Publications for 2007

2007

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The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M. Nucleic acids research Volume 36 (2008) p.D1028-33 DOI: 10.1093/nar/gkm978
Remediation of the protein data bank archive.
Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Nucleic acids research Volume 36 (2008) p.D426-33 DOI: 10.1093/nar/gkm937
The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world.
Orchard S, Hermjakob H. Briefings in bioinformatics Volume 9 (2008) p.166-173 DOI: 10.1093/bib/bbm061
Proteomics: from technology development to biomarker applications.
Orchard S. Expert review of proteomics Volume 4 (2007) p.709-710 DOI: 10.1586/14789450.4.6.709
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Analyzing large-scale proteomics projects with latent semantic indexing.
Klie S, Martens L, Vizcaíno JA, Côté R, Jones P, Apweiler R, Hinneburg A, Hermjakob H. Journal of proteome research Volume 7 (2008) p.182-191 DOI: 10.1021/pr070461k
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The universal protein resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 36 (2008) p.D190-5 DOI: 10.1093/nar/gkm895
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, Castro M, Cox T, Demiralp F, Eberhardt R, Faruque N, Hoad G, Jang M, Kulikova T, Labarga A, Leinonen R, Leonard S, Lin Q, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Plaister S, Robinson S, Sobhany S, Vaughan R, Wu D, Zhu W, Apweiler R, Hubbard T, Birney E. Nucleic acids research Volume 36 (2008) p.D5-12 DOI: 10.1093/nar/gkm1018
PRIDE: new developments and new datasets.
Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H. Nucleic acids research Volume 36 (2008) p.D878-83 DOI: 10.1093/nar/gkm1021
Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. BMC bioinformatics Volume 8 (2007) p.S1-S1
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Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Bioinformatics (Oxford, England) Volume 24 (2008) p.11-17 DOI: 10.1093/bioinformatics/btm547
Ensembl 2008.
Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. Nucleic acids research Volume 36 (2008) p.D707-14 DOI: 10.1093/nar/gkm988
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miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. Nucleic acids research Volume 36 (2008) p.D154-8 DOI: 10.1093/nar/gkm952
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W. Bioinformatics (Oxford, England) Volume 24 (2008) p.1100-1101 DOI: 10.1093/bioinformatics/btm518
The HGNC Database in 2008: a resource for the human genome.
Bruford EA, Lush MJ, Wright MW, Sneddon TP, Povey S, Birney E. Nucleic acids research Volume 36 (2008) p.D445-8 DOI: 10.1093/nar/gkm881
Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Favia AD, Nobeli I, Glaser F, Thornton JM. Journal of molecular biology Volume 375 (2008) p.855-874 DOI: 10.1016/j.jmb.2007.10.065
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Double Dutch for duplications.
Birney E. Nature genetics Volume 39 (2007) p.1303-1304 DOI: 10.1038/ng1107-1303
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Evolutionary genomics: come fly with us.
Birney E. Nature Volume 450 (2007) p.184-185 DOI: 10.1038/450184a
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Classification and nomenclature of all human homeobox genes.
Holland PW, Booth HA, Bruford EA. BMC biology Volume 5 (2007) p.47 DOI: 10.1186/1741-7007-5-47
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H. BMC bioinformatics Volume 8 (2007) p.401 DOI: 10.1186/1471-2105-8-401
ENFIN a network to enhance integrative systems biology.
Kahlem P, Birney E. Annals of the New York Academy of Sciences Volume 1115 (2007) p.23-31 DOI: 10.1196/annals.1407.016
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Evidence for lifespan extension and delayed age-related biomarkers in insulin receptor substrate 1 null mice.
Selman C, Lingard S, Choudhury AI, Batterham RL, Claret M, Clements M, Ramadani F, Okkenhaug K, Schuster E, Blanc E, Piper MD, Al-Qassab H, Speakman JR, Carmignac D, Robinson IC, Thornton JM, Gems D, Partridge L, Withers DJ. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 22 (2008) p.807-818 DOI: 10.1096/fj.07-9261com
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. BMC biology Volume 5 (2007) p.44 DOI: 10.1186/1741-7007-5-44
In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R. Molecular biotechnology Volume 38 (2008) p.165-177 DOI: 10.1007/s12033-007-9003-x
4DXpress: a database for cross-species expression pattern comparisons.
Haudry Y, Berube H, Letunic I, Weeber PD, Gagneur J, Girardot C, Kapushesky M, Arendt D, Bork P, Brazma A, Furlong EE, Wittbrodt J, Henrich T. Nucleic acids research Volume 36 (2008) p.D847-53 DOI: 10.1093/nar/gkm797
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 EW, Binz PA, Jones AR, Paton N, Pizarro A, Creasy DM, Wojcik J, Hermjakob H. Proteomics Volume 7 (2007) p.3436-3440 DOI: 10.1002/pmic.200700658
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Construction, visualisation, and clustering of transcription networks from microarray expression data.
Freeman TC, Goldovsky L, Brosch M, van Dongen S, Mazière P, Grocock RJ, Freilich S, Thornton J, Enright AJ. PLoS computational biology Volume 3 (2007) p.2032-2042 DOI: 10.1371/journal.pcbi.0030206
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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. Nature biotechnology Volume 25 (2007) p.1127-1133 DOI: 10.1038/nbt1347
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Current approaches to gene regulatory network modelling.
Schlitt T, Brazma A. BMC bioinformatics Volume 8 Suppl 6 (2007) p.S9 DOI: 10.1186/1471-2105-8-s6-s9
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Population genomics of human gene expression.
Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET. Nature genetics Volume 39 (2007) p.1217-1224 DOI: 10.1038/ng2142
Evolution of enzymes and pathways for the biosynthesis of cofactors.
Holliday GL, Thornton JM, Marquet A, Smith AG, Rébeillé F, Mendel R, Schubert HL, Lawrence AD, Warren MJ. Natural product reports Volume 24 (2007) p.972-987 DOI: 10.1039/b703107f
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The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals.
Edwards CA, Rens W, Clarke O, Mungall AJ, Hore T, Graves JA, Dunham I, Ferguson-Smith AC, Ferguson-Smith MA. BMC evolutionary biology Volume 7 (2007) p.157 DOI: 10.1186/1471-2148-7-157
Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.
Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H. Proteomics Volume 7 Suppl 1 (2007) p.28-34 DOI: 10.1002/pmic.200700286
Genome browsing with Ensembl: a practical overview.
Spudich G, Fernández-Suárez XM, Birney E. Briefings in functional genomics & proteomics Volume 6 (2007) p.202-219 DOI: 10.1093/bfgp/elm025
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy.
Martens L, Orchard S, Apweiler R, Hermjakob H. Molecular & cellular proteomics : MCP Volume 6 (2007) p.1666-1667
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Proteomics Data Collection - the 1st ProDaC workshop 26 April 2007 Ecole Normale Supérieur, Lyon, France.
Eisenacher M, Hardt T, Hamacher M, Martens L, Häkkinen J, Levander F, Apweiler R, Meyer HE, Stephan C. Proteomics Volume 7 (2007) p.3034-3037 DOI: 10.1002/pmic.200700554
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
Ward JJ, Thornton JM. PLoS computational biology Volume 3 (2007) p.1993-2002 DOI: 10.1371/journal.pcbi.0030198
Probabilistic models for the study of protein evolution
Thorne JL, Goldman N. Handbook of Statistical Genetics John Wiley and Sons (3 edition) DOI: 10.1002/9780470061619.ch14
PROCOGNATE: a cognate ligand domain mapping for enzymes.
Bashton M, Nobeli I, Thornton JM. Nucleic acids research Volume 36 (2008) p.D618-22 DOI: 10.1093/nar/gkm611
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Tissue-specific histone modification and transcription factor binding in alpha globin gene expression.
De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG, Higgs DR. Blood Volume 110 (2007) p.4503-4510 DOI: 10.1182/blood-2007-06-097964
Statistics of the log-det estimator.
Massingham T, Goldman N. Molecular biology and evolution Volume 24 (2007) p.2277-2285 DOI: 10.1093/molbev/msm160
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Computational prediction of protein-protein interactions.
Skrabanek L, Saini HK, Bader GD, Enright AJ. Molecular biotechnology Volume 38 (2008) p.1-17 DOI: 10.1007/s12033-007-0069-2
The chemistry of protein catalysis.
Holliday GL, Almonacid DE, Mitchell JB, Thornton JM. Journal of molecular biology Volume 372 (2007) p.1261-1277 DOI: 10.1016/j.jmb.2007.07.034
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Experimental design criteria in phylogenetics: where to add taxa.
Geuten K, Massingham T, Darius P, Smets E, Goldman N. Systematic biology Volume 56 (2007) p.609-622 DOI: 10.1080/10635150701499563
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High Performance Proteomics: 7th HUPO Brain Proteome Project Workshop March 7-9, 2007 Wellcome Trust Conference Centre, Hinxton, UK.
Hamacher M, Stephan C, Eisenacher M, Lewczuk P, Wiltfang J, Martens L, Vizcaíno JA, Kwon KH, Yoo JS, Park YM, Beckers J, Horsch M, de Angelis MH, Cho ZH, Apweiler R, Meyer HE. Proteomics Volume 7 (2007) p.2490-2496 DOI: 10.1002/pmic.200700449
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, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. Nature biotechnology Volume 25 (2007) p.894-898 DOI: 10.1038/nbt1324
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The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR, Hermjakob H. Nature biotechnology Volume 25 (2007) p.887-893 DOI: 10.1038/nbt1329
In vivo validation of a computationally predicted conserved Ath5 target gene set.
Del Bene F, Ettwiller L, Skowronska-Krawczyk D, Baier H, Matter JM, Birney E, Wittbrodt J. PLoS genetics Volume 3 (2007) p.1661-1671 DOI: 10.1371/journal.pgen.0030159
Prediction of gene expression in embryonic structures of Drosophila melanogaster.
Samsonova AA, Niranjan M, Russell S, Brazma A. PLoS computational biology Volume 3 (2007) p.e144 DOI: 10.1371/journal.pcbi.0030144
Optimized design and assessment of whole genome tiling arrays.
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Bioinformatics (Oxford, England) Volume 23 (2007) p.i195-204 DOI: 10.1093/bioinformatics/btm200
The PSI formal document process and its implementation on the PSI website.
Vizcaíno JA, Martens L, Hermjakob H, Julian RK, Paton NW. Proteomics Volume 7 (2007) p.2355-2357 DOI: 10.1002/pmic.200700064
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Challenges and standards in integrating surveys of structural variation.
Scherer SW, Lee C, Birney E, Altshuler DM, Eichler EE, Carter NP, Hurles ME, Feuk L. Nature genetics Volume 39 (2007) p.S7-15 DOI: 10.1038/ng2093
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Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
Oeder S, Mages J, Flicek P, Lang R. BMC genomics Volume 8 (2007) p.200 DOI: 10.1186/1471-2164-8-200
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Renaming the DSCR1/Adapt78 gene family as RCAN: regulators of calcineurin.
Davies KJ, Ermak G, Rothermel BA, Pritchard M, Heitman J, Ahnn J, Henrique-Silva F, Crawford D, Canaider S, Strippoli P, Carinci P, Min KT, Fox DS, Cunningham KW, Bassel-Duby R, Olson EN, Zhang Z, Williams RS, Gerber HP, Pérez-Riba M, Seo H, Cao X, Klee CB, Redondo JM, Maltais LJ, Bruford EA, Povey S, Molkentin JD, McKeon FD, Duh EJ, Crabtree GR, Cyert MS, de la Luna S, Estivill X. FASEB journal : official publication of the Federation of American Societies for Experimental Biology Volume 21 (2007) p.3023-3028 DOI: 10.1096/fj.06-7246com
Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation.
Ettwiller L, Paten B, Ramialison M, Birney E, Wittbrodt J. Nature methods Volume 4 (2007) p.563-565 DOI: 10.1038/nmeth1061
Proteomics data validation: why all must provide data.
Martens L, Hermjakob H. Molecular bioSystems Volume 3 (2007) p.518-522 DOI: 10.1039/b705178f
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Correction: Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases.
Allali-Hassani A, Pan W, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards A, Bochkarev A, Plotnikov A, Vedadi M, Arrowsmith C. PLoS biology Volume 5 (2007)
Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N. Systematic biology Volume 56 (2007) p.431-444 DOI: 10.1080/10635150701411279
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Nature Volume 447 (2007) p.799-816 DOI: 10.1038/nature05874
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Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.
Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C. Genome research Volume 17 (2007) p.708-719 DOI: 10.1101/gr.5540007
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The landscape of histone modifications across 1% of the human genome in five human cell lines.
Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I. Genome research Volume 17 (2007) p.691-707 DOI: 10.1101/gr.5704207
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Genome research Volume 17 (2007) p.760-774 DOI: 10.1101/gr.6034307
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Genome sequence of Aedes aegypti, a major arbovirus vector.
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedeo P, Arensburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston JS, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary S, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Birren B, Fraser-Liggett CM, Severson DW. Science (New York, N.Y.) Volume 316 (2007) p.1718-1723 DOI: 10.1126/science.1138878
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Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11.
Nejentsev S, Smink LJ, Smyth D, Bailey R, Lowe CE, Payne F, Masters J, Godfrey L, Lam A, Burren O, Stevens H, Nutland S, Walker NM, Smith A, Twells R, Barratt BJ, Wright C, French L, Chen Y, Deloukas P, Rogers J, Dunham I, Todd JA. BMC genetics Volume 8 (2007) p.24 DOI: 10.1186/1471-2156-8-24
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AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.
Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton MR, Futreal PA, Wooster R. Bioinformatics (Oxford, England) Volume 23 (2007) p.1689-1691 DOI: 10.1093/bioinformatics/btm152
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Structural and chemical profiling of the human cytosolic sulfotransferases.
Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH. PLoS biology Volume 5 (2007) p.e97 DOI: 10.1371/journal.pbio.0050097
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eGenomics: Cataloguing Our Complete Genome Collection III.
Field D, Garrity G, Gray T, Selengut J, Sterk P, Thomson N, Tatusova T, Cochrane G, Glöckner FO, Kottmann R, Lister AL, Tateno Y, Vaughan R. Comparative and Functional Genomics Volume 2007 (2007)
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Characterization of genes encoding novel peptidases in the biocontrol fungus Trichoderma harzianum CECT 2413 using the TrichoEST functional genomics approach.
Suárez MB, Vizcaíno JA, Llobell A, Monte E. Current genetics Volume 51 (2007) p.331-342 DOI: 10.1007/s00294-007-0130-5
Publication Committee meeting. HUPO 5th annual World Congress. Long Beach, CA, USA 30 October 2006.
Orchard S, Heck A, Uhlen M, Ping P. Proteomics Volume 7 (2007) p.1009-1011 DOI: 10.1002/pmic.200700015
The HUPO pre-congress Proteomics Standards Initiative workshop. HUPO 5th annual World Congress. Long Beach, CA, USA 28 October-1 November 2006.
Orchard S, Jones AR, Stephan C, Binz PA. Proteomics Volume 7 (2007) p.1006-1008 DOI: 10.1002/pmic.200700014
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Evolutionary and biomedical insights from the rhesus macaque genome.
Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Science (New York, N.Y.) Volume 316 (2007) p.222-234 DOI: 10.1126/science.1139247
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Recommendations of the 2006 Human Variome Project meeting.
Cotton RG, 2006 Human Variome Project, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M. Nature genetics Volume 39 (2007) p.433-436 DOI: 10.1038/ng2024
An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N. Molecular Biology and Evolution Volume 24 (2007) p.1464-1479 DOI: 10.1093/molbev/msm064
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature.
Laskowski RA. Bioinformatics Volume 23 (2007) p.1824-1827 DOI: 10.1093/bioinformatics/btm085
The geometry of interactions between catalytic residues and their substrates.
Torrance JW, Holliday GL, Mitchell JB, Thornton JM. Journal of molecular biology Volume 369 (2007) p.1140-1152 DOI: 10.1016/j.jmb.2007.03.055
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The implications of alternative splicing in the ENCODE protein complement.
Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A. Proceedings of the National Academy of Sciences of the United States of America Volume 104 (2007) p.5495-5500 DOI: 10.1073/pnas.0700800104
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Patterns of somatic mutation in human cancer genomes.
Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, Edkins S, O'Meara S, Vastrik I, Schmidt EE, Avis T, Barthorpe S, Bhamra G, Buck G, Choudhury B, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Cahill DP, Louis DN, Goldstraw P, Nicholson AG, Brasseur F, Looijenga L, Weber BL, Chiew YE, DeFazio A, Greaves MF, Green AR, Campbell P, Birney E, Easton DF, Chenevix-Trench G, Tan MH, Khoo SK, Teh BT, Yuen ST, Leung SY, Wooster R, Futreal PA, Stratton MR. Nature Volume 446 (2007) p.153-158 DOI: 10.1038/nature05610
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Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol.
Vizcaíno JA, Redondo J, Suárez MB, Cardoza RE, Hermosa R, González FJ, Rey M, Monte E. Applied microbiology and biotechnology Volume 75 (2007) p.853-862 DOI: 10.1007/s00253-007-0885-0
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Mouse Phenotype Database Integration Consortium: integration [corrected] of mouse phenome data resources.
Mouse Phenotype Database Integration Consortium, Hancock JM, Adams NC, Aidinis V, Blake A, Bogue M, Brown SD, Chesler EJ, Davidson D, Duran C, Eppig JT, Gailus-Durner V, Gates H, Gkoutos GV, Greenaway S, Hrabé de Angelis M, Kollias G, Leblanc S, Lee K, Lengger C, Maier H, Mallon AM, Masuya H, Melvin DG, Müller W, Parkinson H, Proctor G, Reuveni E, Schofield P, Shukla A, Smith C, Toyoda T, Vasseur L, Wakana S, Walling A, White J, Wood J, Zouberakis M. Mammalian genome : official journal of the International Mammalian Genome Society Volume 18 (2007) p.157-163 DOI: 10.1007/s00335-007-9004-x
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Cancer informatics in the U.K.: the NCRI informatics initiative.
Reddington F, Wilkinson JM, Clark R, Parkinson H, Kerr P, Begent R. Cancer informatics Volume 2 (2007) p.389-394
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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 SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U. BMC bioinformatics Volume 8 (2007) p.52 DOI: 10.1186/1471-2105-8-52
Shape variation in protein binding pockets and their ligands.
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. Journal of molecular biology Volume 368 (2007) p.283-301 DOI: 10.1016/j.jmb.2007.01.086
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, Gross C. Genome research Volume 17 (2007) p.320-327 DOI: 10.1101/gr.5755407
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ.
Siepen JA, Swainston N, Jones AR, Hart SR, Hermjakob H, Jones P, Hubbard SJ. Proteome science Volume 5 (2007) p.4 DOI: 10.1186/1477-5956-5-4
Entering the implementation era: a report on the HUPO-PSI Fall workshop 25-27 September 2006, Washington DC, USA.
Orchard S, Taylor CF, Jones P, Montechi-Palazzo L, Binz PA, Jones AR, Pizarro A, Julian RK, Hermjakob H. Proteomics Volume 7 (2007) p.337-339 DOI: 10.1002/pmic.200600915
Towards fully automated structure-based function prediction in structural genomics: a case study.
Watson JD, Sanderson S, Ezersky A, Savchenko A, Edwards A, Orengo C, Joachimiak A, Laskowski RA, Thornton JM. Journal of molecular biology Volume 367 (2007) p.1511-1522 DOI: 10.1016/j.jmb.2007.01.063
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Clinical proteomics: A need to define the field and to begin to set adequate standards.
Mischak H, Apweiler R, Banks RE, Conaway M, Coon J, Dominiczak A, Ehrich JH, Fliser D, Girolami M, Hermjakob H, Hochstrasser D, Jankowski J, Julian BA, Kolch W, Massy ZA, Neusuess C, Novak J, Peter K, Rossing K, Schanstra J, Semmes OJ, Theodorescu D, Thongboonkerd V, Weissinger EM, Van Eyk JE, Yamamoto T. Proteomics. Clinical applications Volume 1 (2007) p.148-156 DOI: 10.1002/prca.200600771
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Partial silencing of a hydroxy-methylglutaryl-CoA reductase-encoding gene in Trichoderma harzianum CECT 2413 results in a lower level of resistance to lovastatin and lower antifungal activity.
Cardoza RE, Hermosa MR, Vizcaíno JA, González F, Llobell A, Monte E, Gutiérrez S. Fungal genetics and biology : FG & B Volume 44 (2007) p.269-283 DOI: 10.1016/j.fgb.2006.11.013
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Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T. Genome research Volume 17 (2007) p.175-183 DOI: 10.1101/gr.5509507
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hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.
Lamesch P, Li N, Milstein S, Fan C, Hao T, Szabo G, Hu Z, Venkatesan K, Bethel G, Martin P, Rogers J, Lawlor S, McLaren S, Dricot A, Borick H, Cusick ME, Vandenhaute J, Dunham I, Hill DE, Vidal M. Genomics Volume 89 (2007) p.307-315 DOI: 10.1016/j.ygeno.2006.11.012
New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. Nucleic acids research Volume 35 (2007) p.D224-8 DOI: 10.1093/nar/gkl841
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InterPro and InterProScan: tools for protein sequence classification and comparison.
Mulder N, Apweiler R. Methods in molecular biology (Clifton, N.J.) Volume 396 (2007) p.59-70 DOI: 10.1007/978-1-59745-515-2_5
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Human Proteome Organization Proteomics Standards Initiative: Data Standardization, a View on Developments and Policy.
Martens L, Orchard S, Apweiler R, Hermjakob H. Mol Cell Proteomics Volume 6 (2007) p.1666-1667
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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics.
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J, Hardy N, Hermjakob H, Hubbard SJ, Hussey P, Igra M, Jenkins H, Julian RK Jr, Laursen K, Oliver SG, Paton NW, Sansone SA, Sarkans U, Stoeckert CJ Jr, Taylor CF, Whetzel PL, White JA, Spellman P, Pizarro A. Nat Biotechnol. (2007) p.1127-1133
Proteomic data exchange and storage: the need for common standards and public repositories.
Orchard S, Jones P, Taylor C, Zhu W, Julian RK, Hermjakob H, Apweiler R. Methods in molecular biology (Clifton, N.J.) Volume 367 (2007) p.261-270 DOI: 10.1385/1-59745-275-0:261
Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study.
Rustici G, van Bakel H, Lackner DH, Holstege FC, Wijmenga C, Bähler J, Brazma A. Genome biology Volume 8 (2007) p.R73 DOI: 10.1186/gb-2007-8-5-r73
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ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome.
Taussig MJ, Stoevesandt O, Borrebaeck CA, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M. Nature methods Volume 4 (2007) p.13-17 DOI: 10.1038/nmeth0107-13
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Gene and Protein Sequence Databases.
Martin M, Kulikova T, Pruess M, Apweiler R. Drug Discovery Technologies Elsevier, Oxford (3 edition)
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Evolutionary conservation of regulated longevity assurance mechanisms.
McElwee JJ, Schuster E, Blanc E, Piper MD, Thomas JH, Patel DS, Selman C, Withers DJ, Thornton JM, Partridge L, Gems D. Genome biology Volume 8 (2007) p.R132 DOI: 10.1186/gb-2007-8-7-r132
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM. Bioinformatics (Oxford, England) Volume 23 (2007) p.e104-9 DOI: 10.1093/bioinformatics/btl292
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The Universal Protein Resource (UniProt).
The UniProt Consortium. Nucl. Acids Res. Volume 35 (2007) p.D193-D197
Gene prediction: compare and CONTRAST.
Flicek P. Genome biology Volume 8 (2007) p.233 DOI: 10.1186/gb-2007-8-12-233
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Adding semantics in kinetics models of biochemical pathways
Le-Novere N, Courtot M, Laibe C. Proceedings of the 2nd International Symposium on experimental standard conditions of enzyme characterizations (2007) p.137-153
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Update of the Anopheles gambiae PEST genome assembly.
Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH. Genome biology Volume 8 (2007) p.R5 DOI: 10.1186/gb-2007-8-1-r5
The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R. Methods in molecular biology (Clifton, N.J.) Volume 406 (2007) p.1-21 DOI: 10.1007/978-1-59745-535-0_1
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MCP and HUPO: An Era of New Partnership.
Ping P, Apweiler R, Bergeron J. Mol Cell Proteomics Volume 6 (2007) p.951-952
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Variation of geometrical and phsicochemical properties in protein binding pockets and their ligands
Kahraman A, Morris RJ, Laskowski RA, Thornton JM. BMC Bioinformatics (8 edition)
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Evolving Methods for Macromolecular Crystallography
Watson J, Golovin A, Laskowski R, Henrick K, Thornton JM, Joachimiak A and Edwards A. Structural Bioinformatics: From Protein Structure to Function
Estimation and correction of non-specific binding in a large-scale spike-in experiment.
Schuster EF, Blanc E, Partridge L, Thornton JM. Genome biology Volume 8 (2007) p.R126 DOI: 10.1186/gb-2007-8-6-r126
Correcting for sequence biases in present/absent calls.
Schuster EF, Blanc E, Partridge L, Thornton JM. Genome biology Volume 8 (2007) p.R125 DOI: 10.1186/gb-2007-8-6-r125
Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Genome biology Volume 8 (2007) p.R39 DOI: 10.1186/gb-2007-8-3-r39