Publications for 2007

2007

Probabilistic models for the study of protein evolution
Thorne, J. L., and Goldman N.
Handbook of Statistical Genetics. Volume 1, (2007), Chichester, UK, p.439-459
Knowledge-based prediction for alternate indications and targets for known drugs
Chan, A. W. E., and OVERINGTON J.
234th National ACS Meeting, Boston. (2007),
microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells
Vigorito, E., Perks K. L., ABREU-GOODGER C., Bunting S., Xiang Z., Kohlhaas S., Das P. P., Miska E. A., Rodriguez A., Bradley A., et al.
Immunity. Volume 27, Number 6, (2007), p.847–859
The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics
Jones, A. R., Miller M., Aebersold R., Apweiler R., Ball C. A., BRAZMA A., DeGreef J., Hardy N., Hermjakob H., Hubbard S. J., et al.
Nature Biotechnology. Volume 25, Number 10, (2007), p.1127-1133
Recommendations of the 2006 Human Variome Project meeting.
Cotton, Richard G. H., Project Human Variome 2006, Appelbe William, Auerbach Arleen D., Becker Kevin, Bodmer Walter, Boone Joe D., Boulyjenkov Victor, Brahmachari Samir, Brody Lawrence, et al.
Nat Genet. 4, Volume 39, Number 4, (2007), United States, p.433-6 doi: 10.1038/ng2024
Geminal Bismethylation Prevents Polyketide Oxidation and Dimerization in the Benastatin Pathway This work was financially supported by the BMBF GenoMik program and by a Humboldt research fellowship to AS We are grateful to Dr. P. Krastel, Novartis, for th
Schenk, A., Xu Z., Pfeiffer C., Steinbeck C., and Hertweck C.
Angewandte Chemie International Edition. Volume 46, Number 37, (2007),
Proteomics data validation: why all must provide data
Martens, L., and Hermjakob H.
Mol. BioSyst.. Volume 3, Number 8, (2007), p.518–522
Statistics of the log-det estimator
Massingham, T., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.2277-2285
The implications of alternative splicing in the ENCODE protein complement
Tress, M. L., Martelli P. L., Frankish A., Reeves G. A., Wesselink J. J., Yeats C., Albrecht M., Hegyi H., Giorgetti A., Raimondo D., et al.
Proceedings of the National Academy of Sciences. Volume 104, Number 13, (2007), p.5495
Denoising inferred functional association networks obtained by gene fusion analysis
Kamburov, A., Goldovsky L., Freilich S., Kapazoglou A., Kunin V., Enright A., Tsaftaris A., and Ouzounis C.
BMC genomics. Volume 8, Number 1, (2007), p.460
Evolution of protein complexes by duplication of homomeric interactions
Pereira-Leal, J. B., Levy E. D., Kamp C., and Teichmann S. A.
Genome biology. Volume 8, Number 4, (2007), p.R51
ArrayExpress—a public database of microarray experiments and gene expression profiles
Parkinson, H., KAPUSHESKY M., Shojatalab M., ABEYGUNAWARDENA N., COULSON R., FARNE A., HOLLOWAY E., Kolesnykov N., Lilja P., Lukk M., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D747–D750
The minimum information required for reporting a molecular interaction experiment (MIMIx)
Orchard, S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stümpflen V., Ceol A., Chatr-aryamontri A., Armstrong J., Woollard P., et al.
Nature biotechnology. Volume 25, Number 8, (2007), p.894–898
Inference and validation of Synechocystis protein interaction network using orthology
Michaut, M., Kerrien S., Montecchi-Palazzi L., Chauvat F., Cassier-Chauvat C., Aude J. C., Legrain P., and Hermjakob H.
JOBIM proceedings. (2007), p.229–234
Predicting active site residue annotations in the Pfam database
Mistry, J., Bateman A., and Finn R.
BMC bioinformatics. Volume 8, Number 1, (2007), p.298
Specificity and evolvability in eukaryotic protein interaction networks
Beltrao, P., and Serrano L.
PLoS computational biology. Volume 3, Number 2, (2007), p.e25
Genome browsing with Ensembl: a practical overview
Spudich, G., Fernández-Suárez X. M., and Birney E.
Briefings in functional genomics & proteomics. Volume 6, Number 3, (2007), p.202–219
Evolutionary genomics: come fly with us
Birney, E.
Nature. Volume 450, Number 7167, (2007), p.184–185
Bioinformatics: Using the Molecular Biology Data
Zdobnov, E. M., Lopez R., Apweiler R., and Etzold T.
Essentials of Genomics and Bioinformatics. (2007), p.265–284
Analysis of Assembly and Disassembly Pathways of Non-covalent Homooligomeric Complexes
Erba, E. B., Levy E., Hernandez H., Lane L., Teichmann S., and Robinson C. V.
55 th ASMS Conference Proceedings. (2007),
Gene Expression Databases
BRAZMA, A., and Sarkans U.
eLS. (2007),
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Côté, R.G., Jones P., Martens L., Kerrien S., Reisinger F., Lin Q., Leinonen R., Apweiler R., and Hermjakob H.
BMC bioinformatics. Volume 8, Number 1, (2007), p.401
Web services at the European bioinformatics institute
Labarga, Alberto, Valentin Franck, Anderson Mikael, and Lopez Rodrigo
Nucleic acids research. Volume 35, Number suppl 2, (2007), p.W6–W11
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium, The
Nature. Volume 447, (2007), p.799-816
Evolutionary and biomedical insights from the rhesus macaque genome
Gibbs, R. A., Rogers J., Katze M. G., Bumgarner R., Weinstock G. M., Mardis E. R., Remington K. A., Strausberg R. L., Venter J. C., Wilson R. K., et al.
science. Volume 316, Number 5822, (2007), p.222
Requirement of bic/microRNA-155 for normal immune function
Rodriguez, A., Vigorito E., Clare S., Warren M. V., Couttet P., Soond D. R., Van Dongen S., Grocock R. J., Das P. P., Miska E. A., et al.
Science. Volume 316, Number 5824, (2007), p.608
SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics–exploring current scientific literature for emerging topics
Rebholz-Schuhman, D., Cameron G., Clark D., van Mulligen E., Coatrieux J. L., Barbolla E. D. H., Martin-Sanchez F., Milanesi L., Porro I., Beltrame F., et al.
BMC bioinformatics. Volume 8, Number Suppl 1, (2007), p.S18
The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch, Christoph M., Andrews Robert M., Flicek Paul, Dillon Shane C., Karaöz Ulaş, Clelland Gayle K., Wilcox Sarah, Beare David M., Fowler Joanna C., Couttet Phillippe, et al.
Genome Res. 6, Volume 17, Number 6, (2007), United States, p.691-707 doi: 10.1101/gr.5704207
Bioclipse: an open source workbench for chemo- and bioinformatics.
Spjuth, Ola, Helmus Tobias, Willighagen Egon L., Kuhn Stefan, Eklund Martin, Wagener Johannes, Murray-Rust Peter, Steinbeck Christoph, and Wikberg Jarl E. S.
BMC Bioinformatics. Volume 8, Number 1, (2007), p.59 doi: 10.1186/1471-2105-8-59
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQTM
Siepen, J.A., Swainston N., Jones A. R., Hart S. R., Hermjakob H., Jones P., and Hubbard S. J.
Proteome science. Volume 5, Number 1, (2007), p.4
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper Gregory M., Asimenos George, Thomas Daryl J., Dewey Colin N., Siepel Adam, Birney Ewan, Keefe Damian, Schwartz Ariel S., Hou Minmei, et al.
Genome Research. Volume 17, (2007), p.760-774
The landscape of histone modifications across 1% of the human genome in five human cell lines
Koch, C. M., Andrews R. M., Flicek P., Dillon S. C., Karaöz U., Clelland G. K., Wilcox S., Beare D. M., Fowler J. C., Couttet P., et al.
Genome research. Volume 17, Number 6, (2007), p.691–707
Construction, visualisation, and clustering of transcription networks from microarray expression data
Freeman, T. C., Goldovsky L., Brosch M., Van Dongen S., Mazière P., Grocock R. J., Freilich S., Thornton J., and Enright A. J.
PLoS computational biology. Volume 3, Number 10, (2007), p.e206
The folding and evolution of multidomain proteins
Han, J. H., Batey S., Nickson A. A., Teichmann S. A., and Clarke J.
Nature Reviews Molecular Cell Biology. Volume 8, Number 4, (2007),
Ensembl 2007.
Hubbard, T. J. 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 35, Number Database issue, (2007), England, p.D610-7 doi: 10.1093/nar/gkl996
Clinical proteomics: a need to define the field and to begin to set adequate standards
Mischak, H., Apweiler R., Banks R. E., Conaway M., Coon J., Dominiczak A., Ehrich J. H. H., Fliser D., Girolami M., Hermjakob H., et al.
PROTEOMICS-Clinical Applications. Volume 1, Number 2, (2007), p.148–156
An application of latent topic document analysis to large-scale proteomics databases
Klie, S., Martens L., Vizcaino J.A., Côté R., Jones P., Apweiler R., Hinneburg A., Hermjakob H., and Outstation E.
German Bioinformatics Conference. (2007),
SCOOP: a simple method for identification of novel protein superfamily relationships
Bateman, A., and Finn R. D.
Bioinformatics. Volume 23, Number 7, (2007), p.809–814
New approaches to phylogenetic tree search and their application to large numbers of protein alignments
Whelan, S.
Systematic Biology. Volume 56, (2007), p.727-740
Identification of novel peptide hormones in the human proteome by hidden Markov model screening
Mirabeau, O., Perlas E., Severini C., Audero E., Gascuel O., Possenti R., Birney E., Rosenthal N., and Gross C.
Genome research. Volume 17, Number 3, (2007), p.320–327
ENFIN—a Network to Enhance Integrative Systems Biology
Kahlem, P., and Birney E.
Annals of the New York Academy of Sciences. Volume 1115, Number 1, (2007), p.23–31
EMBL nucleotide sequence database in 2006
Kulikova, T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D16–D20
The (In) dependence of
Talavera, D., Vogel C., Orozco M., Teichmann S. A., and de La Cruz X.
(2007),
Prediction of gene expression in embryonic structures of Drosophila melanogaster
Samsonova, A. A., Niranjan M., Russell S., and BRAZMA A.
PLoS computational biology. Volume 3, Number 7, (2007), p.e144
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
Jones, A. R., Miller M., Aebersold R., Apweiler R., Ball C.A., Brazma A., DeGreef J., Hardy N., Hermjakob H., Hubbard S. J., et al.
Nature biotechnology. Volume 25, Number 10, (2007), p.1127–1133
New developments in the InterPro database
Mulder, Nicola J., Apweiler Rolf, Attwood Teresa K., Bairoch Amos, Bateman Alex, Binns David, Bork Peer, Buillard Virginie, Cerutti Lorenzo, Copley Richard, et al.
Nucleic Acids Research. Volume 35, Number suppl 1, (2007), p.D224–D228
Variation in evolutionary processes at different codon positions
Bofkin, L., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.513-521
Ensembl 2007
Hubbard, T. J. 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 35, Number suppl 1, (2007), p.D610–D617
Reactome–a knowledgebase of human biological pathways
D'Eustachio, P., Croft D., de Bono B., Gopinath G., Gillespie M., Jassal B., Matthews L., Schmidt E., Vastrik I., Wu G., et al.
(2007),
Medical informatics and bioinformatics: a bibliometric study
Bansard, J. Y., REBHOLZ-SCHUHMANN D., Cameron G., Clark D., van Mulligen E., Beltrame F., Barbolla E. D. H., Martin-Sanchez F., Milanesi L., Tollis I., et al.
Information Technology in Biomedicine, IEEE Transactions on. Volume 11, Number 3, (2007), p.237–243
Gene prediction: compare and CONTRAST.
Flicek, Paul
Genome Biol. Volume 8, Number 12, (2007), England, p.233 doi: 10.1186/gb-2007-8-12-233
Geminal bismethylation prevents polyketide oxidation and dimerization in the benastatin pathway.
Schenk, Angéla, Xu Zhongli, Pfeiffer Corina, Steinbeck Christoph, and Hertweck Christian
Angewandte Chemie. International Ed. in English. Volume 46, Number 37, (2007), p.7035–7038 doi: 10.1002/anie.200702033
Analyzing large-scale proteomics projects with latent semantic indexing
Klie, S., Martens L., Vizcaino J.A., Côté R., Jones P., Apweiler R., Hinneburg A., and Hermjakob H.
Journal of proteome research. Volume 7, Number 01, (2007), p.182–191
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, E. H., Cooper G. M., Asimenos G., Thomas D. J., Dewey C. N., Siepel A., Birney E., Keefe D., Schwartz A. S., Hou M., et al.
Genome research. Volume 17, Number 6, (2007), p.760–774
Prediction of microRNA targets
Maziere, P., and Enright A. J.
Drug discovery today. Volume 12, Number 11-12, (2007), p.452–458
Evolution of genes and genomes on the Drosophila phylogeny
Clark, A. G., Eisen M. B., Smith D. R., Bergman C. M., Oliver B., Markow T. A., Kaufman T. C., Kellis M., Gelbart W., Iyer V. N., et al.
Nature. Volume 450, Number 7167, (2007), p.203–218
Evolution of genes and genomes on the Drosophila phylogeny.
Consortium, Drosophila Genomes 12, Clark Andrew G., Eisen Michael B., Smith Douglas R., Bergman Casey M., Oliver Brian, Markow Therese A., Kaufman Thomas C., Kellis Manolis, Gelbart William, et al.
Nature. 11, Volume 450, Number 7167, (2007), England, p.203-18 doi: 10.1038/nature06341
The minimum information about a proteomics experiment (MIAPE)
Taylor, C.F., Paton N.W., Lilley K. S., Binz P.A., Julian R. K., Jones A. R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., et al.
Nature biotechnology. Volume 25, Number 8, (2007), p.887–893
MIACA–Minimum Information About a Cellular Assay, and the Cellular Assay Object Model
Wiemann, S., Mehrle E., Hahne F., Hermjakob H., Apweiler R., Arlt D., Bechtel S., Bielke W., Birmingham A., Boese Q., et al.
(2007),
Reuse of structural domain–domain interactions in protein networks
Schuster-Böckler, B., and Bateman A.
BMC bioinformatics. Volume 8, Number 1, (2007), p.259
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
Ettwiller, L., Paten B., Ramialison M., Birney E., and Wittbrodt J.
Nature methods. Volume 4, Number 7, (2007), p.563–565
In vivo validation of a computationally predicted conserved Ath5 target gene set
Del Bene, F., Ettwiller L., Skowronska-Krawczyk D., Baier H., Matter J. M., Birney E., and Wittbrodt J.
PLoS genetics. Volume 3, Number 9, (2007), p.e159
Web services at the European bioinformatics institute
LABARGA, A., Valentin F., Anderson M., and Lopez R.
Nucleic acids research. Volume 35, Number suppl 2, (2007), p.W6–W11
Evolution of genes and genomes on the Drosophila phylogeny. Nature
Clark, A. G., Eisen M. B., Smith D. R., and others
Nature. Volume 450, (2007),
PASSIM–an open source software system for managing information in biomedical studies
Viksna, J., Celms E., Opmanis M., Podnieks K., Rucevskis P., Zarins A., Barrett A., Neogi S. G., KRESTYANINOVA M., McCarthy M. I., et al.
BMC bioinformatics. Volume 8, Number 1, (2007), p.52
Broadening the horizon–level 2.5 of the HUPO-PSI format for molecular interactions
Kerrien, S., Orchard S., Montecchi-Palazzi L., Aranda B., Quinn A. F., Vinod N., Bader G.D., Xenarios I., Wojcik J., Sherman D., et al.
BMC biology. Volume 5, Number 1, (2007), p.44
Clustal W and Clustal X version 2.0
Larkin, MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al.
Bioinformatics. Volume 23, Number 21, (2007), p.2947–2948
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium, The, Birney E., Stamatoyannopoulos J. A., Dutta A., Guigó R., Gingeras T. R., Margulies E. H., Weng Z., Snyder M., Dermitzakis E. T., et al.
Nature. Volume 447, Number 7146, (2007), p.799–816
Double Dutch for duplications
Birney, E.
Nature genetics. Volume 39, Number 11, (2007), p.1303–1304
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
Itoh, T., Tanaka T., Barrero R. A., Yamasaki C., Fujii Y., Hilton P. B., Antonio B. A., Aono H., Apweiler R., Bruskiewich R., et al.
Genome research. Volume 17, Number 2, (2007), p.175–183 doi:
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
Oeder, Sebastian, Mages Joerg, Flicek Paul, and Lang Roland
BMC Genomics. Volume 8, (2007), England, p.200 doi: 10.1186/1471-2164-8-200
Userscripts for the life sciences
Willighagen, E. L., O'Boyle N. M., Gopalakrishnan H., Jiao D., Guha R., Steinbeck C., and Wild D. J.
BMC Bioinformatics. Volume 8, Number 1, (2007), p.487
Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23–25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France
Orchard, S., Montechi-Palazzi L., Deutsch E.W., Binz P.A., Jones A. R., Paton N., Pizarro A., Creasy D. M., Wojcik J., and Hermjakob H.
Proteomics. Volume 7, Number 19, (2007), p.3436–3440
CAALIGN: a program for pairwise and multiple protein-structure alignment
Oldfield, T. J.
Acta Crystallographica D. Volume 63, Issue Part 4, (2007), p.514-525 doi: 10.1107/S0907444907000844
An empirical codon model for protein sequence evolution
Kosiol, C., Holmes I., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.1464-1479
Challenges and standards in integrating surveys of structural variation
Scherer, S. W., Lee C., Birney E., Altshuler D. M., Eichler E. E., Carter N. P., Hurles M. E., and Feuk L.
Nature genetics. Volume 39, (2007), p.S7–S15
A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway
O’Carroll, D., Mecklenbrauker I., Das P. P., Santana A., Koenig U., Enright A. J., Miska E. A., and Tarakhovsky A.
Genes & development. Volume 21, Number 16, (2007), p.1999
ArrayExpress - A public database of microarray experiments and gene expression profiles
Parkinson, H., KAPUSHESKY M., Shojatalab M., ABEYGUNAWARDENA N., COULSON R., FARNE A., HOLLOWAY E., Kolesnykov N., Lilja P., Lukk M., et al.
Nucleic Acids Research. Volume 35, Number SUPPL. 1, (2007), p.D747-D750
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Consortium, ENCODE Project, Birney Ewan, Stamatoyannopoulos John A., Dutta Anindya, Guigó Roderic, Gingeras Thomas R., Margulies Elliott H., Weng Zhiping, Snyder Michael, Dermitzakis Emmanouil T., et al.
Nature. 6, Volume 447, Number 7146, (2007), England, p.799-816
IntAct—open source resource for molecular interaction data
Kerrien, S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D561–D565
Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25–27 September 2006, Washington DC, USA
Orchard, S., Taylor C.F., Jones P., Montechi-Palazzo L., Binz P.A., Jones A. R., Pizarro A., Julian Jr R. K., and Hermjakob H.
Proteomics. Volume 7, Number 3, (2007), p.337–339
The tify family previously known as ZIM
Vanholme, B., Grunewald W., Bateman A., Kohchi T., and Gheysen G.
Trends in plant science. Volume 12, Number 6, (2007), p.239–244
Management, presentation and interpretation of genome scans using GSCANDB
Taylor, M., Valdar W., Kumar A., Flint J., and Mott R.
Bioinformatics. Volume 23, (2007), p.1545-1549
Optimized design and assessment of whole genome tiling arrays
Gräf, S., Nielsen F. G. G., Kurtz S., Huynen M. A., Birney E., Stunnenberg H., and Flicek P.
Bioinformatics. Volume 23, Number 13, (2007), p.i195–i204
Estimating the neutral rate of nucleotide substitution using introns
Hoffman, M. M., and Birney E.
Molecular biology and evolution. Volume 24, Number 2, (2007), p.522–531
New developments in the InterPro database
Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., et al.
Nucleic Acids Research. Volume 35, Number suppl 1, (2007), p.D224–D228 doi:
Computational identification of site-specific transcription factors in Drosophila
Adryan, B., and Teichmann S. A.
Fly. Volume 1, Number 3, (2007), p.142–145
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study
RUSTICI, G., Van Bakel H., Lackner D. H., Holstege F. C., Wijmenga C., Bähler J., BRAZMA A., and others
Genome Biol. Volume 8, Number 5, (2007), p.R73
The implications of alternative splicing in the ENCODE protein complement
Tress, M. L., Martelli P. L., Frankish A., Reeves G. A., Wesselink J. J., Yeats C., Albrecht M., Hegyi H., Giorgetti A., Raimondo D., et al.
Proceedings of the National Academy of Sciences. Volume 104, Number 13, (2007), p.5495–5500
Pride Wizard: generation of standards compliant quantitative proteomics data
Swainston, N., Siepen J.A., Jones A. R., Hart S. R., Hermjakob H., Jones P., and Hubbard S. J.
BMC Systems Biology. Volume 1, Number Suppl 1, (2007), p.P27
In the editorial for 2007 Database issue, the name of the editor was spelt incorrectly. The correct name should read
Bateman, A.
Nucleic Acids Research. Volume 35, Number 2, (2007),
A genome-wide Ras-effector interaction network
Kiel, C., Foglierini M., Kuemmerer N., Beltrao P., and Serrano L.
Journal of molecular biology. Volume 370, Number 5, (2007), p.1020–1032
Optimising oligonucleotide array design for ChIP-on-chip
Nielsen, F., Graef S., Zhang X., Kurtz S., Denissov S., Green R., Birney E., Flicek P., Huynen M., and Stunnenberg H.
BMC Bioinformatics. Volume 8, (2007), p.1–1
EMBL Nucleotide Sequence Database in 2006
Kulikova, T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., et al.
Nucleic Acids Res. Volume 35, Number Database issue, (2007), p.D16-20
Optimized design and assessment of whole genome tiling arrays.
Gräf, Stefan, Nielsen Fiona G. G., Kurtz Stefan, Huynen Martijn A., Birney Ewan, Stunnenberg Henk, and Flicek Paul
Bioinformatics. 7, Volume 23, Number 13, (2007), England, p.i195-204 doi: 10.1093/bioinformatics/btm200
Geminal bismethylation prevents polyketide oxidation and dimerization in the benastatin pathway
Schenk, A., Xu Z., Pfeiffer C., Steinbeck C., and Hertweck C.
Angewandte Chemie. Volume 119, Number 37, (2007), p.7165–7168
The PSI formal document process and its implementation on the PSI website
Vizcaino, J.A., Martens L., Hermjakob H., Julian R. K., and Paton N.W.
Proteomics. Volume 7, Number 14, (2007), p.2355–2357
Bioinformatics: Using the Molecular Biology Data
Zdobnov, Evgeni M., Lopez Rodrigo, Apweiler Rolf, and Etzold Thure
Essentials of Genomics and Bioinformatics. (2007), p.265–284
MATLIGN: a motif clustering, comparison and matching tool
Kankainen, M., and Löytynoja A.
BMC Bioinformatics. Volume 8, (2007), p.189
Reactome: a knowledge base of biologic pathways and processes
Vastrik, I., D'Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., et al.
Genome biology. Volume 8, Number 3, (2007), p.R39
Genomic analysis of human microRNA transcripts
Saini, H. K., Griffiths-Jones S., and Enright A. J.
Proceedings of the National Academy of Sciences. Volume 104, Number 45, (2007), p.17719
PASSIM - An open source software system for managing information in biomedical studies
Viksna, J., Celms E., Opmanis M., Podnieks K., Rucevskis P., Zarins A., Barrett A., Neogi S. G., KRESTYANINOVA M., McCarthy M. I., et al.
BMC Bioinformatics. Volume 8, (2007),
Population genomics of human gene expression.
Stranger, Barbara E., Nica Alexandra C., Forrest Matthew S., Dimas Antigone, Bird Christine P., Beazley Claude, Ingle Catherine E., Dunning Mark, Flicek Paul, Koller Daphne, et al.
Nat Genet. 10, Volume 39, Number 10, (2007), United States, p.1217-24 doi: 10.1038/ng2142
ChEBI: a database and ontology for chemical entities of biological interest
Degtyarenko, K., Matos P., ENNIS M., and HASTINGS J.
Nucleic Acids Research. (2007),
Human Proteome Organization Proteomics Standards Initiative Data Standardization, a View on Developments and Policy
Martens, L., Orchard S., Apweiler R., and Hermjakob H.
Molecular & Cellular Proteomics. Volume 6, Number 9, (2007), p.1666–1667
Resource aware taxon selection for maximizing phylogenetic diversity
Pardi, F., and Goldman N.
Systematic Biology. Volume 56, (2007), p.431-444
VectorBase: a home for invertebrate vectors of human pathogens
Lawson, D., Arensburger P., Atkinson P., Besansky N. J., Bruggner R. V., Butler R., Campbell K. S., Christophides G. K., Christley S., Dialynas E., et al.
Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D503–D505
Clustal W and Clustal X version 2.0
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