Michael Tress - Publications

Affiliations: 
Centro Nacional de Biotecnología, Madrid, Comunidad de Madrid, Spain 

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML. Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Research. PMID 30395326 DOI: 10.1093/nar/gky1146  0.72
2018 Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, ... ... Tress ML, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. PMID 30357393 DOI: 10.1093/nar/gky955  0.44
2018 Abascal F, Juan D, Jungreis I, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML. Loose ends: almost one in five human genes still have unresolved coding status. Nucleic Acids Research. PMID 29982784 DOI: 10.1093/nar/gky587  0.72
2018 Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. 28: 1096. PMID 29967126 DOI: 10.1101/gr.239137.118  0.64
2018 Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, et al. SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Research. PMID 29440222 DOI: 10.1101/gr.222976.117  0.64
2017 Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML. APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Research. PMID 29069475 DOI: 10.1093/nar/gkx997  1
2017 Tress ML, Abascal F, Valencia A. Most Alternative Isoforms Are Not Functionally Important. Trends in Biochemical Sciences. 42: 408-410. PMID 28483377 DOI: 10.1016/j.tibs.2017.04.002  1
2016 Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, ... ... Tress ML, et al. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology. 17: 251. PMID 27964752 DOI: 10.1186/s13059-016-1090-1  1
2016 Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends in Biochemical Sciences. PMID 27712956 DOI: 10.1016/j.tibs.2016.08.008  1
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Tress ML, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/s13059-016-1037-6  1
2015 Ezkurdia I, Calvo E, Del Pozo A, Vázquez J, Valencia A, Tress ML. The potential clinical impact of the release of two drafts of the human proteome. Expert Review of Proteomics. 12: 579-593. PMID 26496066 DOI: 10.1586/14789450.2015.1103186  1
2015 Abascal F, Ezkurdia I, Rodriguez-Rivas J, Rodriguez JM, Del Pozo A, Vázquez J, Valencia A, Tress ML. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. Plos Computational Biology. 11: e1004325. PMID 26061177 DOI: 10.1371/journal.pcbi.1004325  1
2015 Rodriguez JM, Carro A, Valencia A, Tress ML. APPRIS WebServer and WebServices. Nucleic Acids Research. PMID 25990727 DOI: 10.1093/nar/gkv512  1
2015 Abascal F, Tress ML, Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biology and Evolution. 7: 1392-403. PMID 25931610 DOI: 10.1093/gbe/evv076  1
2015 Ezkurdia I, Vázquez J, Valencia A, Tress M. Correction to "Analyzing the first drafts of the human proteome". Journal of Proteome Research. 14: 1991. PMID 25756922 DOI: 10.1021/acs.jproteome.5b00186  1
2015 Abascal F, Tress ML, Valencia A. Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinformatics (Oxford, England). PMID 25735770 DOI: 10.1093/bioinformatics/btv132  1
2015 Ezkurdia I, Rodriguez JM, Carrillo-de Santa Pau E, Vázquez J, Valencia A, Tress ML. Most highly expressed protein-coding genes have a single dominant isoform. Journal of Proteome Research. 14: 1880-7. PMID 25732134 DOI: 10.1021/pr501286b  1
2014 Ezkurdia I, Vázquez J, Valencia A, Tress M. Analyzing the first drafts of the human proteome. Journal of Proteome Research. 13: 3854-5. PMID 25014353 DOI: 10.1021/pr500572z  1
2014 Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Human Molecular Genetics. 23: 5866-78. PMID 24939910 DOI: 10.1093/hmg/ddu309  1
2014 Maietta P, Lopez G, Carro A, Pingilley BJ, Leon LG, Valencia A, Tress ML. FireDB: a compendium of biological and pharmacologically relevant ligands. Nucleic Acids Research. 42: D267-72. PMID 24243844 DOI: 10.1093/nar/gkt1127  1
2013 Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Research. 41: D110-7. PMID 23161672 DOI: 10.1093/nar/gks1058  1
2012 Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, ... ... Tress M, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Research. 22: 1760-74. PMID 22955987 DOI: 10.1101/gr.135350.111  1
2012 Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A. Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Research. 22: 1231-42. PMID 22588898 DOI: 10.1101/gr.130062.111  1
2012 Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function. Molecular Biology and Evolution. 29: 2265-83. PMID 22446687 DOI: 10.1093/molbev/mss100  1
2012 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, ... ... Tress ML, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/journal.pone.0028213  1
2011 Ezkurdia I, Tress ML. Protein structural domains: definition and prediction. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. Unit2.14. PMID 22045561 DOI: 10.1002/0471140864.ps0214s66  1
2011 Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML. firestar--advances in the prediction of functionally important residues. Nucleic Acids Research. 39: W235-41. PMID 21672959 DOI: 10.1093/nar/gkr437  1
2010 Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins. 78: 1980-91. PMID 20408174 DOI: 10.1002/prot.22714  1
2009 López G, Ezkurdia I, Tress ML. Assessment of ligand binding residue predictions in CASP8. Proteins. 77: 138-46. PMID 19714771 DOI: 10.1002/prot.22557  1
2009 Ezkurdia I, Graña O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins. 77: 196-209. PMID 19714769 DOI: 10.1002/prot.22554  1
2009 Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins. 77: 10-7. PMID 19603487 DOI: 10.1002/prot.22497  1
2009 Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Briefings in Bioinformatics. 10: 233-46. PMID 19346321 DOI: 10.1093/bib/bbp021  1
2009 Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, Bork P, von Heijne G, Valencia A, Ouzounis CA, Casadio R, Brunak S. Sequence-based feature prediction and annotation of proteins. Genome Biology. 10: 206. PMID 19226438 DOI: 10.1186/gb-2009-10-2-206  1
2008 Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biology. 9: R162. PMID 19017398 DOI: 10.1186/gb-2008-9-11-r162  1
2008 Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/bioinformatics/btm547  1
2008 Tress ML, Casadio R, Giorgetti A, Hallin PF, Juncker AS, Kulberkyte E, Martelli P, Raimondo D, Reeves GA, Thornton JM, Tramontano A, Wang K, Wesselink JJ, Valencia A. Alternative splicing in the ENCODE protein complement Modern Genome Annotation: the Biosapiens Network. 453-484. DOI: 10.1007/978-3-211-75123-7_20  1
2008 Watson JD, Thornton JM, Tress ML, Lopez G, Valencia A, Redfern O, Orengo CA, Sommer I, Domingues FS. Structure to function Modern Genome Annotation: the Biosapiens Network. 239-262. DOI: 10.1007/978-3-211-75123-7_12  1
2008 Bujnicki JM, Tress M, Lopez G, Valencia A. Integrating Prediction of Structure, Function, and Interactions Prediction of Protein Structures, Functions, and Interactions. 259-279. DOI: 10.1002/9780470741894.ch11  1
2007 Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/prot.21675  1
2007 Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND. Assessment of intramolecular contact predictions for CASP7. Proteins. 69: 152-8. PMID 17671976 DOI: 10.1002/prot.21637  1
2007 Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M. Domain definition and target classification for CASP7. Proteins. 69: 10-8. PMID 17654725 DOI: 10.1002/prot.21686  1
2007 López G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins. 69: 165-74. PMID 17654548 DOI: 10.1002/prot.21651  1
2007 López G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Research. 35: W573-7. PMID 17584799 DOI: 10.1093/nar/gkm297  1
2007 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, ... ... Tress ML, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  0.44
2007 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, et al. The implications of alternative splicing in the ENCODE protein complement. Proceedings of the National Academy of Sciences of the United States of America. 104: 5495-500. PMID 17372197 DOI: 10.1073/pnas.0700800104  1
2007 Lopez G, Valencia A, Tress M. FireDB--a database of functionally important residues from proteins of known structure. Nucleic Acids Research. 35: D219-23. PMID 17132832 DOI: 10.1093/nar/gkl897  1
2006 Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM. TreeDet: a web server to explore sequence space. Nucleic Acids Research. 34: W110-5. PMID 16844971 DOI: 10.1093/nar/gkl203  1
2006 Tress ML, Cozzetto D, Tramontano A, Valencia A. An analysis of the Sargasso Sea resource and the consequences for database composition. Bmc Bioinformatics. 7: 213. PMID 16623953 DOI: 10.1186/1471-2105-7-213  1
2005 Graña O, Baker D, MacCallum RM, Meiler J, Punta M, Rost B, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins. 61: 214-24. PMID 16187364 DOI: 10.1002/prot.20739  1
2005 Tress M, Ezkurdia I, Graña O, López G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 61: 27-45. PMID 16187345 DOI: 10.1002/prot.20720  1
2005 Tress M, Tai CH, Wang G, Ezkurdia I, López G, Valencia A, Lee B, Dunbrack RL. Domain definition and target classification for CASP6. Proteins. 61: 8-18. PMID 16187342 DOI: 10.1002/prot.20717  1
2005 Tress M, de Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A. Scoring docking models with evolutionary information. Proteins. 60: 275-80. PMID 15981273 DOI: 10.1002/prot.20570  1
2005 Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A. Empirical limits for template-based protein structure prediction: the CASP5 example. Febs Letters. 579: 1203-7. PMID 15710414 DOI: 10.1016/j.febslet.2005.01.014  1
2004 Tress ML, Graña O, Valencia A. SQUARE--determining reliable regions in sequence alignments. Bioinformatics (Oxford, England). 20: 974-5. PMID 14764569 DOI: 10.1093/bioinformatics/bth032  1
2003 Tress ML, Jones D, Valencia A. Predicting reliable regions in protein alignments from sequence profiles. Journal of Molecular Biology. 330: 705-18. PMID 12850141  1
1999 Jones DT, Tress M, Bryson K, Hadley C. Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure. Proteins. 104-11. PMID 10526358 DOI: 10.1002/(SICI)1097-0134(1999)37:3+<104::AID-PROT14>3.0.CO;2-P  1
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