Publications for 2010


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

PRIDE: Data submission and analysis.
Vizcaíno JA, Reisinger F, Côté R, Martens L.
Current protocols in protein science Volume Chapter 25 (2010) p.Unit 25.4

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

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

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.
Molecular systems biology Volume 6 (2010) p.399

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 genetics Volume 6 (2010) p.e1000881

Domain-ligand mapping for enzymes.
Bashton M, Thornton JM.
Journal of molecular recognition : JMR Volume 23 (2010) p.194-208

Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity.
Oliva R, Calamita G, Thornton JM, Pellegrini-Calace M.
Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.4135-4140

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

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

WormBase: a comprehensive resource for nematode research.
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW.
Nucleic acids research Volume 38 (2010) p.D463-7

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

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.

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

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

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

Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes.
Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.1849-1865

OntoFox: web-based support for ontology reuse.
Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.
BMC research notes Volume 3 (2010) p.175 Web Services, a free and integrated toolkit for computational modelling software.
Li C, Courtot M, Le Novère N, Laibe C.
Briefings in bioinformatics Volume 11 (2010) p.270-277

Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.
Genome research 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 genetics Volume 6 (2010) p.e1001249

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

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

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

Construction of signaling pathways and identification of drug effects on the liver cancer cell HepG2.
Alexopoulos LG, Melas IN, Chairakaki AD, Saez-Rodriguez J, Mitsos A.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference Volume 2010 (2010) p.6717-6720

Mining proteomic MS/MS data for MRM transitions.
Chem Mead JA, Bianco L, Bessant C.
Methods in molecular biology (Clifton, N.J.) Volume 604 (2010) p.187-199

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

The genome of Streptococcus mitis B6--what is a commensal?
Denapaite D, Brückner R, Nuhn M, Reichmann P, Henrich B, Maurer P, Schähle Y, Selbmann P, Zimmermann W, Wambutt R, Hakenbeck R.
PloS one Volume 5 (2010) p.e9426

Identification of genes for small non-coding RNAs that belong to the regulon of the two-component regulatory system CiaRH in Streptococcus.
Marx P, Nuhn M, Kovács M, Hakenbeck R, Brückner R.
BMC genomics Volume 11 (2010) p.661

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

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.
Journal of virology Volume 84 (2010) p.8732-8742

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

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 (New York, N.Y.) Volume 330 (2010) p.641-646

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 biology Volume 11 (2010) p.R88

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 research Volume 38 (2010) p.W689-94

The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium.
Nucleic acids research Volume 38 (2010) p.D331-5

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 research Volume 38 (2010) p.W695-9

Anterior development in the parthenogenetic and viviparous form of the pea aphid, Acyrthosiphon pisum: hunchback and orthodenticle expression.
Huang TY, Cook CE, Davis GK, Shigenobu S, Chen RP, Chang CC.
Insect molecular biology Volume 19 Suppl 2 (2010) p.75-85

OrChem: an open source chemistry search engine for Oracle.
Rijnbeek ML, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.P28-P28

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

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.
Nature biotechnology Volume 28 (2010) p.650-653

Progress on an open source computer-assisted structure elucidation suite (SENECA).
Kuhn S, Steinbeck C.
Journal of Cheminformatics Volume 2 (2010) p.P34-P34

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

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 research Volume 38 (2010) p.D52-6

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 biology Volume 11 (2010) p.R27

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, Turner JA, Zheng J, OBI consortium.
Journal of biomedical semantics Volume 1 Suppl 1 (2010) p.S7

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.
Standards in genomic sciences Volume 3 (2010) p.259-266

Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach.
Kafkas Ş, Varoğlu E, Rebholz-Schuhmann D, Taneri B.
BMC Bioinformatics Volume 11 (2010) p.P1-P1

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

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

Highlights of the 'gene nomenclature across species' meeting.
Bruford EA.
Human genomics Volume 4 (2010) p.213-217

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

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

The Universal Protein Resource (UniProt) in 2010.
UniProt Consortium.
Nucleic acids research Volume 38 (2010) p.D142-8

The European Bioinformatics Institute's data resources.
Brooksbank C, Cameron G, Thornton J.
Nucleic acids research Volume 38 (2010) p.D17-25

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.
Briefings in bioinformatics Volume 11 (2010) p.552-562

From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.
Hinz U, UniProt Consortium.
Cellular and molecular life sciences : CMLS Volume 67 (2010) p.1049-1064

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 research Volume 38 (2010) p.4466-4475

The Ontology Lookup Service: bigger and better.
Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.
Nucleic acids research Volume 38 (2010) p.W155-60

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

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

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.
Briefings in bioinformatics Volume 11 (2010) p.544-551

FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database.
Pfreundt U, James DP, Tweedie S, Wilson D, Teichmann SA, Adryan B.
Nucleic acids research Volume 38 (2010) p.D443-7

Molecular fragments chemoinformatics.
Kuhn H, Neumann S, Steinbeck C, Wittekindt C, Zielesny A.
Journal of Cheminformatics Volume 2 (2010) p.P14-P14

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

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.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.1-10

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 research Volume 38 (2010) p.D525-31

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

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

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 research Volume 38 (2010) p.D249-54

The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources.
Cochrane GR, Galperin MY.
Nucleic acids research Volume 38 (2010) p.D1-4

IPD--the Immuno Polymorphism Database.
Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG.
Nucleic acids research Volume 38 (2010) p.D863-9

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 : the journal of biological databases and curation Volume 2010 (2010) p.baq014

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

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.
Nature methods Volume 7 (2010) p.S42-55

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
The Plant cell Volume 22 (2010) p.2530-2536

Molecular interactions and data standardisation.
Orchard S, Kerrien S.
Methods in molecular biology (Clifton, N.J.) Volume 604 (2010) p.309-318

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.
Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.
Molecular & cellular proteomics : MCP Volume 9 (2010) p.2642-2653

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

Allele-specific and heritable chromatin signatures in humans.
Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR.
Human molecular genetics Volume 19 (2010) p.R204-9

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

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 : the journal of biological databases and curation Volume 2010 (2010) p.baq018

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 research Volume 20 (2010) p.249-256

Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins.
Berka K, Laskowski RA, Hobza P, Vondrášek J.
Journal of chemical theory and computation Volume 6 (2010) p.2191-2203

Protein structure databases.
Laskowski RA.
Methods in molecular biology (Clifton, N.J.) Volume 609 (2010) p.59-82

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

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

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 research Volume 20 (2010) p.791-803

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 (New York, N.Y.) Volume 328 (2010) p.235-239

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

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 (Oxford, England) Volume 26 (2010) p.2069-2070

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 (New York, N.Y.) Volume 328 (2010) p.710-722

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.
Standards in genomic sciences Volume 3 (2010) p.93-96

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 research Volume 38 (2010) p.D39-45

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.
Standards in genomic sciences Volume 3 (2010) p.232-234

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.
Standards in genomic sciences Volume 2 (2010) p.357-360

Archiving next generation sequencing data.
Shumway M, Cochrane G, Sugawara H.
Nucleic acids research Volume 38 (2010) p.D870-1

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 research Volume 38 (2010) p.D557-62

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.
Standards in genomic sciences Volume 3 (2010) p.254-258

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, Reubenacker 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.
Nature biotechnology Volume 28 (2010) p.935-942

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

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

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 research Volume 38 (2010) p.D570-6

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.
Human mutation Volume 31 (2010) p.1374-1381

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 medicine Volume 2 (2010) p.24

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 research Volume 87 (2010) p.95-110

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

Integration of chemical information with protein sequences and 3D structures.
Golovin A, Henrick K, Kleywegt G.
Journal of Cheminformatics Volume 2 (2010) p.O17-O17

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

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.
Nature chemical biology Volume 6 (2010) p.785

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.
Molecular cell Volume 38 (2010) p.603-613

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 (Oxford, England) Volume 26 (2010) p.1112-1118

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 research Volume 38 (2010) p.4325-4336

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 (New York, N.Y.) Volume 328 (2010) p.1036-1040

The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli.
Petty NK, Bulgin R, Crepin VF, Cerdeño-Tárraga AM, Schroeder GN, Quail MA, Lennard N, Corton C, Barron A, Clark L, Toribio AL, Parkhill J, Dougan G, Frankel G, Thomson NR.
Journal of bacteriology Volume 192 (2010) p.525-538

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

Digital expression profiling of novel diatom transcripts provides insight into their biological functions.
Maheswari U, Jabbari K, Petit JL, Porcel BM, Allen AE, Cadoret JP, De Martino A, Heijde M, Kaas R, La Roche J, Lopez PJ, Martin-Jézéquel V, Meichenin A, Mock T, Schnitzler Parker M, Vardi A, Armbrust EV, Weissenbach J, Katinka M, Bowler C.
Genome biology Volume 11 (2010) p.R85

Role of open chemical data in aiding drug discovery and design.
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Future medicinal chemistry Volume 2 (2010) p.903-907

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

Comparative ecophysiology and genomics of the toxic unicellular alga Fibrocapsa japonica.
Guidi-Rontani C, Maheswari U, Jabbari K, Bowler C.
The New phytologist Volume 185 (2010) p.446-458

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 research Volume 38 (2010) p.D563-9

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.
Nature genetics Volume 42 (2010) p.813-814

The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam.
Nguyen NT, Ha V, Tran NV, Stabler R, Pham DT, Le TM, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J, Nguyen VM, Tran TT, Pham MV, Cao TT, Wren B, Farrar J, Baker S.
PLoS neglected tropical diseases Volume 4 (2010) p.e702

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 systems biology Volume 4 (2010) p.92

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.
Nature medicine Volume 16 (2010) p.586-91, 1p following 591

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

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

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.
Clinical trials (London, England) Volume 7 (2010) p.S5-S32

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 research Volume 38 (2010) p.D690-8

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

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

Large scale comparison of global gene expression patterns in human and mouse.
Zheng-Bradley X, Rung J, Parkinson H, Brazma A.
Genome biology Volume 11 (2010) p.R124

Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis.
Patrick S, Blakely GW, Houston S, Moore J, Abratt VR, Bertalan M, Cerdeño-Tárraga AM, Quail MA, Corton N, Corton C, Bignell A, Barron A, Clark L, Bentley SD, Parkhill J.
Microbiology (Reading, England) Volume 156 (2010) p.3255-3269

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 genetics Volume 6 (2010) p.e1000976

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

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 research Volume 20 (2010) p.578-588

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

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 research Volume 70 (2010) p.2911-2923

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

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.
Journal of biomolecular NMR Volume 48 (2010) p.85-92

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.
Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.13830-13835

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, Ball CA.
Bioinformatics (Oxford, England) Volume 26 (2010) p.2470-2471

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

The Proteomics Identifications database: 2010 update.
Vizcaíno JA, Côté R, Reisinger F, Barsnes H, Foster JM, Rameseder J, Hermjakob H, Martens L.
Nucleic acids research Volume 38 (2010) p.D736-42

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.
The Journal of experimental medicine Volume 207 (2010) p.1351-1358

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

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.
Molecular cancer Volume 9 (2010) p.290

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 research Volume 38 (2010) p.D308-17

Mining Unique-m Substrings from Genomes
Ye K, Jia Z, Wang Y, Flicek P, Apweiler R.
Journal of proteomics & bioinformatics Volume 3 (2010) p.99-100

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 biology Volume 8 (2010) p.

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 discovery today Volume 15 (2010) p.804-811

Pyrazolopyridazine alpha-2-delta-1 ligands for the treatment of neuropathic pain.
Myatt JW, Healy MP, Bravi GS, Billinton A, Johnson CN, Matthews KL, Jandu KS, Meng W, Hersey A, Livermore DG, Douault CB, Witherington J, Bit RA, Rowedder JE, Brown JD, Clayton NM.
Bioorganic & medicinal chemistry letters Volume 20 (2010) p.4683-4688

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

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

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 genetics Volume 11 (2010) p.25

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

The publication and database deposition of molecular interaction data.
Orchard S, Aranda B, Hermjakob H.
Current protocols in protein science Volume Chapter 25 (2010) p.Unit 25.3

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 genetics Volume 6 (2010) p.e1001023

Transcription factor families inferred from genome sequences of photosynthetic stramenopiles.
Rayko E, Maumus F, Maheswari U, Jabbari K, Bowler C.
The New phytologist Volume 188 (2010) p.52-66

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

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 research Volume 38 (2010) p.W78-83

International network of cancer genome projects.
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Nature Volume 464 (2010) p.993-998