Publications for 2006

2006

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Annotation of environmental OMICS data: application to the transcriptomics domain.
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D.
OMICS Volume 10 (2006) p.172-178

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

Using ontologies to annotate microarray experiments.
Whetzel PL, Parkinson H, Stoeckert CJ Jr.
Methods Enzymol Volume 411 (2006) p.325-339

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

Cancer informatics in the U.K.: the NCRI informatics initiative.
Reddington F, Wilkinson JM, Clark R, Parkinson H, Kerr P, Begent R.
Cancer Inform Volume 2 (2006) p.389-394

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

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

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

The MGED Ontology: a resource for semantics-based description of microarray experiments.
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, Sansone SA, Taylor C, White J, Stoeckert CJ Jr.
Bioinformatics Volume 22 (2006) p.866-873

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Development of FuGO: an ontology for functional genomics investigations.
Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ Jr, Taylor C, White J, Wood A, FuGO Working Group.
OMICS Volume 10 (2006) p.199-204

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

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

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

MIAME/Plant - adding value to plant microarrray experiments.
Zimmermann P, Schildknecht B, Craigon D, Garcia-Hernandez M, Gruissem W, May S, Mukherjee G, Parkinson H, Rhee S, Wagner U, Hennig L.
Plant Methods Volume 2 (2006) p.1

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