies A, Mironenko T, Parker A, Perry J, Raine K, Richardson D, Shepherd R, Small A, Smith R, Solomon H, Stephens P, Teague J, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Reinhold W, Weinstein JN, Stratton MR, Futreal PA, Wooster R.
Mol Cancer Ther Volume 5 (2006) p.2606-2612

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island.
Devi SM, Ahmed I, Khan AA, Rahman SA, Alvi A, Sechi LA, Ahmed N.
BMC Genomics Volume 7 (2006) p.191

Target hub proteins serve as master regulators of development in yeast.
Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M.
Genes Dev Volume 20 (2006) p.435-448

Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA.
J Mol Evol Volume 63 (2006) p.513-525

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.
Hermjakob H.
Proteomics Volume 6 Suppl 2 (2006) p.34-38

Dry work in a wet world: computation in systems biology.
Kahlem P, Birney E.
Mol Syst Biol Volume 2 (2006) p.40

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.
Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM.
Genome Biol Volume 7 (2006) p.r89

Top-down standards will not serve systems biology.
Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N.
Nature Volume 440 (2006) p.24

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N.
Nucleic Acids Res Volume 34 (2006) p.d327-31

A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.
Hunter C, Smith R, Cahill DP, Stephens P, Stevens C, Teague J, Greenman C, Edkins S, Bignell G, Davies H, O'Meara S, Parker A, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gorton M, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Kosmidou V, Laman R, Lugg R, Menzies A, Perry J, Petty R, Raine K, Richardson D, Shepherd R, Small A, Solomon H, Tofts C, Varian J, West S, Widaa S, Yates A, Easton DF, Riggins G, Roy JE, Levine KK, Mueller W, Batchelor TT, Louis DN, Stratton MR, Futreal PA, Wooster R.
Cancer Res Volume 66 (2006) p.3987-3991

Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413.
Vizcaíno JA, González FJ, Suárez MB, Redondo J, Heinrich J, Delgado-Jarana J, Hermosa R, Gutiérrez S, Monte E, Llobell A, Rey M.
BMC Genomics Volume 7 (2006) p.193

ThPTR2, a di/tri-peptide transporter gene from Trichoderma harzianum.
Vizcaíno JA, Cardoza RE, Hauser M, Hermosa R, Rey M, Llobell A, Becker JM, Gutiérrez S, Monte E.
Fungal Genet Biol Volume 43 (2006) p.234-246

Cloning and characterization of the erg1 gene of Trichoderma harzianum: effect of the erg1 silencing on ergosterol biosynthesis and resistance to terbinafine.
Cardoza RE, Vizcaíno JA, Hermosa MR, Sousa S, González FJ, Llobell A, Monte E, Gutiérrez S.
Fungal Genet Biol Volume 43 (2006) p.164-178

ArrayExpress service for reviewers/editors of DNA microarray papers.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI.
Nat Biotechnol Volume 24 (2006) p.1321-1322

ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression.
Blake J, Schwager C, Kapushesky M, Brazma A.
Bioinformatics Volume 22 (2006) p.765-767

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice.
Selman C, Kerrison ND, Cooray A, Piper MD, Lingard SJ, Barton RH, Schuster EF, Blanc E, Gems D, Nicholson JK, Thornton JM, Partridge L, Withers DJ.
Physiol Genomics Volume 27 (2006) p.187-200

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
J Mol Biol Volume 356 (2006) p.928-944

Design optimization methods for genomic DNA tiling arrays.
Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M.
Genome Res Volume 16 (2006) p.271-281

Concept of sample in OMICS technology.
Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D.
OMICS Volume 10 (2006) p.127-137

An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM.
J Mol Biol Volume 359 (2006) p.238-247

EMBL Nucleotide Sequence Database: developments in 2005.
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 34 (2006) p.d10-5