Publications for 2007


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

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

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM.
Bioinformatics (Oxford, England) Volume 23 (2007) p.e104-9
DOI: 10.1093/bioinformatics/btl292

eGenomics: Cataloguing Our Complete Genome Collection III.
Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Glöckner FO, Kottmann R, Lister AL, Tateno Y, Vaughan R.
Comparative and Functional Genomics Volume 2007 (2007) p.

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

Evolutionary conservation of regulated longevity assurance mechanisms.
McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D.
Genome biology Volume 8 (2007) p.R132
DOI: 10.1186/gb-2007-8-7-r132

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.
Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C.
Genome research Volume 17 (2007) p.708-719
DOI: 10.1101/gr.5540007

Experimental design criteria in phylogenetics: where to add taxa.
Geuten K, Massingham T, Darius P, Smets E, Goldman N.
Systematic biology Volume 56 (2007) p.609-622
DOI: 10.1080/10635150701499563

ENFIN a network to enhance integrative systems biology.
Kahlem P, Birney E.
Annals of the New York Academy of Sciences Volume 1115 (2007) p.23-31
DOI: 10.1196/annals.1407.016

Challenges and standards in integrating surveys of structural variation.
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L.
Nature genetics Volume 39 (2007) p.S7-15
DOI: 10.1038/ng2093

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

Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N.
Systematic biology Volume 56 (2007) p.431-444
DOI: 10.1080/10635150701411279

Statistics of the log-det estimator.
Massingham T, Goldman N.
Molecular biology and evolution Volume 24 (2007) p.2277-2285
DOI: 10.1093/molbev/msm160

Update of the Anopheles gambiae PEST genome assembly.
Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH.
Genome biology Volume 8 (2007) p.R5
DOI: 10.1186/gb-2007-8-1-r5

Construction, visualisation, and clustering of transcription networks from microarray expression data.
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ.
PLoS computational biology Volume 3 (2007) p.2032-2042
DOI: 10.1371/journal.pcbi.0030206

An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N.
Molecular Biology and Evolution Volume 24 (2007) p.1464-1479
DOI: 10.1093/molbev/msm064

Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.
De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG, Higgs DR.
Blood Volume 110 (2007) p.4503-4510
DOI: 10.1182/blood-2007-06-097964

Evolutionary genomics: come fly with us.
Birney E.
Nature Volume 450 (2007) p.184-185
DOI: 10.1038/450184a

Double Dutch for duplications.
Birney E.
Nature genetics Volume 39 (2007) p.1303-1304
DOI: 10.1038/ng1107-1303

The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.
Edwards CA, Rens W, Clarke O, Mungall AJ, Hore T, Graves JA, Dunham I, Ferguson-Smith AC, Ferguson-Smith MA.
BMC evolutionary biology Volume 7 (2007) p.157
DOI: 10.1186/1471-2148-7-157

The minimum information required for reporting a molecular interaction experiment (MIMIx).
Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.
Nature biotechnology Volume 25 (2007) p.894-898
DOI: 10.1038/nbt1324

Proteomics data validation: why all must provide data.
Martens L, Hermjakob H.
Molecular bioSystems Volume 3 (2007) p.518-522
DOI: 10.1039/b705178f

Optimized design and assessment of whole genome tiling arrays.
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P.
Bioinformatics (Oxford, England) Volume 23 (2007) p.i195-204
DOI: 10.1093/bioinformatics/btm200

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

Proteomic data exchange and storage: the need for common standards and public repositories.
Orchard S, Jones P, Taylor C, Zhu W, Julian RK, Hermjakob H, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 367 (2007) p.261-270
DOI: 10.1385/1-59745-275-0:261

Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11.
Nejentsev S, Smink LJ, Smyth D, Bailey R, Lowe CE, Payne F, Masters J, Godfrey L, Lam A, Burren O, Stevens H, Nutland S, Walker NM, Smith A, Twells R, Barratt BJ, Wright C, French L, Chen Y, Deloukas P, Rogers J, Dunham I, Todd JA.
BMC genetics Volume 8 (2007) p.24
DOI: 10.1186/1471-2156-8-24

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France.
Orchard S, Montechi-Palazzi L, Deutsch EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H.
Proteomics Volume 7 (2007) p.3436-3440
DOI: 10.1002/pmic.200700658

Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Mol Cell Proteomics Volume 6 (2007) p.1666-1667

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.
BMC bioinformatics Volume 8 (2007) p.401
DOI: 10.1186/1471-2105-8-401

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H.
Molecular & cellular proteomics : MCP Volume 6 (2007) p.1666-1667

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.
Proteomics Volume 7 Suppl 1 (2007) p.28-34
DOI: 10.1002/pmic.200700286

The PSI formal document process and its implementation on the PSI website.
Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW.
Proteomics Volume 7 (2007) p.2355-2357
DOI: 10.1002/pmic.200700064

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ.
Proteome science Volume 5 (2007) p.4
DOI: 10.1186/1477-5956-5-4

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nat Biotechnol. Volume (2007) p.1127-1133

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/

The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H.
Nature biotechnology Volume 25 (2007) p.887-893
DOI: 10.1038/nbt1329

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.
BMC biology Volume 5 (2007) p.44
DOI: 10.1186/1741-7007-5-44

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

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

Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM.
Journal of molecular biology Volume 367 (2007) p.1511-1522
DOI: 10.1016/j.jmb.2007.01.063

Cancer informatics in the U.K.: the NCRI informatics initiative.
Reddington F, Wilkinson JM, Clark R, Parkinson H, Kerr P, Begent R.
Cancer informatics Volume 2 (2007) p.389-394

Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
Journal of molecular biology Volume 368 (2007) p.283-301
DOI: 10.1016/j.jmb.2007.01.086

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.
Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M.
Genomics Volume 89 (2007) p.307-315
DOI: 10.1016/j.ygeno.2006.11.012

The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 369 (2007) p.1140-1152
DOI: 10.1016/j.jmb.2007.03.055

Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM.
BMC bioinformatics Volume 8 (2007) p.S1-S1

Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK, Hermjakob H.
Proteomics Volume 7 (2007) p.337-339
DOI: 10.1002/pmic.200600915

Clinical proteomics: A need to define the field and to begin to set adequate standards.
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T.
Proteomics. Clinical applications Volume 1 (2007) p.148-156
DOI: 10.1002/prca.200600771

Evolution of enzymes and pathways for the biosynthesis of cofactors.
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ.
Natural product reports Volume 24 (2007) p.972-987
DOI: 10.1039/b703107f

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M.
Nature methods Volume 4 (2007) p.13-17
DOI: 10.1038/nmeth0107-13

Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA.
Bioinformatics Volume 23 (2007) p.1824-1827
DOI: 10.1093/bioinformatics/btm085

Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.
Mouse Phenotype Database Integration Consortium, Hancock JM, Adams NC, Aidinis V, Blake A, Bogue M, Brown SD, Chesler EJ, Davidson D, Duran C, Eppig JT, Gailus-Durner V, Gates H, Gkoutos GV, Greenaway S, Hrabé de Angelis M, Kollias G, Leblanc S, Lee K, Lengger C, Maier H, Mallon AM, Masuya H, Melvin DG, Müller W, Parkinson H, Proctor G, Reuveni E, Schofield P, Shukla A, Smith C, Toyoda T, Vasseur L, Wakana S, Walling A, White J, Wood J, Zouberakis M.
Mammalian genome : official journal of the International Mammalian Genome Society Volume 18 (2007) p.157-163
DOI: 10.1007/s00335-007-9004-x

Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L.
Genome biology Volume 8 (2007) p.R39
DOI: 10.1186/gb-2007-8-3-r39

The Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic acids research Volume 35 (2007) p.D193-7
DOI: 10.1093/nar/gkl929

Proteomics: from technology development to biomarker applications.
Orchard S.
Expert review of proteomics Volume 4 (2007) p.709-710
DOI: 10.1586/14789450.4.6.709

The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.
Orchard S, Jones AR, Stephan C, Binz PA.
Proteomics Volume 7 (2007) p.1006-1008
DOI: 10.1002/pmic.200700014

In vivo validation of a computationally predicted conserved Ath5 target gene set.
Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J.
PLoS genetics Volume 3 (2007) p.1661-1671
DOI: 10.1371/journal.pgen.0030159

InterPro and InterProScan: tools for protein sequence classification and comparison.
Mulder N, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 396 (2007) p.59-70
DOI: 10.1007/978-1-59745-515-2_5

Patterns of somatic mutation in human cancer genomes.
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR.
Nature Volume 446 (2007) p.153-158
DOI: 10.1038/nature05610

Structural and chemical profiling of the human cytosolic sulfotransferases.
Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH.
PLoS Biology Volume 5 (2007) p.e97
DOI: 10.1371/journal.pbio.0050097

Classification and nomenclature of all human homeobox genes.
Holland PW, Booth HA, Bruford EA.
BMC biology Volume 5 (2007) p.47
DOI: 10.1186/1741-7007-5-47

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

MCP and HUPO: An Era of New Partnership.
Ping P, Apweiler R, Bergeron J.
Mol Cell Proteomics Volume 6 (2007) p.951-952

Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome biology Volume 8 (2007) p.R126
DOI: 10.1186/gb-2007-8-6-r126

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods in molecular biology (Clifton, N.J.) Volume 406 (2007) p.1-21
DOI: 10.1007/978-1-59745-535-0_1

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.
Nature Volume 447 (2007) p.799-816
DOI: 10.1038/nature05874

Renaming the DSCR1/Adapt78 gene family as RCAN: regulators of calcineurin.
Davies KJ, Ermak G, Rothermel BA, Pritchard M, Heitman J, Ahnn J, Henrique-Silva F, Crawford D, Canaider S, Strippoli P, Carinci P, Min KT, Fox DS, Cunningham KW, Bassel-Duby R, Olson EN, Zhang Z, Williams RS, Gerber HP, Pérez-Riba M, Seo H, Cao X, Klee CB, Redondo JM, Maltais LJ, Bruford EA, Povey S, Molkentin JD, McKeon FD, Duh EJ, Crabtree GR, Cyert MS, de la Luna S, Estivill X.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 21 (2007) p.3023-3028
DOI: 10.1096/fj.06-7246com

Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM.
Genome biology Volume 8 (2007) p.R125
DOI: 10.1186/gb-2007-8-6-r125

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.
Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton MR, Futreal PA, Wooster R.
Bioinformatics (Oxford, England) Volume 23 (2007) p.1689-1691
DOI: 10.1093/bioinformatics/btm152

Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A.
BMC bioinformatics Volume 8 Suppl 6 (2007) p.S9
DOI: 10.1186/1471-2105-8-s6-s9

Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol.
Vizcaíno JA, Redondo J, Suárez MB, Cardoza RE, Hermosa R, González FJ, Rey M, Monte E.
Applied microbiology and biotechnology Volume 75 (2007) p.853-862
DOI: 10.1007/s00253-007-0885-0

High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, Meyer HE.
Proteomics Volume 7 (2007) p.2490-2496
DOI: 10.1002/pmic.200700449

Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach.
Suárez MB, Vizcaíno JA, Llobell A, Monte E.
Current genetics Volume 51 (2007) p.331-342
DOI: 10.1007/s00294-007-0130-5

Partial silencing of a hydroxy-methylglutaryl-CoA reductase-encoding gene in Trichoderma harzianum CECT 2413 results in a lower level of resistance to lovastatin and lower antifungal activity.
Cardoza RE, Hermosa MR, Vizcaíno JA, González F, Llobell A, Monte E, Gutiérrez S.
Fungal genetics and biology : FG & B Volume 44 (2007) p.269-283
DOI: 10.1016/j.fgb.2006.11.013

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A.
Nature biotechnology Volume 25 (2007) p.1127-1133
DOI: 10.1038/nbt1347

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

Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.
Allali-Hassani A, Pan W, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards A, Bochkarev A, Plotnikov A, Vedadi M, Arrowsmith C.
PLoS biology Volume 5 (2007) p.

Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM.
PLoS computational biology Volume 3 (2007) p.1993-2002
DOI: 10.1371/journal.pcbi.0030198

Prediction of gene expression in embryonic structures of Drosophila melanogaster.
Samsonova AA, Niranjan M, Russell S, Brazma A.
PLoS computational biology Volume 3 (2007) p.e144
DOI: 10.1371/journal.pcbi.0030144

PASSIM--an open source software system for managing information in biomedical studies.
Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U.
BMC bioinformatics Volume 8 (2007) p.52
DOI: 10.1186/1471-2105-8-52

New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic acids research Volume 35 (2007) p.D224-8
DOI: 10.1093/nar/gkl841

The Universal Protein Resource (UniProt).
The UniProt Consortium.
Nucl. Acids Res. Volume 35 (2007) p.D193-D197

Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C.
Proteomics Volume 7 (2007) p.3034-3037
DOI: 10.1002/pmic.200700554

Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A.
Genome biology Volume 8 (2007) p.R73
DOI: 10.1186/gb-2007-8-5-r73

Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS.
Science (New York, N.Y.) Volume 316 (2007) p.222-234
DOI: 10.1126/science.1139247

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T.
Genome research Volume 17 (2007) p.175-183
DOI: 10.1101/gr.5509507

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A.
Genome research Volume 17 (2007) p.760-774
DOI: 10.1101/gr.6034307

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

Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J.
Nature methods Volume 4 (2007) p.563-565
DOI: 10.1038/nmeth1061

Gene prediction: compare and CONTRAST.
Flicek P.
Genome biology Volume 8 (2007) p.233
DOI: 10.1186/gb-2007-8-12-233

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

Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006.
Orchard S, Heck A, Uhlen M, Ping P.
Proteomics Volume 7 (2007) p.1009-1011
DOI: 10.1002/pmic.200700015

The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.
Genome research Volume 17 (2007) p.691-707
DOI: 10.1101/gr.5704207

Identification of novel peptide hormones in the human proteome by hidden Markov model screening.
Mirabeau O, Perlas E, Severini C, Audero E, Gascuel O, Possenti R, Birney E, Rosenthal N, Gross C.
Genome research Volume 17 (2007) p.320-327
DOI: 10.1101/gr.5755407

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
Oeder S, Mages J, Flicek P, Lang R.
BMC genomics Volume 8 (2007) p.200
DOI: 10.1186/1471-2164-8-200

The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM.
Journal of molecular biology Volume 372 (2007) p.1261-1277
DOI: 10.1016/j.jmb.2007.07.034

Adding semantics in kinetics models of biochemical pathways
Le-Novere N, Courtot M, Laibe C.
Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations Volume (2007) p.137-153

Population genomics of human gene expression.
Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET.
Nature genetics Volume 39 (2007) p.1217-1224
DOI: 10.1038/ng2142

Recommendations of the 2006 Human Variome Project meeting.
Cotton RG, 2006 Human Variome Project, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M.
Nature genetics Volume 39 (2007) p.433-436
DOI: 10.1038/ng2024

Genome sequence of Aedes aegypti, a major arbovirus vector.
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW.
Science (New York, N.Y.) Volume 316 (2007) p.1718-1723
DOI: 10.1126/science.1138878

The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.
Proceedings of the National Academy of Sciences of the United States of America Volume 104 (2007) p.5495-5500
DOI: 10.1073/pnas.0700800104

Genome browsing with Ensembl: a practical overview.
Spudich G, Fernández-Suárez XM, Birney E.
Briefings in functional genomics & proteomics Volume 6 (2007) p.202-219
DOI: 10.1093/bfgp/elm025

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