Publications for 2008

2008

Debunking minimum information myths: one hat need not fit all.
Orchard S, Taylor CF. New biotechnology Volume 25 (2009) p.171-172 DOI: 10.1016/j.nbt.2008.12.001
ASTD: The Alternative Splicing and Transcript Diversity database.
Koscielny G, Le Texier V, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G Reich J, Guigó R, Bork P, Doeberitz Mv, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D. Genomics Volume 93 (2009) p.213-220 DOI: 10.1016/j.ygeno.2008.11.003
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nGASP--the nematode genome annotation assessment project.
Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, Stein LD. BMC bioinformatics Volume 9 (2008) p.549 DOI: 10.1186/1471-2105-9-549
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Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B. Molecular oncology Volume 3 (2009) p.9-17 DOI: 10.1016/j.molonc.2008.11.003
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Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.
Paten B, Herrero J, Beal K, Birney E. Bioinformatics Volume 25 (2009) p.295-301 DOI: 10.1093/bioinformatics/btn630
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Goldman N, Yang Z. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3889-3892 DOI: 10.1098/rstb.2008.0182
A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3913-3919 DOI: 10.1098/rstb.2008.0170
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Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos JA, Dunham I. Pharmacogenomics Volume 9 (2008) p.1781-1783 DOI: 10.2217/14622416.9.12.1781
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Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S. BMC genomics Volume 9 (2008) p.564 DOI: 10.1186/1471-2164-9-323
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Rayner TF, Rezwan FI, Lukk M, Bradley XZ, Farne A, Holloway E, Malone J, Williams E, Parkinson H. Bioinformatics (Oxford, England) Volume 25 (2009) p.279-280 DOI: 10.1093/bioinformatics/btn617
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Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009.
Galperin MY, Cochrane GR. Nucleic acids research Volume 37 (2009) p.D1-4 DOI: 10.1093/nar/gkn942
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Ensembl 2009.
Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P. Nucleic acids research Volume 37 (2009) p.D690-7 DOI: 10.1093/nar/gkn828
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. Genome research Volume 19 (2009) p.327-335 DOI: 10.1101/gr.073585.107
VectorBase: a data resource for invertebrate vector genomics.
Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E, Hammond M, Hill CA, Konopinski N, Lobo NF, MacCallum RM, Madey G, Megy K, Meyer J, Redmond S, Severson DW, Stinson EO, Topalis P, Birney E, Gelbart WM, Kafatos FC, Louis C, Collins FH. Nucleic acids research Volume 37 (2009) p.D583-7 DOI: 10.1093/nar/gkn857
Charting online OMICS resources: A navigational chart for clinical researchers.
Vizcaíno JA, Mueller M, Hermjakob H, Martens L. Proteomics. Clinical applications Volume 3 (2009) p.18-29 DOI: 10.1002/prca.200800082
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MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions.
Mead JA, Bianco L, Ottone V, Barton C, Kay RG, Lilley KS, Bond NJ, Bessant C. Molecular & cellular proteomics : MCP Volume 8 (2009) p.696-705 DOI: 10.1074/mcp.m800192-mcp200
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.
Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A. Nucleic acids research Volume 37 (2009) p.D868-72 DOI: 10.1093/nar/gkn889
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The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. Nucleic acids research Volume 37 (2009) p.D310-4 DOI: 10.1093/nar/gkn877
PDBsum new things.
Laskowski RA. Nucleic acids research Volume 37 (2009) p.D355-9 DOI: 10.1093/nar/gkn860
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The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.
Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U. Chemico-biological interactions Volume 178 (2009) p.94-98 DOI: 10.1016/j.cbi.2008.10.040
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Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Nucleic acids research Volume 37 (2009) p.D619-22 DOI: 10.1093/nar/gkn863
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Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ. Nature methods Volume 5 (2008) p.1023-1025 DOI: 10.1038/nmeth.1267
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GENETICS. The Human Variome Project.
Cotton RG, Auerbach AD, Axton M, Barash CI, Berkovic SF, Brookes AJ, Burn J, Cutting G, den Dunnen JT, Flicek P, Freimer N, Greenblatt MS, Howard HJ, Katz M, Macrae FA, Maglott D, Möslein G, Povey S, Ramesar RS, Richards CS, Seminara D, Smith TD, Sobrido MJ, Solbakk JH, Tanzi RE, Tavtigian SV, Taylor GR, Utsunomiya J, Watson M. Science (New York, N.Y.) Volume 322 (2008) p.861-862 DOI: 10.1126/science.1167363
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Rapidly evolving human promoter regions.
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Nature genetics Volume 40 (2008) p.1262-3; author reply 1263-4 DOI: 10.1038/ng1108-1262
Petabyte-scale innovations at the European Nucleotide Archive.
Cochrane G, Akhtar R, Bonfield J, Bower L, Demiralp F, Faruque N, Gibson R, Hoad G, Hubbard T, Hunter C, Jang M, Juhos S, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Plaister S, Radhakrishnan R, Robinson S, Sobhany S, Hoopen PT, Vaughan R, Zalunin V, Birney E. Nucleic acids research Volume 37 (2009) p.D19-25 DOI: 10.1093/nar/gkn765
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The GOA database in 2009--an integrated Gene Ontology Annotation resource.
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. Nucleic acids research Volume 37 (2009) p.D396-403 DOI: 10.1093/nar/gkn803
Evolutionary footprints of nucleosome positions in yeast.
Washietl S, Machné R, Goldman N. Trends in genetics : TIG Volume 24 (2008) p.583-587 DOI: 10.1016/j.tig.2008.09.003
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Fusion and fission of genes define a metric between fungal genomes.
Durrens P, Nikolski M, Sherman D. PLoS computational biology Volume 4 (2008) p.e1000200 DOI: 10.1371/journal.pcbi.1000200
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MAPU 2.0: high-accuracy proteomes mapped to genomes.
Gnad F, Oroshi M, Birney E, Mann M. Nucleic acids research Volume 37 (2009) p.D902-6 DOI: 10.1093/nar/gkn773
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FlyBase: enhancing Drosophila Gene Ontology annotations.
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium. Nucleic acids research Volume 37 (2009) p.D555-9 DOI: 10.1093/nar/gkn788
InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. Nucleic acids research Volume 37 (2009) p.D211-5 DOI: 10.1093/nar/gkn785
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. Bioinformatics (Oxford, England) Volume 24 (2008) p.2767-2772 DOI: 10.1093/bioinformatics/btn528
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The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients.
Holden MT, Seth-Smith HM, Crossman LC, Sebaihia M, Bentley SD, Cerdeño-Tárraga AM, Thomson NR, Bason N, Quail MA, Sharp S, Cherevach I, Churcher C, Goodhead I, Hauser H, Holroyd N, Mungall K, Scott P, Walker D, White B, Rose H, Iversen P, Mil-Homens D, Rocha EP, Fialho AM, Baldwin A, Dowson C, Barrell BG, Govan JR, Vandamme P, Hart CA, Mahenthiralingam E, Parkhill J. Journal of bacteriology Volume 191 (2009) p.261-277 DOI: 10.1128/jb.01230-08
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OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.
O'Neill K, Garcia A, Schwegmann A, Jimenez RC, Jacobson D, Hermjakob H. BMC bioinformatics Volume 9 (2008) p.437 DOI: 10.1186/1471-2105-9-437
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Mosaic 22q13 deletions: evidence for concurrent mosaic segmental isodisomy and gene conversion.
Bonaglia MC, Giorda R, Beri S, Bigoni S, Sensi A, Baroncini A, Capucci A, De Agostini C, Gwilliam R, Deloukas P, Dunham I, Zuffardi O. European journal of human genetics : EJHG Volume 17 (2009) p.426-433 DOI: 10.1038/ejhg.2008.195
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Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Genome research Volume 18 (2008) p.1814-1828 DOI: 10.1101/gr.076554.108
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Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome research Volume 18 (2008) p.1829-1843 DOI: 10.1101/gr.076521.108
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The Universal Protein Resource (UniProt) 2009.
UniProt Consortium. Nucleic acids research Volume 37 (2009) p.D169-74 DOI: 10.1093/nar/gkn664
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Proteomics Data Collection - 3rd ProDaC workshop April 22nd 2008, Toledo, Spain.
Eisenacher M, Hardt T, Martens L, Häkkinen J, Apweiler R, Hamacher M, Meyer HE, Stephan C. Proteomics Volume 8 (2008) p.4163-4167 DOI: 10.1002/pmic.200800515
Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain.
Orchard S, Albar JP, Deutsch EW, Binz PA, Jones AR, Creasy D, Hermjakob H. Proteomics Volume 8 (2008) p.4168-4172 DOI: 10.1002/pmic.200800555
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Minimum reporting guidelines for proteomics released by the Proteomics Standards Initiative.
Jones AR, Orchard S. Molecular & cellular proteomics : MCP Volume 7 (2008) p.2067-2068 DOI: 10.1074/mcp.h800010-mcp200
Advanced genomic data mining.
Fernández-Suárez XM, Birney E. PLoS computational biology Volume 4 (2008) p.e1000121 DOI: 10.1371/journal.pcbi.1000121
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Building blocks for automated elucidation of metabolites: machine learning methods for NMR prediction.
Kuhn S, Egert B, Neumann S, Steinbeck C. BMC bioinformatics Volume 9 (2008) p.400 DOI: 10.1186/1471-2105-9-400
Metabolic innovations towards the human lineage.
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM. BMC evolutionary biology Volume 8 (2008) p.247 DOI: 10.1186/1471-2148-8-247
Data storage and analysis in ArrayExpress and Expression Profiler.
Rustici G, Kapushesky M, Kolesnikov N, Parkinson H, Sarkans U, Brazma A. Current protocols in bioinformatics Volume Chapter 7 (2008) p.Unit 7.13 DOI: 10.1002/0471250953.bi0713s23
Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R. Combinatorial chemistry & high throughput screening Volume 11 (2008) p.653-660 DOI: 10.2174/138620708785739925
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MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.
Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H. Genome biology Volume 9 Suppl 2 (2008) p.S5 DOI: 10.1186/gb-2008-9-s2-s5
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Consensus nomenclature for the human ArfGAP domain-containing proteins.
Kahn RA, Bruford E, Inoue H, Logsdon JM, Nie Z, Premont RT, Randazzo PA, Satake M, Theibert AB, Zapp ML, Cassel D. The Journal of cell biology Volume 182 (2008) p.1039-1044 DOI: 10.1083/jcb.200806041
Dasty2, an Ajax protein DAS client.
Jimenez RC, Quinn AF, Garcia A, Labarga A, O'Neill K, Martinez F, Salazar GA, Hermjakob H. Bioinformatics Volume 24 (2008) p.2119-2121 DOI: 10.1093/bioinformatics/btn387
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The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.
Garrick D, De Gobbi M, Samara V, Rugless M, Holland M, Ayyub H, Lower K, Sloane-Stanley J, Gray N, Koch C, Dunham I, Higgs DR. Blood Volume 112 (2008) p.3889-3899 DOI: 10.1182/blood-2008-06-161901
BioJava: an open-source framework for bioinformatics.
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ. Bioinformatics (Oxford, England) Volume 24 (2008) p.2096-2097 DOI: 10.1093/bioinformatics/btn397
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. Nature biotechnology Volume 26 (2008) p.889-896 DOI: 10.1038/nbt.1411
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites.
Najmanovich R, Kurbatova N, Thornton J. Bioinformatics Volume 24 (2008) p.i105-11 DOI: 10.1093/bioinformatics/btn263
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Guidelines for the nomenclature of the human heat shock proteins.
Kampinga HH, Hageman J, Vos MJ, Kubota H, Tanguay RM, Bruford EA, Cheetham ME, Chen B, Hightower LE. Cell stress & chaperones Volume 14 (2009) p.105-111 DOI: 10.1007/s12192-008-0068-7
Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kähäri A, Kulesha E, Macías JR, Reeves GA, Prlić A. BMC bioinformatics Volume 9 Suppl 8 (2008) p.S3 DOI: 10.1186/1471-2105-9-s8-s3
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The speciation of the proteome.
Jungblut PR, Holzhütter HG, Apweiler R, Schlüter H. Chemistry Central journal Volume 2 (2008) p.16 DOI: 10.1186/1752-153x-2-16
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Confounding between recombination and selection, and the Ped/Pop method for detecting selection.
O'Reilly PF, Birney E, Balding DJ. Genome research Volume 18 (2008) p.1304-1313 DOI: 10.1101/gr.067181.107
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Metal ions in biological catalysis: from enzyme databases to general principles.
Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry Volume 13 (2008) p.1205-1218 DOI: 10.1007/s00775-008-0404-5
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A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nature biotechnology Volume 26 (2008) p.779-785 DOI: 10.1038/nbt1414
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Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV. The Plant cell Volume 20 (2008) p.1426-1436 DOI: 10.1105/tpc.108.057976
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Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians.
Smits G, Mungall AJ, Griffiths-Jones S, Smith P, Beury D, Matthews L, Rogers J, Pask AJ, Shaw G, VandeBerg JL, McCarrey JR, SAVOIR Consortium, Renfree MB, Reik W, Dunham I. Nature genetics Volume 40 (2008) p.971-976 DOI: 10.1038/ng.168
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An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S. Genome research Volume 18 (2008) p.1518-1529 DOI: 10.1101/gr.077479.108
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Meeting report: the fifth Genomic Standards Consortium (GSC) workshop.
Field D, Garrity GM, Sansone SA, Sterk P, Gray T, Kyrpides N, Hirschman L, Glöckner FO, Kottmann R, Angiuoli S, White O, Dawyndt P, Thomson N, Gil IS, Morrison N, Tatusova T, Mizrachi I, Vaughan R, Cochrane G, Kagan L, Murphy S, Schriml L, Genomic Standards Consortium. Omics : a journal of integrative biology Volume 12 (2008) p.109-113 DOI: 10.1089/omi.2008.a3b3
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Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.
Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. Omics : a journal of integrative biology Volume 12 (2008) p.137-141 DOI: 10.1089/omi.2008.0017
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Meeting report: the fourth Genomic Standards Consortium (GSC) workshop.
Field D, Glöckner FO, Garrity GM, Gray T, Sterk P, Cochrane G, Vaughan R, Kolker E, Kottmann R, Kyrpides N, Angiuoli S, Dawyndt P, Guralnick R, Goldstein P, Hall N, Hirschman L, Kravitz S, Lister AL, Markowitz V, Thomson N, Whetzel T. Omics : a journal of integrative biology Volume 12 (2008) p.101-108 DOI: 10.1089/omi.2008.0014
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Löytynoja A, Goldman N. Science (New York, N.Y.) Volume 320 (2008) p.1632-1635 DOI: 10.1126/science.1158395
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The evolution of the DLK1-DIO3 imprinted domain in mammals.
Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium, Dunham I, Renfree MB, Ferguson-Smith AC. PLoS biology Volume 6 (2008) p.e135 DOI: 10.1371/journal.pbio.0060135
The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?".
Sansone SA, Rocca-Serra P, Brandizi M, Brazma A, Field D, Fostel J, Garrow AG, Gilbert J, Goodsaid F, Hardy N, Jones P, Lister A, Miller M, Morrison N, Rayner T, Sklyar N, Taylor C, Tong W, Warner G, Wiemann S, Members of the RSBI Working Group. Omics : a journal of integrative biology Volume 12 (2008) p.143-149 DOI: 10.1089/omi.2008.0019
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Calling on a million minds for community annotation in WikiProteins.
Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen GJ, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A. Genome biology Volume 9 (2008) p.R89 DOI: 10.1186/gb-2008-9-5-r89
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InteroPORC: automated inference of highly conserved protein interaction networks.
Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H. Bioinformatics (Oxford, England) Volume 24 (2008) p.1625-1631 DOI: 10.1093/bioinformatics/btn249
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Altered proteome biology of cardiac mitochondria under stress conditions.
Zhang J, Liem DA, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Korge P, Drews O, Maclellan WR, Honda H, Weiss JN, Apweiler R, Ping P. Journal of proteome research Volume 7 (2008) p.2204-2214 DOI: 10.1021/pr070371f
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Finishing the finished human chromosome 22 sequence.
Cole CG, McCann OT, Collins JE, Oliver K, Willey D, Gribble SM, Yang F, McLaren K, Rogers J, Ning Z, Beare DM, Dunham I. Genome biology Volume 9 (2008) p.R78 DOI: 10.1186/gb-2008-9-5-r78
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.
Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H. Nucleic acids research Volume 36 (2008) p.W372-6 DOI: 10.1093/nar/gkn252
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica C, Labarga A, Gould CM, López R, Gibson TJ. BMC bioinformatics Volume 9 (2008) p.229 DOI: 10.1186/1471-2105-9-229
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Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?
Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ. Proteomics Volume 8 (2008) p.1950-1953 DOI: 10.1002/pmic.200800078
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Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Nature Volume 453 (2008) p.175-183 DOI: 10.1038/nature06936
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The minimum information about a genome sequence (MIGS) specification.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone SA, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A. Nature biotechnology Volume 26 (2008) p.541-547 DOI: 10.1038/nbt1360
Evolution of binding sites for zinc and calcium ions playing structural roles.
Torrance JW, Macarthur MW, Thornton JM. Proteins Volume 71 (2008) p.813-830 DOI: 10.1002/prot.21741
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SNP and haplotype mapping for genetic analysis in the rat.
STAR Consortium, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N. Nature genetics Volume 40 (2008) p.560-566 DOI: 10.1038/ng.124
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What everybody should know about the rat genome and its online resources.
Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ. Nature genetics Volume 40 (2008) p.523-527 DOI: 10.1038/ng0508-523
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ISPIDER Central: an integrated database web-server for proteomics.
Siepen JA, Belhajjame K, Selley JN, Embury SM, Paton NW, Goble CA, Oliver SG, Stevens R, Zamboulis L, Martin N, Poulovassillis A, Jones P, Côté R, Hermjakob H, Pentony MM, Jones DT, Orengo CA, Hubbard SJ. Nucleic acids research Volume 36 (2008) p.W485-90 DOI: 10.1093/nar/gkn196
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The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.
Braconi Quintaje S, Orchard S. Molecular & cellular proteomics : MCP Volume 7 (2008) p.1409-1419 DOI: 10.1074/mcp.r700001-mcp200
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A logic-based diagram of signalling pathways central to macrophage activation.
Raza S, Robertson KA, Lacaze PA, Page D, Enright AJ, Ghazal P, Freeman TC. BMC systems biology Volume 2 (2008) p.36 DOI: 10.1186/1752-0509-2-36
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Natural language processing in aid of FlyBase curators.
Karamanis N, Seal R, Lewin I, McQuilton P, Vlachos A, Gasperin C, Drysdale R, Briscoe T. BMC bioinformatics Volume 9 (2008) p.193 DOI: 10.1186/1471-2105-9-193
UniProtJAPI: a remote API for accessing UniProt data.
Patient S, Wieser D, Kleen M, Kretschmann E, Jesus Martin M, Apweiler R. Bioinformatics Volume 24 (2008) p.1321-1322 DOI: 10.1093/bioinformatics/btn122
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Systematic characterization of the murine mitochondrial proteome using functionally validated cardiac mitochondria.
Zhang J, Li X, Mueller M, Wang Y, Zong C, Deng N, Vondriska TM, Liem DA, Yang JI, Korge P, Honda H, Weiss JN, Apweiler R, Ping P. Proteomics Volume 8 (2008) p.1564-1575 DOI: 10.1002/pmic.200700851
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Proteomics Data Collection - 2nd ProDaC Workshop 5 October 2007, Seoul, Korea.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Volume 8 (2008) p.1326-1330 DOI: 10.1002/pmic.200701098
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Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.
Margulies EH, Birney E. Nature reviews. Genetics Volume 9 (2008) p.303-313 DOI: 10.1038/nrg2185
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Levers and fulcrums: progress in cis-regulatory motif models.
Birney E. Nature methods Volume 5 (2008) p.297-298 DOI: 10.1038/nmeth0408-297
6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea.
Orchard S, Martens L, Tasman J, Binz PA, Albar JP, Hermjakob H. Proteomics Volume 8 (2008) p.1331-1333 DOI: 10.1002/pmic.200701086
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Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project.
Kuhn T, Zielesny A, Steinbeck C. Chemistry Central journal Volume 2 (2008) p.P27-P27 DOI: 10.1186/1752-153x-2-s1-p27
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Zerbino DR, Birney E. Genome research Volume 18 (2008) p.821-829 DOI: 10.1101/gr.074492.107
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Charting plant interactomes: possibilities and challenges.
Morsy M, Gouthu S, Orchard S, Thorneycroft D, Harper JF, Mittler R, Cushman JC. Trends in plant science Volume 13 (2008) p.183-191 DOI: 10.1016/j.tplants.2008.01.006
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets.
Mueller M, Vizcaíno JA, Jones P, Côté R, Thorneycroft D, Apweiler R, Hermjakob H, Martens L. Proteomics Volume 8 (2008) p.1138-1148 DOI: 10.1002/pmic.200700761
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Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson DR, Gimenez G, Goo YA, Grimmond S, Henrich T, Herrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Stoeckert CJ, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD. Nature biotechnology Volume 26 (2008) p.305-312 DOI: 10.1038/nbt1391
The InterPro database and tools for protein domain analysis.
Mulder NJ, Apweiler R. Current protocols in bioinformatics Volume Chapter 2 (2008) p.Unit 2.7 DOI: 10.1002/0471250953.bi0207s21
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Performance validation of neural network based (13)c NMR prediction using a publicly available data source.
Blinov KA, Smurnyy YD, Elyashberg ME, Churanova TS, Kvasha M, Steinbeck C, Lefebvre BA, Williams AJ. Journal of chemical information and modeling Volume 48 (2008) p.550-555 DOI: 10.1021/ci700363r
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Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells.
Atkinson SP, Koch CM, Clelland GK, Willcox S, Fowler JC, Stewart R, Lako M, Dunham I, Armstrong L. Stem cells (Dayton, Ohio) Volume 26 (2008) p.1174-1185 DOI: 10.1634/stemcells.2007-0497
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Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Genome research Volume 18 (2008) p.393-403 DOI: 10.1101/gr.7080508
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A systematic library for comprehensive overexpression screens in Saccharomyces cerevisiae.
Jones GM, Stalker J, Humphray S, West A, Cox T, Rogers J, Dunham I, Prelich G. Nature methods Volume 5 (2008) p.239-241 DOI: 10.1038/nmeth.1181
Understanding the molecular machinery of genetics through 3D structures.
Laskowski RA, Thornton JM. Nature reviews. Genetics Volume 9 (2008) p.141-151 DOI: 10.1038/nrg2273
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The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M. Briefings in bioinformatics Volume 9 (2008) p.250-253 DOI: 10.1093/bib/bbn002
Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase.
Megy K, Hammond M, Lawson D, Bruggner RV, Birney E, Collins FH. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Volume 9 (2009) p.308-313 DOI: 10.1016/j.meegid.2007.12.007
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The Gene Ontology - Providing a Functional Role in Proteomic Studies.
Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC. Practical Proteomics Volume 8 (2008) DOI: 10.1002/pmic.200800002
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Wiley-VCH and HUPO: a global effort to advance proteomic science.
Ping P, Bergeron J, Apweiler R. Proteomics Volume 8 (2008) p.4-6 DOI: 10.1002/pmic.200790108
Biological Data Resources at the EMBL-EBI
Lopez R. Revista Colombiana de biotecnologia Volume 10 (2008) p.120–128
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Wiley-VCH and HUPO: A Global Effort to Advance Proteomic Science.
Ping P, Bergeron J, Apweiler R. Proteomics. Clinical applications Volume 2 (2008) p.4-6 DOI: 10.1002/prca.200890001
Data standards and controlled vocabularies for proteomics.
Martens L, Palazzi LM, Hermjakob H. Methods in molecular biology (Clifton, N.J.) Volume 484 (2008) p.279-286 DOI: 10.1007/978-1-59745-398-1_18
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The OWL of Biomedical Investigations
Courtot M, Bug W, Gibson F, Liste AL, Malone J, Schober D, Brinkman RR, Ruttenberg A. Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions Volume 432 (2008)
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Annotating the human proteome: From establishing a parts list to a tool for target identification.
Apweiler R, Mueller M. Cancer Proteomics: From Bench to Bedside. Humana Press Inc, NJ, USA
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The Universal Protein Resource. A Growing Online Protein Database.
O'Donovan C, Martin MJ, Apweiler R. BIOforum Europe Volume 12 (2008) p.32-33
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MIACA – Minimum Information About a Cellular Assay: Standardized description of cell-based functional assay projects
Wiemann S, Mehrle A, Hahne F, Hermjakob H, Apweiler R, Arlt D, Bechtel S, Bielke W, Birmingham A, Smith Q, Bork P, Buchholz F, Cai X, Camon E, Carninci P, Chanda SK, Chen Z, Cusick M, Echeverri C, Eils J, Eils R, Frank R, Fraser A, Girod A, Haedrich B, Hannus M, Harris M, Hayashizaki Y, Hide W, Hofmann O, Huber P, Hyman A, Jensen L, Kallioniemi O, Khvorova A, Koski L, Kraybill B, LaBaer J, Landegren U, Lawerenz C, Lehrach H, Liu F-F, Majety M, Mathey-Prevot B, Medico E, Mills GB, Nomura N, The OBI Consortium, Perrimon N, Pizarro A, Poustka A, Quackenbush J, Rosenfelder H, Sahin O, Salehi-Ashtiani K, Sasse F, Sauermann M, Schimmer AD, Schmidt C, Selfors L, Shamu C, Sönnichsen B, Taylor C, Temple G, Vidal M, Weidlich M, Wrobel DJ, Zhang J.
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The Universal Protein Resource (UniProt).
The UniProt Consortium. Nucl. Acids Res. Volume 36 (2008) p.D190-D195
EBI Proteomics Services
Hermjakob H. Lecture notes in computer science Volume 5109 (2008) p.207 DOI: 10.1007/978-3-540-69828-9_21
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ENFIN - An Integrative Structure for Systems Biology
Reisinger F, Corpas M, Hancock J, Hermjakob H, Birney E, Kahlem P. Data Integration in the Life Sciences: 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008. Proceedings Springer Berlin Heidelberg DOI: 10.1007/978-3-540-69828-9_13
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Methods to Characterize the Structure of Enzyme Binding Sites
Kahraman A and Thornton JM. Computational Structural Biology - Methods and Applications World Scientific Publishing
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Infrastructure for distributed protein annotation
Reeves GA, Prlic A, Jimenez RC, Kulesha E, Hermjakob H. Modern Genome Annotation: The BioSapiens Network Springer Vienna DOI: 10.1007/978-3-211-75123-7_18