Structural and Computational Biology Programme, CNIO   Michael Tress   List of Publications   CNIO

 
Genome Annotation
>19,000 coding genes? Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vázquez J, Valencia A, Tress ML. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet. 2014 23:5866-78. [ paper ]

The GENCODE Consortium. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012 22:1760-74. [ paper ]

The ENCODE Project. An integrated encyclopedia of DNA elements in the human genome. Nature 2012 489:57-74. [ paper ]

The ENCODE Project. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 9:e1001046. [ paper ]

The ENCODE Project. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816(2007). [ paper ]


Alternative Splicing
>Alternative Splicing, Proteome Complexity Tress ML, Abascal F, Valencia A. Alternative Splicing May Not Be the Key to Proteome Complexity. Trends Biochem Sci. 2016 Sep 16. pii: S0968-0004(16)30118-9. [ Article in TIBS ][ PDF ]

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 Comput Biol. 2015 Jun 10;11(6):e1004325. [ Paper ]

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. J Proteome Res. 2015 14:1880-7. [ paper ]

Abascal F, Tress ML, Valencia A. Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. Bioinformatics. 2015 31:2257-61. [ paper ]

Abascal F, Tress ML, Valencia A. The evolutionary fate of alternatively spliced homologous exons after gene duplication. Genome Biol Evol. 2015 7:1392-403. [ paper ]

Rodriguez JM, Carro A, Valencia A, Tress ML. APPRIS WebServer and WebServices. Nucleic Acids Res. 2015 43:W455-9. [ paper ][ APPRIS database ]

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 Res. 2013 41:D110-7. [ paper ][ APPRIS database ]

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. Mol Biol Evol. 2012 29:2265-83. [ paper ]

Tress ML, Bodenmiller B, Aebersold R, Valencia A. Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biol. 2008 9(11):R162.

Tress M, Casadio R, Giorgetti A, Hallin PF, Juncker AS, Kulberkyte E, Martelli PL, Raimondo D, Reeves GA, Thornton JM, Tramontano A, Wang K, Wesselink JJ, Valencia A. "Alternative Splicing in the ENCODE Protein Complement" in Modern Genome Annotation: the Biosapiens Network. D. Frishman and A. Valencia (Eds) Springer, Wien New York 2009. ISBN 978-3-211-75122-0.

Tress ML, Wesselink JJ, Frankish A, Lopez G, Goldman N, Loytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics. 2008. 24:11-17.    [paper][ APPRIS database ]

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PL, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, Lopez G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Storling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramirez 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. The implications of alternative splicing in the ENCODE protein complement. PNAS 104:5495-5500 (2007).    [paper]


Proteomics
>Human Proteome Drafts 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 Rev Proteomics. 2015 12:579-93. [ Paper ]

Ezkurdia I, Vázquez J, Valencia A, Tress M. Analyzing the first drafts of the human proteome. J Proteome Res. 2014 13:3854-5. [ Paper ]

Function Prediction
>CASP 7 Function CAFA function Predictors. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 17:184. [paper]

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 Res. 2014 42:D267-72. [paper][ FireDB ]

Lopez G, Maietta P, Rodriguez JM, Valencia A, Tress ML. firestar--advances in the prediction of functionally important residues. Nucleic Acids Res. 2011 39:W235-41. [paper][ firestar ]

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 Biol. 10:206 (2009).    [paper]

Lopez G, Ezkurdia I, Tress ML. Assessment of ligand binding residue predictions in CASP8. Proteins. 2009 77(S9):138-146.  [paper]

Tress ML, Bujnicki JM, Lopez G, Valencia A. "Integrating Prediction of Structure, Function, and Interactions" in Prediction of Protein Structures, Functions, and Interactions. JM. Bujnicki (Ed) John Wiley & Sons. 2008. ISBN 978-0-470-51767-3.

Watson JD, Thornton JM, Tress ML, Lopez G, Valencia A, Redfern O, Orengo CA, Sommer I, Domingues FS. "Structure to function" in Modern Genome Annotation: the Biosapiens Network. D. Frishman and A. Valencia (Eds) Springer, Wien New York 2009. ISBN 978-3-211-75122-0.

Lopez G, Valencia A, Tress ML. FireDB - a database of functionally important residues from proteins of known structure NAR 35:D219-D223 (2007).    [paper] [ FireDB ]

Lopez G, Valencia A, Tress ML. firestar--prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res. 2007 35(Web Server issue):W573-7.[paper][ firestar ]

Lopez G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins, 69(S8):165-74 (2007).  [paper]


Structural Domains
CASP 8 domains Ezkurdia I, Tress ML. Protein structural domains: definition and prediction. Curr Protoc Protein Sci. 2011 Chapter 2:Unit2.14. [paper]

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins. 2009 77(S9), 196-209.   [paper]

Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins. 2009 77(S9):10-17.  [paper]

Tress ML, 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(S8):137-51 (2007).   [paper]

Clarke ND, Ezkurdia I, Kopp J, Read RJ, Schwede T, Tress M. Domain definition and target classification for CASP7. Proteins, 69(S8):10-18 (2007).  [paper]

Tress ML, Tai C-H, Wang G, Ezkurdia I, López G, Valencia A, Lee BK, Dunbrack R. Domain definition and target classification for CASP6. Proteins, 61(S7):8-18 (2005).  [paper]

Structure Prediction
CASP Tress ML, Ezkurdia I, Graña O, López G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins, 61(S7):27-45 (2005).   [paper]

Tress ML, Tai C-H, Wang G, Ezkurdia I, López G, Valencia A, Lee BK, Dunbrack R. Domain definition and target classification for CASP6. Proteins, 61(S7):8-18 (2005).  [paper]

Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A. Empirical limits for template-based protein structure prediction: the CASP5 example. FEBS Letters, 579:1203 (2005).  [paper]

Tress ML, Graña O, Valencia A. SQUARE-determining reliable regions in sequence alignments. Bioinformatics 20:974-975 (2004). [paper][server][ SQUARE ]

Tress ML, Jones D, Valencia A. Predicting Reliable Regions in Protein Alignments from Sequence Profiles. J. Mol. Biol. 330:705-718 (2003).  [paper] 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. 1999 Suppl 3:104-11. [paper]

Contact Prediction
CASP 8 contacts Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins. 2010 78(8):1980-91.   [paper]

Ezkurdia I, Graña O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins. 2009 77(S9), 196-209.   [paper]

Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND.. Assessment of intramolecular contact predictions for CASP7. Proteins, 69(S8), 152-158:(2007).   [paper]

Graña O, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins, 61(S7), 214-224:(2005).   [paper]


Miscellaneous
Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors Manso L, Mourón S, Tress M, Gómez-López G, Morente M, Ciruelos E, Rubio-Camarillo M, Rodriguez-Peralto JL, Pujana MA, Pisano DG, Quintela-Fandino M. Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance. PLoS One. 2016 May 19;11(5):e0155840. [paper]

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. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012 7:e28213. [paper]

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 Res. 2012 22:1231-42. [paper]

Ezkurdia I, Bartoli L, Fariselli P, Casadio R, Valencia A, Tress ML. Progress and challenges in predicting protein-protein interaction sites. Brief Bioinform. 10:233-246 (2009).  [paper]

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 Res. 34:W110-5 (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 (2006).    [paper]

Tress ML, Juan D, Graña O, Gómez MJ, Gómez-Puertas P, González JM, López G, Valencia A. Scoring Docking Models with Evolutionary Information. Proteins 60:275-280 (2005).  [paper]

Contact: mtress AT cnio.es

Michael Tress
Structural and Computational Biology Programme
Spanish National Cancer Research Centre
Calle Melchor Fernandez Almagro, 3,
28029 MADRID. Tel: (+34) 91 372 8000   Fax: (+34) 912 246 900

Thanks to Petr Sobola for the skater.