Publications for 2010

2010

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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 DOI: 10.4056/sigs.147362
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 DOI: 10.1186/gb-2010-11-12-r124
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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 DOI: 10.1186/1471-2105-11-S12-S12
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SAIL--a software system for sample and phenotype availability across biobanks and cohorts.
Gostev M, Fernandez-Banet J, Rung J, Dietrich J, Prokopenko I, Ripatti S, McCarthy MI, Brazma A, Krestyaninova M. Bioinformatics (Oxford, England) Volume 27 (2011) p.589-591 DOI: 10.1093/bioinformatics/btq693
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Proteomic temporal profile of human brain endothelium after oxidative stress.
Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH. Stroke Volume 42 (2011) p.37-43 DOI: 10.1161/STROKEAHA.110.585703
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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 DOI: 10.1371/journal.pgen.1001249
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A novel strategy for NMR resonance assignment and protein structure determination.
Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH. Journal of biomolecular NMR Volume 49 (2011) p.27-38 DOI: 10.1007/s10858-010-9458-0
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Mechanisms of structure generation during plastic compression of nanofibrillar collagen hydrogel scaffolds: towards engineering of collagen.
Hadjipanayi E, Ananta M, Binkowski M, Streeter I, Lu Z, Cui ZF, Brown RA, Mudera V. Journal of tissue engineering and regenerative medicine Volume 5 (2011) p.505-519 DOI: 10.1002/term.343
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Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus.
Reeve R, Blignaut B, Esterhuysen JJ, Opperman P, Matthews L, Fry EE, de Beer TA, Theron J, Rieder E, Vosloo W, O'Neill HG, Haydon DT, Maree FF. PLoS computational biology Volume 6 (2010) p.e1001027 DOI: 10.1371/journal.pcbi.1001027
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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 DOI: 10.4056/sigs/1403501
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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 DOI: 10.4056/sigs.1383476
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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. Microbiology and molecular biology reviews : MMBR Volume 74 (2010) p.479-503 DOI: 10.1128/MMBR.00017-10
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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 DOI: 10.1002/humu.21379
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N. BMC bioinformatics Volume 11 (2010) p.579 DOI: 10.1186/1471-2105-11-579
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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 DOI: 10.1186/1471-2164-11-661
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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. Genome research Volume 21 (2011) p.456-464 DOI: 10.1101/gr.112656.110
The International Nucleotide Sequence Database Collaboration.
Cochrane G, Karsch-Mizrachi I, Nakamura Y, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 39 (2011) p.D15-8 DOI: 10.1093/nar/gkq1150
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Extending CATH: increasing coverage of the protein structure universe and linking structure with function.
Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, Furnham N, Pellegrini-Calace M, Jones D, Thornton J, Orengo CA. Nucleic acids research Volume 39 (2011) p.D420-6 DOI: 10.1093/nar/gkq1001
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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 research Volume 6 (2010) p.10 DOI: 10.1186/1745-7580-6-10
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Towards BioDBcore: a community-defined information specification for biological databases.
Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, Howe DG, Imanishi T, Kelso J, Landsman D, Lewis SE, Mizrachi IK, Orchard S, Ouellette BF, Ranganathan S, Richardson L, Rocca-Serra P, Schofield PN, Smedley D, Southan C, Tan TW, Tatusova T, Whetzel PL, White O, Yamasaki C, BioDBCore Working Group. Nucleic acids research Volume 39 (2011) p.D7-10 DOI: 10.1093/nar/gkq1173
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Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. Nucleic acids research Volume 39 (2011) p.D1085-94 DOI: 10.1093/nar/gkq1148
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The IMGT/HLA database.
Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG. Nucleic acids research Volume 39 (2011) p.D1171-6 DOI: 10.1093/nar/gkq998
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments.
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E, Kurbatova N, Lukk M, Malone J, Mani R, Pilicheva E, Rustici G, Sharma A, Williams E, Adamusiak T, Brandizi M, Sklyar N, Brazma A. Nucleic acids research Volume 39 (2011) p.D1002-4 DOI: 10.1093/nar/gkq1040
UKPMC: a full text article resource for the life sciences.
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, Hubbard SJ, Kim JH, Lewin I, Lyte V, MacIntyre R, Mansoor S, Mason L, McNaught J, Newbold E, Nobata C, Ong E, Pillai S, Rebholz-Schuhmann D, Rosie H, Rowbotham R, Rupp CJ, Stoehr P, Vaughan P. Nucleic acids research Volume 39 (2011) p.D58-65 DOI: 10.1093/nar/gkq1063
Reactome: a database of reactions, pathways and biological processes.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Nucleic acids research Volume 39 (2011) p.D691-7 DOI: 10.1093/nar/gkq1018
The sequence read archive.
Leinonen R, Sugawara H, Shumway M, International Nucleotide Sequence Database Collaboration. Nucleic acids research Volume 39 (2011) p.D19-21 DOI: 10.1093/nar/gkq1019
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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 DOI: 10.1186/1476-4598-9-290
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Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium. Nucleic acids research Volume 39 (2011) p.D214-9 DOI: 10.1093/nar/gkq1020
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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 DOI: 10.1111/j.1365-294X.2010.04888.x
PDBe: Protein Data Bank in Europe.
Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. Nucleic acids research Volume 39 (2011) p.D402-10 DOI: 10.1093/nar/gkq985
Ensembl 2011.
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM. Nucleic acids research Volume 39 (2011) p.D800-6 DOI: 10.1093/nar/gkq1064
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Organelle proteomics experimental designs and analysis.
Gatto L, Vizcaíno JA, Hermjakob H, Huber W, Lilley KS. Proteomics Volume 10 (2010) p.3957-3969 DOI: 10.1002/pmic.201000244
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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 DOI: 10.1038/nchembio.460
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Make Research Data Public?-Not Always so Simple: A Dialogue for Statisticians and Science Editors.
Sedransk N, Young LJ, Kelner KL, Moffitt RA, Thakar A, Raddick J, Ungvarsky EJ, Carlson RW, Apweiler R, Cox LH, Nolan D, Soper K, Spiegelman C. Statistical Science Volume 25 (2010) p.41-50
The European Nucleotide Archive.
Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G. Nucleic acids research Volume 39 (2011) p.D28-31 DOI: 10.1093/nar/gkq967
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"4D Biology for health and disease" workshop report.
Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJ, Henderson PJ, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GF, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ. New biotechnology Volume 28 (2011) p.291-293 DOI: 10.1016/j.nbt.2010.10.003
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EMDataBank.org: unified data resource for CryoEM.
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. Nucleic acids research Volume 39 (2011) p.D456-64 DOI: 10.1093/nar/gkq880
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Recommended nomenclature for five mammalian carboxylesterase gene families: human, mouse, and rat genes and proteins.
Holmes RS, Wright MW, Laulederkind SJ, Cox LA, Hosokawa M, Imai T, Ishibashi S, Lehner R, Miyazaki M, Perkins EJ, Potter PM, Redinbo MR, Robert J, Satoh T, Yamashita T, Yan B, Yokoi T, Zechner R, Maltais LJ. Mammalian genome : official journal of the International Mammalian Genome Society Volume 21 (2010) p.427-441 DOI: 10.1007/s00335-010-9284-4
genenames.org: the HGNC resources in 2011.
Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. Nucleic acids research Volume 39 (2011) p.D514-9 DOI: 10.1093/nar/gkq892
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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 DOI: 10.1016/j.cell.2010.09.023
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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 DOI: 10.1126/science.1197005
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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 (New York, N.Y.) Volume 330 (2010) p.512-514 DOI: 10.1126/science.1195755
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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 DOI: 10.1038/ng1010-813
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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 DOI: 10.1038/nature09534
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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 (New York, N.Y.) Volume 330 (2010) p.86-88 DOI: 10.1126/science.1191864
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Pathogenomics of Culex quinquefasciatus and meta-analysis of infection responses to diverse pathogens.
Bartholomay LC, Waterhouse RM, Mayhew GF, Campbell CL, Michel K, Zou Z, Ramirez JL, Das S, Alvarez K, Arensburger P, Bryant B, Chapman SB, Dong Y, Erickson SM, Karunaratne SH, Kokoza V, Kodira CD, Pignatelli P, Shin SW, Vanlandingham DL, Atkinson PW, Birren B, Christophides GK, Clem RJ, Hemingway J, Higgs S, Megy K, Ranson H, Zdobnov EM, Raikhel AS, Christensen BM, Dimopoulos G, Muskavitch MA. Science (New York, N.Y.) Volume 330 (2010) p.88-90 DOI: 10.1126/science.1193162
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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. Mammalian genome : official journal of the International Mammalian Genome Society Volume 21 (2010) p.499-508 DOI: 10.1007/s00335-010-9285-3
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 DOI: 10.1093/bioinformatics/btq545
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 DOI: 10.1016/j.jmb.2010.09.018
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 DOI: 10.1093/hmg/ddq404
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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. Nature biotechnology Volume 28 (2010) p.935-942 DOI: 10.1038/nbt.1666
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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 DOI: 10.1099/mic.0.042978-0
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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) DOI: 10.1371/journal.pbio.1000475
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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 (Oxford, England) Volume 26 (2010) p.i540-6 DOI: 10.1093/bioinformatics/btq391
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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 DOI: 10.1002/pmic.201000120
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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 DOI: 10.1038/nature09298
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 DOI: 10.1002/pmic.201090075
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An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium. The Plant cell Volume 22 (2010) p.2530-2536 DOI: 10.1105/tpc.110.078519
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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 DOI: 10.1186/gb-2010-11-8-r88
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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 DOI: 10.1186/gb-2010-11-8-r85
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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 DOI: 10.1371/journal.pone.0012339
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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 DOI: 10.1093/bioinformatics/btq462
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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. Journal of biomedical semantics Volume 1 (2010) p.8 DOI: 10.1186/2041-1480-1-8
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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 DOI: 10.4056/sigs.1022942
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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 DOI: 10.1016/j.drudis.2010.08.004
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mzML--a community standard for mass spectrometry data.
Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW. Molecular & cellular proteomics : MCP Volume 10 (2011) p.R110.000133 DOI: 10.1074/mcp.R110.000133
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 DOI: 10.1186/1471-2105-11-415
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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 DOI: 10.1074/mcp.M110.001594
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 DOI: 10.1007/s10858-010-9439-3
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Enzyme kinetics informatics: from instrument to browser.
Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I. The FEBS journal Volume 277 (2010) p.3769-3779 DOI: 10.1111/j.1742-4658.2010.07778.x
The CoFactor database: organic cofactors in enzyme catalysis.
Fischer JD, Holliday GL, Thornton JM. Bioinformatics (Oxford, England) Volume 26 (2010) p.2496-2497 DOI: 10.1093/bioinformatics/btq442
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 (Oxford, England) Volume 26 (2010) p.2354-2356 DOI: 10.1093/bioinformatics/btq415
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Recommendations for biomarker identification and qualification in clinical proteomics.
Mischak H, Allmaier G, Apweiler R, Attwood T, Baumann M, Benigni A, Bennett SE, Bischoff R, Bongcam-Rudloff E, Capasso G, Coon JJ, D'Haese P, Dominiczak AF, Dakna M, Dihazi H, Ehrich JH, Fernandez-Llama P, Fliser D, Frokiaer J, Garin J, Girolami M, Hancock WS, Haubitz M, Hochstrasser D, Holman RR, Ioannidis JP, Jankowski J, Julian BA, Klein JB, Kolch W, Luider T, Massy Z, Mattes WB, Molina F, Monsarrat B, Novak J, Peter K, Rossing P, Sánchez-Carbayo M, Schanstra JP, Semmes OJ, Spasovski G, Theodorescu D, Thongboonkerd V, Vanholder R, Veenstra TD, Weissinger E, Yamamoto T, Vlahou A. Science translational medicine Volume 2 (2010) p.46ps42 DOI: 10.1126/scitranslmed.3001249
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Heme proteins--diversity in structural characteristics, function, and folding.
Smith LJ, Kahraman A, Thornton JM. Proteins Volume 78 (2010) p.2349-2368 DOI: 10.1002/prot.22747
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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 DOI: 10.1038/msb.2010.54
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 DOI: 10.1093/database/baq018
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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 DOI: 10.1093/nar/gkq653
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Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P. Genome biology Volume 11 (2010) p.402 DOI: 10.1186/gb-2010-11-7-402
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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 DOI: 10.1073/pnas.1008861107
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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 DOI: 10.1371/journal.pgen.1001023
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Mapping of amino acid residues responsible for adhesion of cell culture-adapted foot-and-mouth disease SAT type viruses.
Maree FF, Blignaut B, de Beer TA, Visser N, Rieder EA. Virus research Volume 153 (2010) p.82-91 DOI: 10.1016/j.virusres.2010.07.010
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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 DOI: 10.1111/j.1469-8137.2010.03371.x
Design, Implementation and Updating of Knowledge Bases
Hunter S, Apweiler R, Martin MJ. Knowledge-Based Bioinformatics: From Analysis to Interpretation John Wiley & Sons DOI: 10.1002/9780470669716.ch4
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 DOI: 10.1016/j.jprot.2010.06.008
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 DOI: 10.1093/database/baq014
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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 DOI: 10.1177/1740774510373497
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 DOI: 10.1093/bib/bbq023
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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 DOI: 10.1038/nbt0710-650
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 DOI: 10.1021/ct100007y
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 DOI: 10.1186/1752-0509-4-92
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. In silico and wet lab approaches to study transcriptional regulation Department of Human and Clinical Genetics, Faculty of Medicine, Leiden University Medical Center (LUMC), Leiden University
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So what have data standards ever done for us? The view from metabolomics.
Griffin JL, Steinbeck C. Genome medicine Volume 2 (2010) p.38 DOI: 10.1186/gm159
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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 DOI: 10.1128/JVI.00487-10
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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 DOI: 10.1186/1756-0500-3-175
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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 DOI: 10.1186/2041-1480-1-S1-S7
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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. Proceedings of the National Academy of Sciences of the United States of America Volume 107 (2010) p.12168-12173 DOI: 10.1073/pnas.1003379107
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 DOI: 10.1093/bioinformatics/btq330
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 DOI: 10.1093/bib/bbq021
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PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.
Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA. International journal of legal medicine Volume 125 (2011) p.629-636 DOI: 10.1007/s00414-010-0472-2
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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 DOI: 10.4056/sigs.802738
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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 DOI: 10.1371/journal.pntd.0000702
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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 DOI: 10.1371/journal.pgen.1000976
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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 DOI: 10.1093/nar/gkq482
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Assignment and conformational investigation of asymmetric phenylindenylidene ruthenium complexes bearing N,O-bidentate ligands.
Hendrickx PM, Drozdzak R, Verpoort F, Martins JC. Magnetic resonance in chemistry : MRC Volume 48 (2010) p.443-449 DOI: 10.1002/mrc.2599
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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 DOI: 10.1002/pmic.200900773
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Role of open chemical data in aiding drug discovery and design.
Gaulton A, Overington JP. Future medicinal chemistry Volume 2 (2010) p.903-907 DOI: 10.4155/fmc.10.191
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 DOI: 10.1084/jem.20100458
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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 DOI: 10.1016/j.bmcl.2010.05.026
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Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria.
Deng N, Zhang J, Zong C, Wang Y, Lu H, Yang P, Wang W, Young GW, Wang Y, Korge P, Lotz C, Doran P, Liem DA, Apweiler R, Weiss JN, Duan H, Ping P. Molecular & cellular proteomics : MCP Volume 10 (2011) p.M110.000117 DOI: 10.1074/mcp.M110.000117
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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 DOI: 10.1093/nar/gkq394
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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 research Volume 38 (2010) p.W683-8 DOI: 10.1093/nar/gkq297
Consistent annotation of gene expression arrays.
Ballester B, Johnson N, Proctor G, Flicek P. BMC genomics Volume 11 (2010) p.294 DOI: 10.1186/1471-2164-11-294
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 DOI: 10.1186/1471-2105-11-240
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 DOI: 10.1093/nar/gkq331
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 DOI: 10.1186/1471-2105-11-238
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 DOI: 10.1186/1471-2164-11-293
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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 DOI: 10.1074/mcp.M110.000406
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 DOI: 10.1186/1758-2946-2-S1-P6
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 DOI: 10.1186/1758-2946-2-S1-O17
OrChem: an open source chemistry search engine for Oracle.
Rijnbeek ML, Steinbeck C. Journal of cheminformatics Volume 2 (2010) p.P28-P28 DOI: 10.1186/1758-2946-2-S1-P28
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 DOI: 10.1093/nar/gkq313
Elucidation of the structure and intermolecular interactions of a reversible cyclic-peptide inhibitor of the proteasome by NMR spectroscopy and molecular modeling.
Stauch B, Simon B, Basile T, Schneider G, Malek NP, Kalesse M, Carlomagno T. Angewandte Chemie (International ed. in English) Volume 49 (2010) p.3934-3938 DOI: 10.1002/anie.201000140
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 DOI: 10.1002/pmic.201090034
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 Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, 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 DOI: 10.1126/science.1188021
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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 DOI: 10.1016/j.molcel.2010.03.016
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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 DOI: 10.1101/gr.103499.109
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Comparative proteomics profiling reveals role of smooth muscle progenitors in extracellular matrix production.
Simper D, Mayr U, Urbich C, Zampetaki A, Prokopi M, Didangelos A, Saje A, Mueller M, Benbow U, Newby AC, Apweiler R, Rahman S, Dimmeler S, Xu Q, Mayr M. Arteriosclerosis, thrombosis, and vascular biology Volume 30 (2010) p.1325-1332 DOI: 10.1161/atvbaha.110.204651
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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 DOI: 10.1186/1471-2156-11-25
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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 DOI: 10.1038/nm.2130
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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 DOI: 10.1186/gm145
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Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
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