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Results: 1 to 20 of 25

1.

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML.

Hum Mol Genet. 2014 Jun 16. pii: ddu309. [Epub ahead of print]

PMID:
24939910
[PubMed - as supplied by publisher]
Free Article
2.

FireDB: a compendium of biological and pharmacologically relevant ligands.

Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML.

Nucleic Acids Res. 2014 Jan;42(Database issue):D267-72. doi: 10.1093/nar/gkt1127. Epub 2013 Nov 15.

PMID:
24243844
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

APPRIS: annotation of principal and alternative splice isoforms.

Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML.

Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7. doi: 10.1093/nar/gks1058. Epub 2012 Nov 17.

PMID:
23161672
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.

PMID:
22955616
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

PMID:
22446687
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4.

PMID:
22238572
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Protein structural domains: definition and prediction.

Ezkurdia I, Tress ML.

Curr Protoc Protein Sci. 2011 Nov;Chapter 2:Unit2.14. doi: 10.1002/0471140864.ps0214s66.

PMID:
22045561
[PubMed - indexed for MEDLINE]
8.

firestar--advances in the prediction of functionally important residues.

Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W235-41. doi: 10.1093/nar/gkr437. Epub 2011 Jun 14.

PMID:
21672959
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Predicted residue-residue contacts can help the scoring of 3D models.

Tress ML, Valencia A.

Proteins. 2010 Jun;78(8):1980-91. doi: 10.1002/prot.22714.

PMID:
20408174
[PubMed - indexed for MEDLINE]
10.

Assessment of ligand binding residue predictions in CASP8.

López G, Ezkurdia I, Tress ML.

Proteins. 2009;77 Suppl 9:138-46. doi: 10.1002/prot.22557.

PMID:
19714771
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8.

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML.

Proteins. 2009;77 Suppl 9:196-209. doi: 10.1002/prot.22554.

PMID:
19714769
[PubMed - indexed for MEDLINE]
12.

Target domain definition and classification in CASP8.

Tress ML, Ezkurdia I, Richardson JS.

Proteins. 2009;77 Suppl 9:10-7. doi: 10.1002/prot.22497.

PMID:
19603487
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Progress and challenges in predicting protein-protein interaction sites.

Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML.

Brief Bioinform. 2009 May;10(3):233-46. doi: 10.1093/bib/bbp021. Epub 2009 Apr 3.

PMID:
19346321
[PubMed - indexed for MEDLINE]
Free Article
14.

Sequence-based feature prediction and annotation of proteins.

Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S.

Genome Biol. 2009 Feb 2;10(2):206. doi: 10.1186/gb-2009-10-2-206.

PMID:
19226438
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

Tress ML, Bodenmiller B, Aebersold R, Valencia A.

Genome Biol. 2008;9(11):R162. doi: 10.1186/gb-2008-9-11-r162. Epub 2008 Nov 18.

PMID:
19017398
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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. 2008 Jan 1;24(1):11-7. Epub 2007 Nov 15.

PMID:
18006548
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Assessment of intramolecular contact predictions for CASP7.

Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND.

Proteins. 2007;69 Suppl 8:152-8.

PMID:
17671976
[PubMed - indexed for MEDLINE]
18.

firestar--prediction of functionally important residues using structural templates and alignment reliability.

López G, Valencia A, Tress ML.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W573-7. Epub 2007 Jun 21.

PMID:
17584799
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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. 2007 Jun 14;447(7146):799-816.

PMID:
17571346
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.

PMID:
17372197
[PubMed - indexed for MEDLINE]
Free PMC Article

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