Publications for 2008

2008

MODELLER. A Program for Protein Structure Modeling
Šali, A., Webb B., Madhusudhan MS, Shen MY, Marti-Renom MA, Eswar N., Alber F., Topf M., Oliva B., Fiser A., et al.
(2008),
Proceedings of the 6th Asia-Pacific Bioinformatics Conference: Kyoto, Japan, 14-17 January 2008
BRAZMA, A.
Volume 6, (2008),
The molecular basis of predicting druggability
Al-Lazikani, B., GAULTON A., Paolini G., Lanfear J., OVERINGTON J., and Hopkins A.
(2008),
miRBase: a database of microRNA sequences, targets and nomenclature
Enright, A. J., and Griffiths-Jones S.
MicroRNAs: from basic science to disease biology. (2008), p.157
Detecting the presence and location of selection in proteins
Massingham, T.
Bioinformatics. Volume I: Data, Sequence Analysis and Evolution, (2008), Totowa, NJ, USA, p.311-329
Inferring trees
Whelan, S.
Bioinformatics. Volume I: Data, Sequence Analysis and Evolution, (2008), Totowa, NJ, USA, p.287-309
Gaussian process product models for nonparametric nonstationarity
Adams, R. P., and Stegle O.
Proceedings of the 25th international conference on Machine learning. (2008), p.1–8
Advanced genomic data mining
Fernández-Suárez, X. M., and Birney E.
PLoS computational biology. Volume 4, Number 9, (2008), p.e1000121
In silico characterization of proteins: UniProt, InterPro and Integr8
Mulder, N. J., Kersey P., Pruess M., and Apweiler R.
Molecular biotechnology. Volume 38, Number 2, (2008), p.165–177
Tight regulation of unstructured proteins: from transcript synthesis to protein degradation
Gsponer, J., Futschik M. E., Teichmann S. A., and Babu M. M.
Science. Volume 322, Number 5906, (2008), p.1365–1368
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs.
Paten, Benedict, Herrero Javier, Beal Kathryn, Fitzgerald Stephen, and Birney Ewan
Genome Res. 11, Volume 18, Number 11, (2008), United States, p.1814-28 doi: 10.1101/gr.076554.108
The first RSBI (ISA-TAB) workshop:“can a simple format work for complex studies?”
Sansone, S. A., Rocca-Serra P., BRANDIZI M., BRAZMA A., Field D., Fostel J., Garrow A. G., Gilbert J., Goodsaid F., Hardy N., et al.
OMICS A Journal of Integrative Biology. Volume 12, Number 2, (2008), p.143–149
InteroPORC: automated inference of highly conserved protein interaction networks
Michaut, M., Kerrien S., Montecchi-Palazzi L., Chauvat F., Cassier-Chauvat C., Aude J. C., Legrain P., and Hermjakob H.
Bioinformatics. Volume 24, Number 14, (2008), p.1625–1631
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
Cochrane, Guy, Akhtar Ruth, Aldebert Philippe, Althorpe Nicola, Baldwin Alastair, Bates Kirsty, Bhattacharyya Sumit, Bonfield James, Bower Lawrence, Browne Paul, et al.
Nucleic Acids Research. Volume 36, Number suppl 1, (2008), p.D5–D12
Statistical and computational challenges in molecular phylogenetics and evolution
Goldman, N., and Yang Z.
Philosophical Transactions of the Royal Society of London. Volume B 363, (2008), p.3889-3892
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm
Sánchez, I. E., Beltrao P., Stricher F., Schymkowitz J., Ferkinghoff-Borg J., Rousseau F., and Serrano L.
PLoS computational biology. Volume 4, Number 4, (2008), p.e1000052
Detecting microRNA binding and siRNA off-target effects from expression data
Van Dongen, S., ABREU-GOODGER C., and Enright A. J.
Nature methods. Volume 5, Number 12, (2008), p.1023–1025
Meeting report: the fourth Genomic Standards Consortium (GSC) workshop
Field, D., Glockner F. O., Garrity G. M., Gray T., Sterk P., Cochrane G., VAUGHAN R., Kolker E., Kottmann R., Kyrpides N., et al.
OMICS. Volume 12, Number 2, (2008), p.101-8
Chance and necessity in chromosomal gene distributions
Hermsen, R., ten Wolde P. R., and Teichmann S.
Trends in Genetics. Volume 24, Number 5, (2008), p.216–219
SNP and haplotype mapping for genetic analysis in the rat.
Consortium, STAR, Saar Kathrin, Beck Alfred, Bihoreau Marie-Thérèse T., Birney Ewan, Brocklebank Denise, Chen Yuan, Cuppen Edwin, Demonchy Stephanie, Dopazo Joaquin, et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.560-6 doi: 10.1038/ng.124
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project
Taylor, C.F., Field D., Sansone S.A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.A., Bogue M., Booth T., et al.
Nature biotechnology. Volume 26, Number 8, (2008), p.889–896
OntoDas–a tool for facilitating the construction of complex queries to the Gene Ontology
O'Neill, K., Garcia A., Schwegmann A., Jimenez R.C., Jacobson D., and Hermjakob H.
BMC bioinformatics. Volume 9, Number 1, (2008), p.437
Herramientas para el manejo de datos biológicos en el EMBL-EBI
Lopez, Rodrigo
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
The RNA WikiProject: community annotation of RNA families
Daub, J., Gardner P. P., Tate J., Ramsköld D., Manske M., Scott W. G., Weinberg Z., Griffiths-Jones S., and Bateman A.
Rna. Volume 14, Number 12, (2008), p.2462–2464
A model of evolution and structure for multiple sequence alignment
Löytynoja, A., and Goldman N.
Philosophical Transactions of the Royal Society of London. Volume B 363, (2008), p.3913-3919
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Rakyan, V. K., Down T. A., Thorne N. P., Flicek P., Kulesha E., Gräf S., Tomazou E. M., Bäckdahl L., Johnson N., Herberth M., et al.
Genome research. Volume 18, Number 9, (2008), p.1518–1529
Genome-wide nucleotide-level mammalian ancestor reconstruction
Paten, B., Herrero J., Fitzgerald S., Beal K., Flicek P., Holmes I., and Birney E.
Genome research. Volume 18, Number 11, (2008), p.1829–1843
A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
Chica, C., LABARGA A., Gould C. M., López R., and Gibson T. J.
BMC bioinformatics. Volume 9, Number 1, (2008), p.229
The rice annotation project database (RAP-DB): 2008 update
Tanaka, T., Antonio B. A., Kikuchi S., Matsumoto T., Nagamura Y., Numa H., Sakai H., Wu J., Itoh T., Sasaki T., et al.
Nucleic acids research. Volume 36, Number Database issue, (2008), p.D1028 doi:
Integrating biological data - the Distributed Annotation System.
Jenkinson, Andrew M., Albrecht Mario, Birney Ewan, Blankenburg Hagen, Down Thomas, Finn Robert D., Hermjakob Henning, Hubbard Tim Jp, Jimenez Rafael C., Jones Philip, et al.
BMC Bioinformatics. 7, Volume 9 Suppl 8, (2008), p.S3 doi: 10.1186/1471-2105-9-S8-S3
Epigenomics at the tipping point. Foreword.
Stamatoyannopoulos, John A., and Dunham Ian
Pharmacogenomics. 12, Volume 9, Number 12, (2008), England, p.1781-3 doi: 10.2217/14622416.9.12.1781
Dasty2, an Ajax protein DAS client
Jimenez, R.C., Quinn A. F., Garcia A., Labarga A., O'Neill K., Martinez F., Salazar G. A., and Hermjakob H.
Bioinformatics. (2008),
Inference of Synechocystis protein interaction network
Michaut, M., Kerrien S., Montecchi-Palazzi L., Cassier-Chauvat C., Chauvat F., Aude J. C., Legrain P., and Hermjakob H.
JOBIM proceedings. (2008), p.99–104
MEROPS: the peptidase database
Rawlings, N. D., Morton F. R., Kok C. Y., Kong J., and Barrett A. J.
Nucleic Acids Research. Volume 36, Number suppl 1, (2008), p.D320–D325
Rapidly evolving human promoter regions
Taylor, M. S., Massingham T., Hayashizaki Y., Carninci P., Goldman N., and Semple C. A. M.
Nature Genetics. Volume 40, (2008), p.1262-1263
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
O’Reilly, P. F., Birney E., and Balding D. J.
Genome research. Volume 18, Number 8, (2008), p.1304–1313
Building a Biological Space Based on Protein Sequence Similarities and Biological Ontologies
Kersey, P., Lonsdale D., Mulder N. J., Petryszak R., and Apweiler R.
Combinatorial Chemistry &\# 38; High Throughput Screening. Volume 11, Number 8, (2008), p.653–660
Common variants near MC4R are associated with fat mass, weight and risk of obesity
Loos, R. J. F., Lindgren C. M., Li S., Wheeler E., Zhao J. H., Prokopenko I., Inouye M., Freathy R. M., Attwood A. P., Beckmann J. S., et al.
Nature genetics. Volume 40, Number 6, (2008), p.768–775
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Rakyan, Vardhman K., Down Thomas A., Thorne Natalie P., Flicek Paul, Kulesha Eugene, Gräf Stefan, Tomazou Eleni M., Bäckdahl Liselotte, Johnson Nathan, Herberth Marlis, et al.
Genome Res. 8, Volume 18, Number 9, (2008), p.1518-29 doi: 10.1101/gr.077479.108
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
Deutsch, E. W., Ball C. A., Berman J. J., Bova G. S., BRAZMA A., Bumgarner R. E., Campbell D., Causton H. C., Christiansen J. H., Daian F., et al.
Nature biotechnology. Volume 26, Number 3, (2008), p.305–312
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
Mueller, M., Vizcaino J.A., Jones P., Côté R., Thorneycroft D., Apweiler R., Hermjakob H., and Martens L.
Proteomics. Volume 8, Number 6, (2008), p.1138–1148
Modeling of C/EBPalpha mutant acute myeloid leukemia reveals a common expression signature of committed myeloid leukemia-initiating cells
Kirstetter, P., Schuster M. B., Bereshchenko O., Moore S., Dvinge H., Kurz E., Theilgaard-Mönch K., Mansson R., Pedersen T.A., Pabst T., et al.
Cancer Cell. Apr, Volume 13, Number 4, (2008), p.299–310
Dinucleotide controlled null models for comparative RNA gene prediction
Gesell, T., and Washietl S.
BMC Bioinformatics. Volume 9, (2008), p.248
Analyzing protein interaction networks using structural information
Kiel, C., Beltrao P., and Serrano L.
Annu. Rev. Biochem.. Volume 77, (2008), p.415–441
miRBase: tools for microRNA genomics
Griffiths-Jones, S., Saini H. K., Van Dongen S., and Enright A. J.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D154–D158
Meeting report: the fifth Genomic Standards Consortium (GSC) workshop
Field, D., Garrity G. M., Sansone S. A., Sterk P., Gray T., Kyrpides N., Hirschman L., Glockner F. O., Kottmann R., Angiuoli S., et al.
OMICS. Volume 12, Number 2, (2008), p.109-13
Functional protein divergence in the evolution of Homo sapiens
Lopez-Bigas, N., De S., Teichmann S. A., and others
Genome Biol. Volume 9, Number 2, (2008), p.R33
What everybody should know about the rat genome and its online resources.
Twigger, Simon N., Pruitt Kim D., Fernández-Suárez Xosé M., Karolchik Donna, Worley Kim C., Maglott Donna R., Brown Garth, Weinstock George, Gibbs Richard A., Kent Jim, et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.523-7 doi: 10.1038/ng0508-523
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction
Kuhn, S., Egert B., Neumann S., and Steinbeck C.
BMC Bioinformatics. Volume 9, Number 1, (2008), p.400
6th HUPO Annual World Congress–Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea
Orchard, S., Martens L., Tasman J., Binz P.A., Albar J.P., and Hermjakob H.
Proteomics. Volume 8, Number 7, (2008), p.1331–1333
Biological Data Resources at the EMBL-EBI
Lopez, Rodrigo
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
Identifying protein domains with the Pfam database
Coggill, P., Finn R. D., and Bateman A.
Curr Protoc Bioinformatics. Volume 2, Number 2.5, (2008),
Singleton SNPs in the human genome and implications for genome-wide association studies
Ke, X., Taylor M. S., and Cardon L. R.
European Journal of Human Genetics. Volume 16, (2008), p.506-515
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Down, T. A., Rakyan V. K., Turner D. J., Flicek P., Li H., Kulesha E., Gräf S., Johnson N., Herrero J., Tomazou E. M., et al.
Nature biotechnology. Volume 26, Number 7, (2008), p.779–785
Integrating biological data–the distributed annotation system
Jenkinson, A., Albrecht M., Birney E., Blankenburg H., Down T., Finn R., Hermjakob H., Hubbard T., Jimenez R., Jones P., et al.
BMC bioinformatics. Volume 9, Number Suppl 8, (2008), p.S3
Genomes and evolution: multidimensional approaches to understanding diversity.
Teichmann, S., and Patel N. H.
Current opinion in genetics & development. Volume 18, Number 6, (2008), p.469
TreeFam: 2008 Update.
Ruan, Jue, Li Heng, Chen Zhongzhong, Coghlan Avril, Coin Lachlan James M., Guo Yiran, Hériché Jean-Karim K., Hu Yafeng, Kristiansen Karsten, Li Ruiqiang, et al.
Nucleic Acids Res. 1, Volume 36, Number Database issue, (2008), England, p.D735-40 doi: 10.1093/nar/gkm1005
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Côté, R.G., Jones P., Martens L., Apweiler R., and Hermjakob H.
Nucleic acids research. Volume 36, Number suppl 2, (2008), p.W372–W376
EBI Proteomics Services
Hermjakob, H.
Data Integration in the Life Sciences. (2008), p.207–207
A Unified View of Protein Sequence and Structure Using the Distributed Anno-tation System
Prlic, A., Down T., Bateman A., Hubbard T., Orengo C., Dibley M., and Finn R. D.
(2008),
The genome of the simian and human malaria parasite Plasmodium knowlesi
Pain, A., Bohme U., Berry A. E., Mungall K., Finn R. D., Jackson A. P., Mourier T., Mistry J., Pasini E. M., Aslett M. A., et al.
Nature. Volume 455, (2008), p.799-803
What everybody should know about the rat genome and its online resources
Twigger, S. N., Pruitt K. D., Fernandez-Suarez X. M., Karolchik D., Worley K. C., Maglott D. R., Brown G., Weinstock G., Gibbs R. A., Kent J., et al.
Nature genetics. Volume 40, Number 5, (2008), p.523–527
Herramientas para el manejo de datos biológicos en el EMBL-EBI
Lopez, R.
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
The first RSBI (ISA-TAB) workshop: "Can a simple format work for complex studies?"
Sansone, S. - A., Rocca-Serra P., BRANDIZI M., BRAZMA A., Field D., Fostel J., Garrow A. G., Gilbert J., Goodsaid F., Hardy N., et al.
OMICS A Journal of Integrative Biology. Volume 12, Number 2, (2008), p.143-149
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson, David S., Li Wei, Gordon Benjamin D., Bhattacharjee Arindam, Curry Bo, Ghosh Jayati, Brizuela Leonardo, Carroll Jason S., Brown Myles, Flicek Paul, et al.
Genome Res. 3, Volume 18, Number 3, (2008), United States, p.393-403 doi: 10.1101/gr.7080508
The BREW workshop series: a stimulating experience in PhD education
Giegerich, R., BRAZMA A., Jonassen I., Ukkonen E., and Vingron M.
Briefings in bioinformatics. Volume 9, Number 3, (2008), p.250–253
ISPIDER Central: an integrated database web-server for proteomics
Siepen, J.A., Belhajjame K., Selley J.N., Embury S.M., Paton N.W., Goble C.A., Oliver S. G., Stevens R., Zamboulis L., Martin N., et al.
Nucleic acids research. Volume 36, Number suppl 2, (2008), p.W485–W490
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila
Kind, J., Vaquerizas J.M., Gebhardt P., Gentzel M., Luscombe N.M., Bertone P., and Akhtar A.
Cell. May, Volume 133, Number 5, (2008), p.813–828
Distribution of phylogenetic diversity under random extinction
Faller, B., Pardi F., and Steel M.
Journal of Theoretical Biology. Volume 251, (2008), p.286-296
Evolvability and hierarchy in rewired bacterial gene networks
Isalan, M., Lemerle C., Michalodimitrakis K., Horn C., Beltrao P., Raineri E., Garriga-Canut M., and Serrano L.
Nature. Volume 452, Number 7189, (2008), p.840–845
An integrated resource for genome-wide identification and analysis
Rakyan, V. K., Down T. A., Thorne N. P., Flicek P., Kulesha E., Graf S., Tomazou E. M., Backdahl L., Johnson N., Herberth M., et al.
(2008),
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 M. J., Angiuoli S. V., et al.
Nat Biotechnol. Volume 26, Number 5, (2008), p.541-7 doi:
Structure and distribution of pentapeptide repeats in bacteria
Bateman, A., Murzin A. G., and Teichmann S. A.
Protein science. Volume 7, Number 6, (2008), p.1477–1480
Progress and prospects in rat genetics: a community view.
Aitman, Timothy J., Critser John K., Cuppen Edwin, Dominiczak Anna, Fernandez-Suarez Xose M., Flint Jonathan, Gauguier Dominique, Geurts Aron M., Gould Michael, Harris Peter C., et al.
Nat Genet. 5, Volume 40, Number 5, (2008), United States, p.516-22 doi: 10.1038/ng.147
Performance Validation of Neural Network Based 13C NMR Prediction Using a Publicly Available Data Source
Blinov, K. A., Smurnyy Y. D., Elyashberg M. E., Churanova T. S., Kvasha M., Steinbeck C., Lefebvre B. A., and Williams A. J.
Journal of Chemical Information and Modeling. Volume 48, Number 3, (2008), p.550–555
Annual spring meeting of the Proteomics Standards Initiative 23–25 April 2008, Toledo, Spain
Orchard, S., Albar J.P., Deutsch E.W., Binz P.A., Jones A. R., Creasy D., and Hermjakob H.
Proteomics. Volume 8, Number 20, (2008), p.4168–4172
Using the molecular biology data
Zdobnov, Evgeni M., Lopez Rodrigo, Apweiler Rolf, and Etzold Thure
Biotechnology Set, Second Edition. (2008), p.281–300
Pfam 10 years on: 10 000 families and still growing
SAMMUT, S. J., Finn R. D., and Bateman A.
Briefings in bioinformatics. Volume 9, Number 3, (2008), p.210–219
PhyloWidget: web-based visualizations for the tree of life
Jordan, G. E., and Piel W. H.
Bioinformatics. Volume 24, (2008), p.1641-1642
Genome analysis of the platypus reveals unique signatures of evolution
Warren, W. C., Hillier L. D. W., Graves J. A. M., Birney E., Ponting C. P., Grützner F., Belov K., Miller W., Clarke L., Chinwalla A. T., et al.
Nature. Volume 453, Number 7192, (2008), p.175–183
SNP and haplotype mapping for genetic analysis in the rat
Saar, K., Beck A., Bihoreau M. T., Birney E., Brocklebank D., Chen Y., Cuppen E., Demonchy S., Dopazo J., Flicek P., et al.
Nature genetics. Volume 40, Number 5, (2008), p.560–566
A logic-based diagram of signalling pathways central to macrophage activation
Raza, S., Robertson K., Lacaze P., Page D., Enright A., Ghazal P., and Freeman T.
BMC systems biology. Volume 2, Number 1, (2008), p.36
Accounting for non-genetic factors improves the power of eQTL studies
Stegle, O., Kannan A., Durbin R., and Winn J.
Research in Computational Molecular Biology. (2008), p.411–422
Sequences and topology: from genome structure to protein structure.
Teichmann, S. A., and Grishin N. V.
Current opinion in structural biology. Volume 18, Number 3, (2008), p.340
Ensembl 2008.
Flicek, P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic Acids Res. 1, Volume 36, Number Database issue, (2008), England, p.D707-14 doi: 10.1093/nar/gkm988
Integrating biological data–the distributed annotation system
Jenkinson, A.M., Albrecht M., Birney E., Blankenburg H., Down T., Finn R. D., Hermjakob H., Hubbard T. J. P., Jimenez R.C., Jones P., et al.
BMC bioinformatics. Volume 9, Number Suppl 8, (2008), p.S3
Infrastructure for distributed protein annotation
Reeves, GA, Prlić A., Jimenez RC, Kulesha E., and Hermjakob H.
Modern Genome Annotation: The Biosapiens Network. (2008), p.413
Databases, data tombs and dust in the wind
Wren, J. D., and Bateman A.
Bioinformatics. Volume 24, Number 19, (2008), p.2127–2128
Arabidopsis reactome: a foundation knowledgebase for plant systems biology
Tsesmetzis, N., Couchman M., Higgins J., Smith A., Doonan J. H., Seifert G. J., Schmidt E. E., Vastrik I., Birney E., Wu G., et al.
The Plant Cell Online. Volume 20, Number 6, (2008), p.1426–1436
Biological Data Resources at the EMBL-EBI
Lopez, R.
Revista Colombiana de Biotecnolog{\'ıa. Volume 10, Number 2, (2008), p.120–128
Data storage and analysis in ArrayExpress and Expression Profiler.
RUSTICI, G., KAPUSHESKY M., KOLESNIKOV N., Parkinson H., Sarkans U., and BRAZMA A.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Volume Chapter 7, (2008),
Finishing the finished human chromosome 22 sequence.
Cole, Charlotte G., McCann Owen T., Collins John E., Oliver Karen, Willey David, Gribble Susan M., Yang Fengtang, McLaren Karen, Rogers Jane, Ning Zemin, et al.
Genome Biol. Volume 9, Number 5, (2008), England, p.R78 doi: 10.1186/gb-2008-9-5-r78
From gene expression profiling to gene regulation
COULSON, R., Manke T., Palin K., Roider H., Sand O., Van Helden J., Ukkonen E., Vingron M., and BRAZMA A.
(2008),
The Protein Feature Ontology: a tool for the unification of protein feature annotations
Reeves, G. A., Eilbeck K., Magrane M., O'Donovan C., Montecchi-Palazzi L., Harris M. A., Orchard S., Jimenez R.C., Prlić A., Hubbard T. J. P., et al.
Bioinformatics. Volume 24, Number 23, (2008), p.2767–2772 doi:
The universal protein resource (UniProt)
Consortium, Uniprot, and others
Nucleic Acids Res. Volume 36, Number D190-D195, (2008), p.61–79
Levers and fulcrums: progress in cis-regulatory motif models
Birney, E., and others
Nature methods. Volume 5, Number 4, (2008), p.297–298
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
Cochrane, G., Akhtar R., Aldebert P., Althorpe N., Baldwin A., Bates K., Bhattacharyya S., Bonfield J., Bower L., Browne P., et al.
Nucleic Acids Res. Volume 36, Number Database issue, (2008), p.D5-12
DBD––taxonomically broad transcription factor predictions: new content and functionality
WILSON, D., Charoensawan V., Kummerfeld S. K., and Teichmann S. A.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D88–D92
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Down, Thomas A., Rakyan Vardhman K., Turner Daniel J., Flicek Paul, Li Heng, Kulesha Eugene, Gräf Stefan, Johnson Nathan, Herrero Javier, Tomazou Eleni M., et al.
Nat Biotechnol. 7, Volume 26, Number 7, (2008), United States, p.779-85 doi: 10.1038/nbt1414
Data storage and analysis in ArrayExpress and Expression Profiler
RUSTICI, G., KAPUSHESKY M., KOLESNIKOV N., Parkinson H., Sarkans U., and BRAZMA A.
Current Protocols in Bioinformatics. (2008), p.7–13
Data standards and controlled vocabularies for proteomics
Martens, L., Palazzi L. M., and Hermjakob H.
Methods Mol Biol. Volume 484, (2008), p.279–286
Data curation+ process curation= data integration+ science
Goble, Carole, Stevens Robert, Hull Duncan, Wolstencroft Katy, and Lopez Rodrigo
Briefings in bioinformatics. Volume 9, Number 6, (2008), p.506–517
The Pfam protein families database
Finn, R. D., Tate J., Mistry J., Coggill P. C., SAMMUT S. J., Hotz H. R., Ceric G., Forslund K., Eddy S. R., Sonnhammer E. L. L., et al.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D281–D288
Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients
Huggett, J. F., Taylor M. S., Kocjan G., Evans H. E., Morris-Jones S., Gant V., Novak T., Costello A. M., Zumla A., and Miller R. F.
Thorax. Volume 63, (2008), p.154-159
Ensembl 2008
Flicek, P., Aken BL, Beal K., Ballester B., Caccamo M., Chen Y., Clarke L., Coates G., Cunningham F., Cutts T., et al.
Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D707–D714
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs
Paten, B., Herrero J., Beal K., Fitzgerald S., and Birney E.
Genome research. Volume 18, Number 11, (2008), p.1814–1828
Annotation of mammalian primary microRNAs
Saini, H., Enright A., and Griffiths-Jones S.
BMC genomics. Volume 9, Number 1, (2008), p.564
Gaussian process robust regression for noisy heart rate data
Stegle, O., Fallert S. V., MacKay DJ, and Brage S.
Biomedical Engineering, IEEE Transactions on. Volume 55, Number 9, (2008), p.2143–2151
Networks for all
Ahnert, S. E., and Teichmann S. A.
Genome Biology. Volume 9, Number 10, (2008), p.324
Genome analysis of the platypus reveals unique signatures of evolution.
Warren, Wesley C., Hillier LaDeana W., Marshall Graves Jennifer A., Birney Ewan, Ponting Chris P., Grützner Frank, Belov Katherine, Miller Webb, Clarke Laura, Chinwalla Asif T., et al.
Nature. 5, Volume 453, Number 7192, (2008), England, p.175-83 doi: 10.1038/nature06936
PRIDE: new developments and new datasets
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InteroPORC: an automated tool to predict highly conserved protein interaction networks
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Remediation of the Protein Data Bank archive
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Profile Comparer: a program for scoring and aligning profile hidden Markov models
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4DXpress: a database for cross-species expression pattern comparisons
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Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
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A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences
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Strategies for measuring evolutionary conservation of RNA secondary structures
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Velvet: algorithms for de novo short read assembly using de Bruijn graphs
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DDBJ with new system and face
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Genomic-scale prioritization of drug targets: the TDR Targets database
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