Publications for 2006

2006

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

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

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

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nature cell biology Volume 8 (2006) p.1183-1189

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Conformational diversity of ligands bound to proteins.
Stockwell GR, Thornton JM.
Journal of molecular biology Volume 356 (2006) p.928-944

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

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

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

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

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

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 microbiologica Volume 51 (2006) p.114-120

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

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

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

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

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

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

Bioinformatics database infrastructure for biotechnology research.
Whitfield EJ, Pruess M, Apweiler R.
Journal of biotechnology Volume 124 (2006) p.629-639

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 Volume (2006) p.33-38

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

[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

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

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

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

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

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

Data standards: a call to action.
Brooksbank C, Quackenbush J.
Omics : a journal of integrative biology Volume 10 (2006) p.94-99

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

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

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

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

Cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM.
Journal of molecular biology Volume 364 (2006) p.836-852

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

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

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

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

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

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

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

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

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

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

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

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 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 Research Volume 34 (2006) p.D187-91

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

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

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

Standards for systems biology.
Brazma A, Krestyaninova M, Sarkans U.
Nature reviews. Genetics Volume 7 (2006) p.593-605

MGED standards: work in progress.
Ball CA, Brazma A.
Omics : a journal of integrative biology Volume 10 (2006) p.138-144

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

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

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

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