Publications for 2006

2006

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GOAnnotator: linking protein GO annotations to evidence text.
Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D. Journal of biomedical discovery and collaboration Volume 1 (2006) p.19 DOI: 10.1186/1747-5333-1-19
EMBL Nucleotide Sequence Database in 2006.
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R. Nucleic acids research Volume 35 (2007) p.D16-20 DOI: 10.1093/nar/gkl913
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Ensembl 2007.
Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E. Nucleic acids research Volume 35 (2007) p.D610-7 DOI: 10.1093/nar/gkl996
IntAct--open source resource for molecular interaction data.
Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H. Nucleic acids research Volume 35 (2007) p.D561-5 DOI: 10.1093/nar/gkl958
VectorBase: a home for invertebrate vectors of human pathogens.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Emmert D, Hammond M, Hill CA, Kennedy RC, Lobo NF, MacCallum MR, Madey G, Megy K, Redmond S, Russo S, Severson DW, Stinson EO, Topalis P, Zdobnov EM, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH. Nucleic acids research Volume 35 (2007) p.D503-5 DOI: 10.1093/nar/gkl960
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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. Mechanisms of ageing and development Volume 127 (2006) p.922-936 DOI: 10.1016/j.mad.2006.10.002
Annotating the human proteome: beyond establishing a parts list.
Mueller M, Martens L, Apweiler R. Biochimica et biophysica acta Volume 1774 (2007) p.175-191 DOI: 10.1016/j.bbapap.2006.11.011
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The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.
Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA. Nucleic acids research Volume 35 (2007) p.D291-7 DOI: 10.1093/nar/gkl959
ArrayExpress--a public database of microarray experiments and gene expression profiles.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A. Nucleic acids research Volume 35 (2007) p.D747-50 DOI: 10.1093/nar/gkl995
Estimating the neutral rate of nucleotide substitution using introns.
Hoffman MM, Birney E. Molecular biology and evolution Volume 24 (2007) p.522-531 DOI: 10.1093/molbev/msl179
Variation in evolutionary processes at different codon positions.
Bofkin L, Goldman N. Molecular biology and evolution Volume 24 (2007) p.513-521 DOI: 10.1093/molbev/msl178
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The Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 35 (2007) p.D193-7 DOI: 10.1093/nar/gkl929
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, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. BMC bioinformatics Volume 7 (2006) p.489 DOI: 10.1186/1471-2105-7-489
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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. Molecular cancer therapeutics Volume 5 (2006) p.2606-2612 DOI: 10.1158/1535-7163.mct-06-0433
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms.
Holliday GL, Almonacid DE, Bartlett GJ, O'Boyle NM, Torrance JW, Murray-Rust P, Mitchell JB, Thornton JM. Nucleic acids research Volume 35 (2007) p.D515-20 DOI: 10.1093/nar/gkl774
Linking publication, gene and protein data.
Kersey P, Apweiler R. Nature cell biology Volume 8 (2006) p.1183-1189 DOI: 10.1038/ncb1495
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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. American journal of human genetics Volume 79 (2006) p.1119-1124 DOI: 10.1086/510137
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ArrayExpress service for reviewers/editors of DNA microarray papers.
Brazma A, Parkinson H, ArrayExpress team, EMBL-EBI. Nature biotechnology Volume 24 (2006) p.1321-1322 DOI: 10.1038/nbt1106-1321
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Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.
Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ. Molecular psychiatry Volume 12 (2007) p.74-86 DOI: 10.1038/sj.mp.4001880
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 biology Volume 7 (2006) p.R89 DOI: 10.1186/gb-2006-7-10-r89
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Protein superfamily evolution and the last universal common ancestor (LUCA).
Ranea JA, Sillero A, Thornton JM, Orengo CA. Journal of molecular evolution Volume 63 (2006) p.513-525 DOI: 10.1007/s00239-005-0289-7
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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 DOI: 10.1186/1471-2105-7-428
Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM. Journal of molecular biology Volume 364 (2006) p.836-852 DOI: 10.1016/j.jmb.2006.09.041
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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 crystallographica. Section D, Biological crystallography Volume 62 (2006) p.1184-1195 DOI: 10.1107/s090744490602991x
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HCOP: a searchable database of human orthology predictions.
Eyre TA, Wright MW, Lush MJ, Bruford EA. Briefings in bioinformatics Volume 8 (2007) p.2-5 DOI: 10.1093/bib/bbl030
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Gaining knowledge from previously unexplained spectra-application of the PTM-Explorer software to detect PTM in HUPO BPP MS/MS data.
Chamrad DC, Körting G, Schäfer H, Stephan C, Thiele H, Apweiler R, Meyer HE, Marcus K, Blüggel M. Proteomics Volume 6 (2006) p.5048-5058 DOI: 10.1002/pmic.200600189
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HUPO Brain Proteome Project: summary of the pilot phase and introduction of a comprehensive data reprocessing strategy.
Hamacher M, Apweiler R, Arnold G, Becker A, Blüggel M, Carrette O, Colvis C, Dunn MJ, Fröhlich T, Fountoulakis M, van Hall A, Herberg F, Ji J, Kretzschmar H, Lewczuk P, Lubec G, Marcus K, Martens L, Palacios Bustamante N, Park YM, Pennington SR, Robben J, Stühler K, Reidegeld KA, Riederer P, Rossier J, Sanchez JC, Schrader M, Stephan C, Tagle D, Thiele H, Wang J, Wiltfang J, Yoo JS, Zhang C, Klose J, Meyer HE. Proteomics Volume 6 (2006) p.4890-4898 DOI: 10.1002/pmic.200600295
The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.
Hermjakob H. Proteomics Volume 6 Suppl 2 (2006) p.34-38 DOI: 10.1002/pmic.200600537
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Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.
Stephan C, Reidegeld KA, Hamacher M, van Hall A, Marcus K, Taylor C, Jones P, Müller M, Apweiler R, Martens L, Körting G, Chamrad DC, Thiele H, Blüggel M, Parkinson D, Binz PA, Lyall A, Meyer HE. Proteomics Volume 6 (2006) p.5015-5029 DOI: 10.1002/pmic.200600294
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A comparison of the HUPO Brain Proteome Project pilot with other proteomics studies.
Martens L, Müller M, Stephan C, Hamacher M, Reidegeld KA, Meyer HE, Blüggel M, Vandekerckhove J, Gevaert K, Apweiler R. Proteomics Volume 6 (2006) p.5076-5086 DOI: 10.1002/pmic.200600291
Functional annotation of proteins identified in human brain during the HUPO Brain Proteome Project pilot study.
Mueller M, Martens L, Reidegeld KA, Hamacher M, Stephan C, Blüggel M, Körting G, Chamrad D, Scheer C, Marcus K, Meyer HE, Apweiler R. Proteomics Volume 6 (2006) p.5059-5075 DOI: 10.1002/pmic.200600194
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The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome Project pilot study results.
Reidegeld KA, Müller M, Stephan C, Blüggel M, Hamacher M, Martens L, Körting G, Chamrad DC, Parkinson D, Apweiler R, Meyer HE, Marcus K. Proteomics Volume 6 (2006) p.4997-5014 DOI: 10.1002/pmic.200600305
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Flicek P, Brent MR. Genome biology Volume 7 Suppl 1 (2006) p.S8.1-9 DOI: 10.1186/gb-2006-7-s1-s8
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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 biology Volume 7 Suppl 1 (2006) p.S2.1-31 DOI: 10.1186/gb-2006-7-s1-s2
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A comparison of the phenotypic and genetic stability of recombinant Trichoderma spp. generated by protoplast- and Agrobacterium-mediated transformation.
Cardoza RE, Vizcaino JA, Hermosa MR, Monte E, Gutiérrez S. Journal of microbiology (Seoul, Korea) Volume 44 (2006) p.383-395
Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U. Nature reviews. Genetics Volume 7 (2006) p.593-605 DOI: 10.1038/nrg1922
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 DOI: 10.1002/pmic.200600452
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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. Nature genetics Volume 38 (2006) p.853 DOI: 10.1038/ng0806-853a
HUPO Publications Committee Meeting: 21 April 2006, San Francisco, CA, USA.
Orchard S, Ping P. Proteomics Volume 6 (2006) p.4436-4438 DOI: 10.1002/pmic.200600453
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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. Physiological genomics Volume 27 (2006) p.187-200 DOI: 10.1152/physiolgenomics.00084.2006
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RPS6KA2, a putative tumour suppressor gene at 6q27 in sporadic epithelial ovarian cancer.
Bignone PA, Lee KY, Liu Y, Emilion G, Finch J, Soosay AE, Charnock FM, Beck S, Dunham I, Mungall AJ, Ganesan TS. Oncogene Volume 26 (2007) p.683-700 DOI: 10.1038/sj.onc.1209827
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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 DOI: 10.1186/1471-2164-7-193
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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. Molecular & cellular proteomics : MCP Volume 5 (2006) p.1996-2007 DOI: 10.1074/mcp.t600020-mcp200
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Dry work in a wet world: computation in systems biology.
Kahlem P, Birney E. Molecular systems biology Volume 2 (2006) p.40 DOI: 10.1038/msb4100080
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[InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study]
Mulder N, Fleischmann W, Kanapin A, Arwailer R. Biofizika Volume 51 (2006) p.656-660
Bioinformatics database infrastructure for biotechnology research.
Whitfield EJ, Pruess M, Apweiler R. Journal of biotechnology Volume 124 (2006) p.629-639 DOI: 10.1016/j.jbiotec.2006.04.006
Proteomic Data Standardization, Deposition and Exchange
Orchard S, Hermjakob H, Pruess M, Apweiler R. Proteomics in Drug Research Wiley-VCH Verlag GmbH & Co. KGaA DOI: 10.1002/3527608230.ch2
Picking pyknons out of the human genome.
Meynert A, Birney E. Cell Volume 125 (2006) p.836-838 DOI: 10.1016/j.cell.2006.05.019
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Structural genomics on membrane proteins: comparison of more than 100 GPCRs in 3 expression systems.
Lundstrom K, Wagner R, Reinhart C, Desmyter A, Cherouati N, Magnin T, Zeder-Lutz G, Courtot M, Prual C, André N, Hassaine G, Michel H, Cambillau C, Pattus F. Journal of structural and functional genomics Volume 7 (2006) p.77-91 DOI: 10.1007/s10969-006-9011-2
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A bioinformatician's view of the metabolome.
Nobeli I, Thornton JM. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 28 (2006) p.534-545 DOI: 10.1002/bies.20414
Integrating biological data through the genome.
Reeves GA, Thornton JM, BioSapiens Network of Excellence. Human molecular genetics Volume 15 Spec No 1 (2006) p.R81-7 DOI: 10.1093/hmg/ddl086
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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 research Volume 66 (2006) p.3987-3991 DOI: 10.1158/0008-5472.can-06-0127
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An analysis of intron positions in relation to nucleotides, amino acids, and protein secondary structure.
Whamond GS, Thornton JM. Journal of molecular biology Volume 359 (2006) p.238-247 DOI: 10.1016/j.jmb.2006.03.029
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Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.
Zhang R, Skarina T, Evdokimova E, Edwards A, Savchenko A, Laskowski R, Cuff ME, Joachimiak A. Acta crystallographica. Section F, Structural biology and crystallization communications Volume 62 (2006) p.335-339 DOI: 10.1107/s1744309106009651
UniSave: the UniProtKB sequence/annotation version database.
Leinonen R, Nardone F, Zhu W, Apweiler R. Bioinformatics Volume 22 (2006) p.1284-1285 DOI: 10.1093/bioinformatics/btl105
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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. Mechanisms of ageing and development Volume 127 (2006) p.458-472 DOI: 10.1016/j.mad.2006.01.006
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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 DOI: 10.1038/440024a
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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 DOI: 10.1002/pmic.200600069
Modelling in molecular biology: describing transcription regulatory networks at different scales.
Schlitt T, Brazma A. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.483-494 DOI: 10.1098/rstb.2005.1806
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Introduction. Bioinformatics: from molecules to systems.
Jones DT, Sternberg MJ, Thornton JM. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 361 (2006) p.389-391 DOI: 10.1098/rstb.2005.1811
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 DOI: 10.1186/1471-2105-7-97
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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 genetics and biology : FG & B Volume 43 (2006) p.234-246 DOI: 10.1016/j.fgb.2005.12.003
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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 genetics and biology : FG & B Volume 43 (2006) p.164-178 DOI: 10.1016/j.fgb.2005.11.002
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The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.
Hermjakob H, Apweiler R. Expert review of proteomics Volume 3 (2006) p.1-3 DOI: 10.1586/14789450.3.1.1
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 DOI: 10.1002/pmic.200500868
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 DOI: 10.1002/prot.20769
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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. Bioinformatics (Oxford, England) Volume 22 (2006) p.866-873 DOI: 10.1093/bioinformatics/btl005
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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 DOI: 10.1186/1746-4811-2-1
Data standards: a call to action.
Brooksbank C, Quackenbush J. Omics : a journal of integrative biology Volume 10 (2006) p.94-99 DOI: 10.1089/omi.2006.10.94
The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).
Taylor CF, Hermjakob H, Julian RK, Garavelli JS, Aebersold R, Apweiler R. Omics : a journal of integrative biology Volume 10 (2006) p.145-151 DOI: 10.1089/omi.2006.10.145
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Function Prediction with Protein Signatures and InterPro
Mulder NJ, Apweiler R. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Nova Science Publishers, Inc, , New York, USA
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Genomics and the Genome Era.
Mulder NJ, Apweiler R. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Nova Science Publishers, Inc, , New York, USA
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Integr8: Navigating Genome Reviews and the Proteome Analysis Database.
Kersey P, Kulikova T, Pruess M, Apweiler R. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Nova Science Publishers, Inc, , New York, USA
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Guilt by association: using protein interactions and expression patterns to predict protein function
Orchard S, Hermjakob H. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins Nova Science Publishers
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 research Volume 34 (2006) p.D659-63 DOI: 10.1093/nar/gkj138
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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. Nature biotechnology Volume 24 (2006) p.21-2; author reply 23 DOI: 10.1038/nbt0106-21a
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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, Swedlow J, Taylor RC, Walashek L, Zhou Y, Liu AY, True LD. Omics : a journal of integrative biology Volume 10 (2006) p.205-208 DOI: 10.1089/omi.2006.10.205
Data storage and analysis in ArrayExpress.
Brazma A, Kapushesky M, Parkinson H, Sarkans U, Shojatalab M. Methods in enzymology Volume 411 (2006) p.370-386 DOI: 10.1016/s0076-6879(06)11020-4
Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R. Omics : a journal of integrative biology Volume 10 (2006) p.114-118 DOI: 10.1089/omi.2006.10.114
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Sequence clustering as a method of protein functional annotation
Petryszak R, Kersey P. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins Nova Science Publishers
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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 DOI: 10.1002/gcc.20265
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Integr8: Navigating Genome Reviews and the Proteome Analysis Database
Kersey P, Kulikova T, Pruess M. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins 9781594549953
Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R. Methods of biochemical analysis Volume 49 (2006) p.397-414
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Introduction. Bioinformatics: From Molecules to Systems
Jones DT, Sternberg MJE, Thornton JM. Philosophical Transactions of the Royal Society of London Series B - Biological Sciences (361 edition)
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The HUPO Brain Proteome Project.
Reidegeld KA, Hamacher M, Meyer HE, Stephan C, Blueggel M, Koerting G, Chamrad D, Scheer C, Thiele H, Taylor CF, Mueller M, Apweiler R, Jones P, Martens L. European Pharmaceutical Review (2006) p.33-38
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 : a journal of integrative biology Volume 10 (2006) p.105-113 DOI: 10.1089/omi.2006.10.105
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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 research Volume 34 (2006) p.D187-91 DOI: 10.1093/nar/gkj161
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Concept of sample in OMICS technology.
Morrison N, Cochrane G, Faruque N, Tatusova T, Tateno Y, Hancock D, Field D. Omics : a journal of integrative biology Volume 10 (2006) p.127-137 DOI: 10.1089/omi.2006.10.127
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MGED standards: work in progress.
Ball CA, Brazma A. Omics : a journal of integrative biology Volume 10 (2006) p.138-144 DOI: 10.1089/omi.2006.10.138
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Ensembl’s annotation pipeline and its use in eukaryotic genomes
Fernandez XM, Searle S, Birney E. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins Nova Science Publishers
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, 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 research Volume 34 (2006) p.D556-61 DOI: 10.1093/nar/gkj133
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 research Volume 34 (2006) p.D327-31 DOI: 10.1093/nar/gkj087
E-MSD: improving data deposition and structure quality.
Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S. Nucleic acids research Volume 34 (2006) p.D287-90 DOI: 10.1093/nar/gkj163
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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, Taylor C, White J, Wood A, FuGO Working Group. Omics : a journal of integrative biology Volume 10 (2006) p.199-204 DOI: 10.1089/omi.2006.10.199
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 research Volume 34 (2006) p.D10-5 DOI: 10.1093/nar/gkj130
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Curator driven protein sequence analysis and annotation
Magrane M, O'Donovan C. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins Nova Science Publishers
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Using ontologies to annotate microarray experiments.
Whetzel PL, Parkinson H, Stoeckert CJ. Methods in enzymology Volume 411 (2006) p.325-339 DOI: 10.1016/s0076-6879(06)11017-4
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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 : a journal of integrative biology Volume 10 (2006) p.172-178 DOI: 10.1089/omi.2006.10.172
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. Nucleic acids research Volume 34 (2006) p.D689-91 DOI: 10.1093/nar/gkj092