Publications for 2010

2010

Free computational resources for designing selected reaction monitoring transitions.
Cham Mead JA, Bianco L, Bessant C.
Proteomics Volume 10 (2010) p.1106-1126

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU.
BMC Bioinformatics Volume 11 (2010) p.112

A large-scale protein-function database.
Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K.
Nat Chem Biol Volume 6 (2010) p.785

Progress on an open source computer-assisted structure elucidation suite (SENECA).
Kuhn S, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.p34-p34

The structures and physicochemical properties of organic cofactors in biocatalysis.
Fischer JD, Holliday GL, Rahman SA, Thornton JM.
J Mol Biol Volume 403 (2010) p.803-824

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M.
Proc Natl Acad Sci U S A Volume 107 (2010) p.4135-4140

Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences.
Lawniczak MK, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ.
Science Volume 330 (2010) p.512-514

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.
Shankar R, Parkinson H, Burdett T, Hastings E, Liu J, Miller M, Srinivasa R, White J, Brazma A, Sherlock G, Stoeckert CJ Jr, Ball CA.
Bioinformatics Volume 26 (2010) p.2470-2471

MRMaid-DB: a repository of published SRM transitions.
Cham JA, Bianco L, Barton C, Bessant C.
J Proteome Res Volume 9 (2010) p.620-625

BioCatalogue: a universal catalogue of web services for the life sciences.
Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.
Nucleic Acids Res Volume 38 (2010) p.w689-94

Molecular fragments chemoinformatics.
Kuhn H, Neumann S, Steinbeck C, Wittekindt C, Zielesny A.
Journal of Cheminformatics Volume 2 (2010) p.p14-p14

OrChem: an open source chemistry search engine for Oracle.
Rijnbeek ML, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.p28-p28

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic Acids Res Volume 38 (2010) p.d331-5

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease.
McKinney EF, Lyons PA, Carr EJ, Hollis JL, Jayne DR, Willcocks LC, Koukoulaki M, Brazma A, Jovanovic V, Kemeny DM, Pollard AJ, Macary PA, Chaudhry AN, Smith KG.
Nat Med Volume 16 (2010) p.586-91, 1p following 591

Mining proteomic MS/MS data for MRM transitions.
Chem Mead JA, Bianco L, Bessant C.
Methods Mol Biol Volume 604 (2010) p.187-199

Molecular interactions and data standardisation.
Orchard S, Kerrien S.
Methods Mol Biol Volume 604 (2010) p.309-318

A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA.
Nature Volume 467 (2010) p.1061-1073

Ontology engineering.
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF.
Nat Biotechnol Volume 28 (2010) p.128-130

Fast and efficient searching of biological data resources--using EB-eye.
Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R.
Brief Bioinform Volume 11 (2010) p.375-384

IPD--the Immuno Polymorphism Database.
Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG.
Nucleic Acids Res Volume 38 (2010) p.d863-9

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.
Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.
Science Volume 330 (2010) p.86-88

DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.
Schuster E, McElwee JJ, Tullet JM, Doonan R, Matthijssens F, Reece-Hoyes JS, Hope IA, Vanfleteren JR, Thornton JM, Gems D.
Mol Syst Biol Volume 6 (2010) p.399

Integrating common and rare genetic variation in diverse human populations.
International HapMap 3 Consortium, Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L, Dermitzakis E, Bonnen PE, Altshuler DM, Gibbs RA, de Bakker PI, Deloukas P, Gabriel SB, Gwilliam R, Hunt S, Inouye M, Jia X, Palotie A, Parkin M, Whittaker P, Yu F, Chang K, Hawes A, Lewis LR, Ren Y, Wheeler D, Gibbs RA, Muzny DM, Barnes C, Darvishi K, Hurles M, Korn JM, Kristiansson K, Lee C, McCarrol SA, Nemesh J, Dermitzakis E, Keinan A, Montgomery SB, Pollack S, Price AL, Soranzo N, Bonnen PE, Gibbs RA, Gonzaga-Jauregui C, Keinan A, Price AL, Yu F, Anttila V, Brodeur W, Daly MJ, Leslie S, McVean G, Moutsianas L, Nguyen H, Schaffner SF, Zhang Q, Ghori MJ, McGinnis R, McLaren W, Pollack S, Price AL, Schaffner SF, Takeuchi F, Grossman SR, Shlyakhter I, Hostetter EB, Sabeti PC, Adebamowo CA, Foster MW, Gordon DR, Licinio J, Manca MC, Marshall PA, Matsuda I, Ngare D, Wang VO, Reddy D, Rotimi CN, Royal CD, Sharp RR, Zeng C, Brooks LD, McEwen JE.
Nature Volume 467 (2010) p.52-58

Visualizing chromosome mosaicism and detecting ethnic outliers by the method of "rare" heterozygotes and homozygotes (RHH).
McGinnis RE, Deloukas P, McLaren WM, Inouye M.
Hum Mol Genet Volume 19 (2010) p.2539-2553

Diversity of human copy number variation and multicopy genes.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler EE.
Science Volume 330 (2010) p.641-646

The Renal Gene Ontology Annotation Initiative.
Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.
Organogenesis Volume 6 (2010) p.71-75

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J.
Nucleic Acids Res Volume 38 (2010) p.4325-4336

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.
Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG, Stanier P, Kwiatkowski D, Deloukas P, Dermitzakis ET, Tavaré S, Moore GE, Dunham I.
BMC Genet Volume 11 (2010) p.25

Protein structure databases.
Laskowski RA.
Methods Mol Biol Volume 609 (2010) p.59-82

Regulation of lifespan, metabolism, and stress responses by the Drosophila SH2B protein, Lnk.
Slack C, Werz C, Wieser D, Alic N, Foley A, Stocker H, Withers DJ, Thornton JM, Hafen E, Partridge L.
PLoS Genet Volume 6 (2010) p.e1000881

On the diversity of physicochemical environments experienced by identical ligands in binding pockets of unrelated proteins.
Kahraman A, Morris RJ, Laskowski RA, Favia AD, Thornton JM.
Proteins Volume 78 (2010) p.1120-1136

The (non)malignancy of cancerous amino acidic substitutions.
Talavera D, Taylor MS, Thornton JM.
Proteins Volume 78 (2010) p.518-529

A new bioinformatics analysis tools framework at EMBL-EBI.
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R.
Nucleic Acids Res Volume 38 (2010) p.w695-9

ATR-X syndrome protein targets tandem repeats and influences allele-specific expression in a size-dependent manner.
Law MJ, Lower KM, Voon HP, Hughes JR, Garrick D, Viprakasit V, Mitson M, De Gobbi M, Marra M, Morris A, Abbott A, Wilder SP, Taylor S, Santos GM, Cross J, Ayyub H, Jones S, Ragoussis J, Rhodes D, Dunham I, Higgs DR, Gibbons RJ.
Cell Volume 143 (2010) p.367-378

The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM.
Bioinformatics Volume 26 (2010) p.2496-2497

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
J Mol Recognit Volume 23 (2010) p.194-208

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution.
Dhami P, Saffrey P, Bruce AW, Dillon SC, Chiang K, Bonhoure N, Koch CM, Bye J, James K, Foad NS, Ellis P, Watkins NA, Ouwehand WH, Langford C, Andrews RM, Dunham I, Vetrie D.
PLoS One Volume 5 (2010) p.e12339

ArchSchema: a tool for interactive graphing of related Pfam domain architectures.
Tamuri AU, Laskowski RA.
Bioinformatics Volume 26 (2010) p.1260-1261

So what have data standards ever done for us? The view from metabolomics.
Griffin JL, Steinbeck C.
Genome Med Volume 2 (2010) p.38

Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM.
Proteins Volume 78 (2010) p.2349-2368

International network of cancer genome projects.
International Cancer Genome Consortium, Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hubbard TJ, Jiang T, Jones SM, Li Q, López-Bigas N, Luo R, Muthuswamy L, Ouellette BF, Pearson JV, Puente XS, Quesada V, Raphael BJ, Sander C, Shibata T, Speed TP, Stein LD, Stuart JM, Teague JW, Totoki Y, Tsunoda T, Valencia A, Wheeler DA, Wu H, Zhao S, Zhou G, Stein LD, Guigó R, Hubbard TJ, Joly Y, Jones SM, Kasprzyk A, Lathrop M, López-Bigas N, Ouellette BF, Spellman PT, Teague JW, Thomas G, Valencia A, Yoshida T, Kennedy KL, Axton M, Dyke SO, Futreal PA, Gerhard DS, Gunter C, Guyer M, Hudson TJ, McPherson JD, Miller LJ, Ozenberger B, Shaw KM, Kasprzyk A, Stein LD, Zhang J, Haider SA, Wang J, Yung CK, Cros A, Liang Y, Gnaneshan S, Guberman J, Hsu J, Bobrow M, Chalmers DR, Hasel KW, Joly Y, Kaan TS, Kennedy KL, Knoppers BM, Lowrance WW, Masui T, Nicolás P, Rial-Sebbag E, Rodriguez LL, Vergely C, Yoshida T, Grimmond SM, Biankin AV, Bowtell DD, Cloonan N, deFazio A, Eshleman JR, Etemadmoghadam D, Gardiner BB, Kench JG, Scarpa A, Sutherland RL, Tempero MA, Waddell NJ, Wilson PJ, McPherson JD, Gallinger S, Tsao MS, Shaw PA, Petersen GM, Mukhopadhyay D, Chin L, DePinho RA, Thayer S, Muthuswamy L, Shazand K, Beck T, Sam M, Timms L, Ballin V, Lu Y, Ji J, Zhang X, Chen F, Hu X, Zhou G, Yang Q, Tian G, Zhang L, Xing X, Li X, Zhu Z, Yu Y, Yu J, Yang H, Lathrop M, Tost J, Brennan P, Holcatova I, Zaridze D, Brazma A, Egevard L, Prokhortchouk E, Banks RE, Uhlén M, Cambon-Thomsen A, Viksna J, Ponten F, Skryabin K, Stratton MR, Futreal PA, Birney E, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Martin S, Reis-Filho JS, Richardson AL, Sotiriou C, Stunnenberg HG, Thoms G, van de Vijver M, van't Veer L, Calvo F, Birnbaum D, Blanche H, Boucher P, Boyault S, Chabannon C, Gut I, Masson-Jacquemier JD, Lathrop M, Pauporté I, Pivot X, Vincent-Salomon A, Tabone E, Theillet C, Thomas G, Tost J, Treilleux I, Calvo F, Bioulac-Sage P, Clément B, Decaens T, Degos F, Franco D, Gut I, Gut M, Heath S, Lathrop M, Samuel D, Thomas G, Zucman-Rossi J, Lichter P, Eils R, Brors B, Korbel JO, Korshunov A, Landgraf P, Lehrach H, Pfister S, Radlwimmer B, Reifenberger G, Taylor MD, von Kalle C, Majumder PP, Sarin R, Rao TS, Bhan MK, Scarpa A, Pederzoli P, Lawlor RA, Delledonne M, Bardelli A, Biankin AV, Grimmond SM, Gress T, Klimstra D, Zamboni G, Shibata T, Nakamura Y, Nakagawa H, Kusada J, Tsunoda T, Miyano S, Aburatani H, Kato K, Fujimoto A, Yoshida T, Campo E, López-Otín C, Estivill X, Guigó R, de Sanjosé S, Piris MA, Montserrat E, González-Díaz M, Puente XS, Jares P, Valencia A, Himmelbauer H, Quesada V, Bea S, Stratton MR, Futreal PA, Campbell PJ, Vincent-Salomon A, Richardson AL, Reis-Filho JS, van de Vijver M, Thomas G, Masson-Jacquemier JD, Aparicio S, Borg A, Børresen-Dale AL, Caldas C, Foekens JA, Stunnenberg HG, van't Veer L, Easton DF, Spellman PT, Martin S, Barker AD, Chin L, Collins FS, Compton CC, Ferguson ML, Gerhard DS, Getz G, Gunter C, Guttmacher A, Guyer M, Hayes DN, Lander ES, Ozenberger B, Penny R, Peterson J, Sander C, Shaw KM, Speed TP, Spellman PT, Vockley JG, Wheeler DA, Wilson RK, Hudson TJ, Chin L, Knoppers BM, Lander ES, Lichter P, Stein LD, Stratton MR, Anderson W, Barker AD, Bell C, Bobrow M, Burke W, Collins FS, Compton CC, DePinho RA, Easton DF, Futreal PA, Gerhard DS, Green AR, Guyer M, Hamilton SR, Hubbard TJ, Kallioniemi OP, Kennedy KL, Ley TJ, Liu ET, Lu Y, Majumder P, Marra M, Ozenberger B, Peterson J, Schafer AJ, Spellman PT, Stunnenberg HG, Wainwright BJ, Wilson RK, Yang H.
Nature Volume 464 (2010) p.993-998

ChEBI: a chemistry ontology and database.
de Matos P, Dekker A, Ennis M, Hastings J, Haug K, Turner S, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.p6-p6

Unifying themes in microbial associations with animal and plant hosts described using the gene ontology.
Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, Lindeberg M, Meng S, Chibucos MC, Tseng TT, Lomax J, Biehl B, Ireland A, Bird D, Dean RA, Glasner JD, Perna N, Setubal JC, Collmer A, Tyler BM.
Microbiol Mol Biol Rev Volume 74 (2010) p.479-503

HLA class I binding of HBZ determines outcome in HTLV-1 infection.
Macnamara A, Rowan A, Hilburn S, Kadolsky U, Fujiwara H, Suemori K, Yasukawa M, Taylor G, Bangham CR, Asquith B.
PLoS Pathog Volume 6 (2010) p.e1001117

Chemical fragments that hydrogen bond to Asp, Glu, Arg, and His side chains in protein binding sites.
Chan AW, Laskowski RA, Selwood DL.
J Med Chem Volume 53 (2010) p.3086-3094

A global map of human gene expression.
Lukk M, Kapushesky M, Nikkilä J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A.
Nat Biotechnol Volume 28 (2010) p.322-324

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.
Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubío JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguadé M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR.
Proc Natl Acad Sci U S A Volume 107 (2010) p.12168-12173

Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.
Nat Methods Volume 7 (2010) p.s42-55

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets.
Lee K, Thorneycroft D, Achuthan P, Hermjakob H, Ideker T.
Plant Cell Volume 22 (2010) p.997-1005

Public data archives for genomic structural variation.
Church DM, Lappalainen I, Sneddon TP, Hinton J, Maguire M, Lopez J, Garner J, Paschall J, DiCuccio M, Yaschenko E, Scherer SW, Feuk L, Flicek P.
Nat Genet Volume 42 (2010) p.813-814

Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC).
Hilner JE, Perdue LH, Sides EG, Pierce JJ, Wägner AM, Aldrich A, Loth A, Albret L, Wagenknecht LE, Nierras C, Akolkar B, T1DGC.
Clin Trials Volume 7 (2010) p.s5-s32

Ensembl variation resources.
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P.
BMC Genomics Volume 11 (2010) p.293

Minimum information about a protein affinity reagent (MIAPAR).
Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PA, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D.
Nat Biotechnol Volume 28 (2010) p.650-653

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic Acids Res Volume 38 (2010) p.d142-8

PDBe: Protein Data Bank in Europe.
Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ.
Nucleic Acids Res Volume 38 (2010) p.d308-17

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cell Mol Life Sci Volume 67 (2010) p.1049-1064

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.
Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL.
Stand Genomic Sci Volume 3 (2010) p.259-266

iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M, Down TA, Saini H, Enright A, Hubbard TJ.
Bioinformatics Volume 26 (2010) p.843-844

The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.
Swertz MA, Dijkstra M, Adamusiak T, van der Velde JK, Kanterakis A, Roos ET, Lops J, Thorisson GA, Arends D, Byelas G, Muilu J, Brookes AJ, de Brock EO, Jansen RC, Parkinson H.
BMC Bioinformatics Volume 11 Suppl 12 (2010) p.s12

A new strategy for genome assembly using short sequence reads and reduced representation libraries.
Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.
Genome Res Volume 20 (2010) p.249-256

A small-cell lung cancer genome with complex signatures of tobacco exposure.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman C, Varela I, Nik-Zainal S, Davies HR, Ordoñez GR, Mudie LJ, Latimer C, Edkins S, Stebbings L, Chen L, Jia M, Leroy C, Marshall J, Menzies A, Butler A, Teague JW, Mangion J, Sun YA, McLaughlin SF, Peckham HE, Tsung EF, Costa GL, Lee CC, Minna JD, Gazdar A, Birney E, Rhodes MD, McKernan KJ, Stratton MR, Futreal PA, Campbell PJ.
Nature Volume 463 (2010) p.184-190

Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Hum Mol Genet Volume 19 (2010) p.r204-9

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 8.
Kyrpides N, Field D, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J.
Stand Genomic Sci Volume 3 (2010) p.93-96

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010.
Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O.
Stand Genomic Sci Volume 3 (2010) p.232-234

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases.
Antonov AV, Schmidt EE, Dietmann S, Krestyaninova M, Hermjakob H.
Nucleic Acids Res Volume 38 (2010) p.w78-83

Modeling Competition of Transcription Factors for DNA Binding Sites Improves Binding Site Predictions
Hestand MS, Hoffman MM, Birney E, van Ommen G-JB, den Dunnen JT, A.C. ’t Hoen P.
Volume (2010) p.45-62

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression.
Murray MJ, Saini HK, van Dongen S, Palmer RD, Muralidhar B, Pett MR, Piipari M, Thornton CM, Nicholson JC, Enright AJ, Coleman N.
Mol Cancer Volume 9 (2010) p.290

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA.
Bioinformatics Volume 26 (2010) p.2354-2356

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.
Cavalieri D, Rivero D, Beltrame L, Buschow SI, Calura E, Rizzetto L, Gessani S, Gauzzi MC, Reith W, Baur A, Bonaiuti R, Brandizi M, De Filippo C, D'Oro U, Draghici S, Dunand-Sauthier I, Gatti E, Granucci F, Gündel M, Kramer M, Kuka M, Lanyi A, Melief CJ, van Montfoort N, Ostuni R, Pierre P, Popovici R, Rajnavolgyi E, Schierer S, Schuler G, Soumelis V, Splendiani A, Stefanini I, Torcia MG, Zanoni I, Zollinger R, Figdor CG, Austyn JM.
Immunome Res Volume 6 (2010) p.10

Gene expression atlas at the European bioinformatics institute.
Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A.
Nucleic Acids Res Volume 38 (2010) p.d690-8

A CTCF-independent role for cohesin in tissue-specific transcription.
Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, Carroll JS, Flicek P, Odom DT.
Genome Res Volume 20 (2010) p.578-588

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A.
Nucleic Acids Res Volume 38 (2010) p.d563-9

The miR-144/451 locus is required for erythroid homeostasis.
Rasmussen KD, Simmini S, Abreu-Goodger C, Bartonicek N, Di Giacomo M, Bilbao-Cortes D, Horos R, Von Lindern M, Enright AJ, O'Carroll D.
J Exp Med Volume 207 (2010) p.1351-1358

Efficient inhibition of miR-155 function in vivo by peptide nucleic acids.
Fabani MM, Abreu-Goodger C, Williams D, Lyons PA, Torres AG, Smith KG, Enright AJ, Gait MJ, Vigorito E.
Nucleic Acids Res Volume 38 (2010) p.4466-4475

Characterization and prediction of protein nucleolar localization sequences.
Scott MS, Boisvert FM, McDowall MD, Lamond AI, Barton GJ.
Nucleic Acids Res Volume 38 (2010) p.7388-7399

Modeling biomedical experimental processes with OBI.
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J, OBI consortium.
J Biomed Semantics Volume 1 Suppl 1 (2010) p.s7

SylArray: a web server for automated detection of miRNA effects from expression data.
Bartonicek N, Enright AJ.
Bioinformatics Volume 26 (2010) p.2900-2901

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.
Swertz MA, Velde KJ, Tesson BM, Scheltema RA, Arends D, Vera G, Alberts R, Dijkstra M, Schofield P, Schughart K, Hancock JM, Smedley D, Wolstencroft K, Goble C, de Brock EO, Jones AR, Parkinson HE, Coordination of Mouse Informatics Resources (CASIMIR), Genotype-To-Phenotype (GEN2PHEN) Consortiums, Jansen RC.
Genome Biol Volume 11 (2010) p.r27

Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs.
Santhakumar D, Forster T, Laqtom NN, Fragkoudis R, Dickinson P, Abreu-Goodger C, Manakov SA, Choudhury NR, Griffiths SJ, Vermeulen A, Enright AJ, Dutia B, Kohl A, Ghazal P, Buck AH.
Proc Natl Acad Sci U S A Volume 107 (2010) p.13830-13835

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Workshop at the Pacific Symposium on Biocomputing 2010.
Hirschman L, Sterk P, Field D, Wooley J, Cochrane G, Gilbert J, Kolker E, Kyrpides N, Meyer F, Mizrachi I, Nakamura Y, Sansone SA, Schriml L, Tatusova T, White O, Yilmaz P.
Stand Genomic Sci Volume 2 (2010) p.357-360

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
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Nucleic Acids Res Volume 38 (2010) p.d1-4

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC.
PLoS Genet Volume 6 (2010) p.e1001023

Meeting Report: BioSharing at ISMB 2010.
Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A.
Stand Genomic Sci Volume 3 (2010) p.254-258

Straightforward and complete deposition of NMR data to the PDBe.
Penkett CJ, van Ginkel G, Velankar S, Swaminathan J, Ulrich EL, Mading S, Stevens TJ, Fogh RH, Gutmanas A, Kleywegt GJ, Henrick K, Vranken WF.
J Biomol NMR Volume 48 (2010) p.85-92

An international bioinformatics infrastructure to underpin the Arabidopsis community.
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Plant Cell Volume 22 (2010) p.2530-2536

Visualizing the drug target landscape.
Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L.
Drug Discov Today Volume 15 (2010) p.3-15

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.
Smedley D, Schofield P, Chen CK, Aidinis V, Ainali C, Bard J, Balling R, Birney E, Blake A, Bongcam-Rudloff E, Brookes AJ, Cesareni G, Chandras C, Eppig J, Flicek P, Gkoutos G, Greenaway S, Gruenberger M, Hériché JK, Lyall A, Mallon AM, Muddyman D, Reisinger F, Ringwald M, Rosenthal N, Schughart K, Swertz M, Thorisson GA, Zouberakis M, Hancock JM.
Database (Oxford) Volume 2010 (2010) p.baq014

The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.
Nature Volume 464 (2010) p.757-762

eHive: an artificial intelligence workflow system for genomic analysis.
Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J.
BMC Bioinformatics Volume 11 (2010) p.240

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT.
Science Volume 328 (2010) p.1036-1040

Journal club. A computational geneticist looks at mechanisms of chromosomal evolution.
Flicek P.
Nature Volume 463 (2010) p.713

Mining Unique-m Substrings from Genomes
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R.
J Proteomics Bioinform Volume 3 (2010) p.99-100

Public Data Resources as the Foundation for a Worldwide Metagenomics Data Infrastructure
Cochrane G, Martin MJ, Apweiler R.
Volume (2010) p.79

Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation.
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gräf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, van Steensel B.
Mol Cell Volume 38 (2010) p.603-613

Role of open chemical data in aiding drug discovery and design.
Gaulton A, Overington JP.
Future Med Chem Volume 2 (2010) p.903-907

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.
Sudbery I, Enright AJ, Fraser AG, Dunham I.
BMC Genomics Volume 11 (2010) p.175

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.
Palmer RD, Murray MJ, Saini HK, van Dongen S, Abreu-Goodger C, Muralidhar B, Pett MR, Thornton CM, Nicholson JC, Enright AJ, Coleman N, Children's Cancer and Leukaemia Group.
Cancer Res Volume 70 (2010) p.2911-2923

Practical application of bioinformatics by the multidisciplinary VIZIER consortium.
Gorbalenya AE, Lieutaud P, Harris MR, Coutard B, Canard B, Kleywegt GJ, Kravchenko AA, Samborskiy DV, Sidorov IA, Leontovich AM, Jones TA.
Antiviral Res Volume 87 (2010) p.95-110

An effective model for natural selection in promoters.
Hoffman MM, Birney E.
Genome Res Volume 20 (2010) p.685-692

Consistent annotation of gene expression arrays.
Ballester B, Johnson N, Proctor G, Flicek P.
BMC Genomics Volume 11 (2010) p.294

Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H.
Nucleic Acids Res Volume 38 (2010) p.d870-1

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome Biol Volume 11 (2010) p.402

EMMA--mouse mutant resources for the international scientific community.
Wilkinson P, Sengerova J, Matteoni R, Chen CK, Soulat G, Ureta-Vidal A, Fessele S, Hagn M, Massimi M, Pickford K, Butler RH, Marschall S, Mallon AM, Pickard A, Raspa M, Scavizzi F, Fray M, Larrigaldie V, Leyritz J, Birney E, Tocchini-Valentini GP, Brown S, Herault Y, Montoliu L, de Angelis MH, Smedley D.
Nucleic Acids Res Volume 38 (2010) p.d570-6

A database and API for variation, dense genotyping and resequencing data.
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F.
BMC Bioinformatics Volume 11 (2010) p.238

Safeguarding the integrity of protein archive.
Berman HM, Kleywegt GJ, Nakamura H, Markley JL, Burley SK.
Nature Volume 463 (2010) p.425

Heritable individual-specific and allele-specific chromatin signatures in humans.
McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E.
Science Volume 328 (2010) p.235-239

The systematic annotation of the three main GPCR families in Reactome.
Jassal B, Jupe S, Caudy M, Birney E, Stein L, Hermjakob H, D'Eustachio P.
Database (Oxford) Volume 2010 (2010) p.baq018

Elevated cyclic AMP levels in T lymphocytes transformed by human T-cell lymphotropic virus type 1.
Kress AK, Schneider G, Pichler K, Kalmer M, Fleckenstein B, Grassmann R.
J Virol Volume 84 (2010) p.8732-8742

MapMi: automated mapping of microRNA loci.
Guerra-Assunção JA, Enright AJ.
BMC Bioinformatics Volume 11 (2010) p.133

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic Acids Res Volume 38 (2010) p.d736-42

A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease.
Perreau VM, Orchard S, Adlard PA, Bellingham SA, Cappai R, Ciccotosto GD, Cowie TF, Crouch PJ, Duce JA, Evin G, Faux NG, Hill AF, Hung YH, James SA, Li QX, Mok SS, Tew DJ, White AR, Bush AI, Hermjakob H, Masters CL.
Proteomics Volume 10 (2010) p.2377-2395

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.
BMC Bioinformatics Volume 11 (2010) p.415

The IntAct molecular interaction database in 2010.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.
Nucleic Acids Res Volume 38 (2010) p.d525-31

implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Hermjakob H.
Proteomics Volume 10 (2010) p.1895-1898

Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS.
Proteomics Volume 10 (2010) p.3957-3969

The Ontology Lookup Service: bigger and better.
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.
Nucleic Acids Res Volume 38 (2010) p.w155-60

BioXSD: the common data-exchange format for everyday bioinformatics web services.
Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I.
Bioinformatics Volume 26 (2010) p.i540-6

A draft sequence of the Neandertal genome.
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.
Science Volume 328 (2010) p.710-722

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.
PLoS Biol Volume 8 (2010) p.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.
Gibson F, Hoogland C, Martinez-Bartolomé S, Medina-Aunon JA, Albar JP, Babnigg G, Wipat A, Hermjakob H, Almeida JS, Stanislaus R, Paton NW, Jones AR.
Proteomics Volume 10 (2010) p.3073-3081

CDK-Taverna: an open workflow environment for cheminformatics.
Kuhn T, Willighagen EL, Zielesny A, Steinbeck C.
BMC Bioinformatics Volume 11 (2010) p.159

Chemical Entities of Biological Interest: an update.
de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C.
Nucleic Acids Res Volume 38 (2010) p.d249-54

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation.
Abad-Zapatero C, Perišić O, Wass J, Bento AP, Overington J, Al-Lazikani B, Johnson ME.
Drug Discov Today Volume 15 (2010) p.804-811

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.
Nature Volume 464 (2010) p.768-772

Ensembl's 10th year.
Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM.
Nucleic Acids Res Volume 38 (2010) p.d557-62

Chromosomal mapping of pancreatic islet morphological features and regulatory hormones in the spontaneously diabetic (Type 2) Goto-Kakizaki rat.
Finlay C, Argoud K, Wilder SP, Ouali F, Ktorza A, Kaisaki PJ, Gauguier D.
Mamm Genome Volume 21 (2010) p.499-508

Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.
Genome Res Volume 20 (2010) p.180-189

Functional comparison of innate immune signaling pathways in primates.
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.
PLoS Genet Volume 6 (2010) p.e1001249

Genomic-scale capture and sequencing of endogenous DNA from feces.
Perry GH, Marioni JC, Melsted P, Gilad Y.
Mol Ecol Volume 19 (2010) p.5332-5344

A community standard format for the representation of protein affinity reagents.
Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H.
Mol Cell Proteomics Volume 9 (2010) p.1-10

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.
Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.
Mol Cell Proteomics Volume 9 (2010) p.2642-2653

The publication and database deposition of molecular interaction data.
Orchard S, Aranda B, Hermjakob H.
Curr Protoc Protein Sci Volume Chapter 25 (2010) p.unit 25.3

The consequence of natural selection on genetic variation in the mouse.
Reuveni E, Birney E, Gross CT.
Genomics Volume 95 (2010) p.196-202

Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea.
Orchard S, Jones A, Albar JP, Cho SY, Kwon KH, Lee C, Hermjakob H.
Proteomics Volume 10 (2010) p.3062-3066

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C.
RNA Volume 16 (2010) p.991-1006

Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research.
Vizcaíno JA, Foster JM, Martens L.
J Proteomics Volume 73 (2010) p.2136-2146

The EMBRACE web service collection.
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G.
Nucleic Acids Res Volume 38 (2010) p.w683-8

Towards a rigorous assessment of systems biology models: the DREAM3 challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PLoS One Volume 5 (2010) p.e9202

Logic-based models for the analysis of cell signaling networks.
Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.
Biochemistry Volume 49 (2010) p.3216-3224

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.
Li C, Courtot M, Le Novère N, Laibe C.
Brief Bioinform Volume 11 (2010) p.270-277

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.
Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C.
BMC Syst Biol Volume 4 (2010) p.92

Discovery of drug mode of action and drug repositioning from transcriptional responses.
Iorio F, Bosotti R, Scacheri E, Belcastro V, Mithbaokar P, Ferriero R, Murino L, Tagliaferri R, Brunetti-Pierri N, Isacchi A, di Bernardo D.
Proc Natl Acad Sci U S A Volume 107 (2010) p.14621-14626

Improvements to services at the European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, Cheng Y, Demiralp F, Faruque N, Goodgame N, Gibson R, Hoad G, Hunter C, Jang M, Leonard S, Lin Q, Lopez R, Maguire M, McWilliam H, Plaister S, Radhakrishnan R, Sobhany S, Slater G, Ten Hoopen P, Valentin F, Vaughan R, Zalunin V, Zerbino D, Cochrane G.
Nucleic Acids Res Volume 38 (2010) p.d39-45

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, Chen Y, McLaren WM, Larsson P, Vaughan BW, Béroud C, Dobson G, Lehväslaiho H, Taschner PE, den Dunnen JT, Devereau A, Birney E, Brookes AJ, Maglott DR.
Genome Med Volume 2 (2010) p.24

Large scale comparison of global gene expression patterns in human and mouse.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome Biol Volume 11 (2010) p.r124

Bioinformatics training: selecting an appropriate learning content management system--an example from the European Bioinformatics Institute.
Wright VA, Vaughan BW, Laurent T, Lopez R, Brooksbank C, Schneider MV.
Brief Bioinform Volume 11 (2010) p.552-562

Modeling sample variables with an Experimental Factor Ontology.
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H.
Bioinformatics Volume 26 (2010) p.1112-1118

Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes.
Naukkarinen J, Surakka I, Pietiläinen KH, Rissanen A, Salomaa V, Ripatti S, Yki-Järvinen H, van Duijn CM, Wichmann HE, Kaprio J, Taskinen MR, Peltonen L, ENGAGE Consortium.
PLoS Genet Volume 6 (2010) p.e1000976

Interaction modes at protein hetero-dimer interfaces.
Vaishnavi A, Sowmya G, Kalaivanii J, Ilakya S, Kangueane U, Kangueane P.
Bioinformation Volume 4 (2010) p.310-319

Non-redundant patent sequence databases with value-added annotations at two levels.
Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R.
Nucleic Acids Res Volume 38 (2010) p.d52-6

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, Behmoaras J, Fernandez-Suarez XM, Johnson MD, McLaren WM, Patone G, Petretto E, Plessy C, Rockland KS, Rockland C, Saar K, Zhao Y, Carninci P, Flicek P, Kurtz T, Cuppen E, Pravenec M, Hubner N, Jones SJ, Birney E, Aitman TJ.
Genome Res Volume 20 (2010) p.791-803

A standard variation file format for human genome sequences.
Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K.
Genome Biol Volume 11 (2010) p.r88

Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.
PLoS ONE Volume 5 (2010) p.

How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010.
Kohonen-Corish MR, Al-Aama JY, Auerbach AD, Axton M, Barash CI, Bernstein I, Béroud C, Burn J, Cunningham F, Cutting GR, den Dunnen JT, Greenblatt MS, Kaput J, Katz M, Lindblom A, Macrae F, Maglott D, Möslein G, Povey S, Ramesar R, Richards S, Seminara D, Sobrido MJ, Tavtigian S, Taylor G, Vihinen M, Winship I, Cotton RG, Human Variome Project Meeting.
Hum Mutat Volume 31 (2010) p.1374-1381

The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.
Nat Biotechnol Volume 28 (2010) p.935-942

Bioinformatics training: a review of challenges, actions and support requirements.
Schneider MV, Watson J, Attwood T, Rother K, Budd A, McDowall J, Via A, Fernandes P, Nyronen T, Blicher T, Jones P, Blatter MC, De Las Rivas J, Judge DP, van der Gool W, Brooksbank C.
Brief Bioinform Volume 11 (2010) p.544-551

Identification of small molecules enhancing autophagic function from drug network analysis.
Iorio F, Isacchi A, di Bernardo D, Brunetti-Pierri N.
Autophagy Volume 6 (2010) p.1204-1205

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N.
BMC Bioinformatics Volume 11 (2010) p.579

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
Bioinformatics Volume 26 (2010) p.2069-2070

The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J.
Nucleic Acids Res Volume 38 (2010) p.d17-25