|
|
|
Ezkurdia I, Graña O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins, 77(S9), 196-209:(2009). [paper]
Tress ML, Ezkurdia I, Richardson JS. Target domain definition and classification in CASP8. Proteins, 77(S9):10-17 (2009). [paper]
Lopez G, Ezkurdia I, Tress ML. Assessment of ligand binding residue predictions in CASP8. Proteins, 77(S9):138-146 (2009). [paper]
|
| Expression of Alternative Isoforms |
|
We demonstrated that alternatively splice variants are expressed in as proteins Drosophila, and that they are expressed in sufficient quantities and are stable enough to be detectable in proteomics experiments.
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.
|
| Alternative Splice Isoforms in ENCODE |
|
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]
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]
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).
|
| Predicting Functionally Important Residues |
|
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 database]
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 server]
Tress ML, Jones D, Valencia A. Predicting Reliable Regions in Protein Alignments from Sequence Profiles. J. Mol. Biol. 330:705-718 (2003). [paper]
Tress ML, Graña O, Valencia A. SQUARE-determining reliable regions in sequence alignments. Bioinformatics 20:974-975 (2004). [pdf] [server]
|
The BioSapiens consortium have released a book detailing the work done by the Network of Excellence and a series of follow-up articles.
D. Frishman and A. Valencia (Eds) Modern Genome Annotation. The BioSapiens Network. Springer, Wien New York 2009. ISBN 978-3-211-75122-0
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]
|
CASP7.5, the second between CASP meeting, was held at The Spanish National Cancer Research Centre in Madrid on April 21-23, 2008.
|
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]
Izarzugaza JM, Graña O, Tress ML, Valencia A, Clarke ND.. Assessment of intramolecular contact predictions for CASP7. Proteins, 69(S8), 152-158:(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]
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]
|
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]
Graña O, Tress ML, Valencia A. CASP6 assessment of contact prediction. Proteins, 61(S7), 214-224:(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]
|
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]
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]
|
|
|
|
Traffic - Indispensible in Gallardon's Madrid
|
|
|
|
|
Unchecked Traffic + Sun - Find out one day too late how crap the air was.
|
|
|
|
|
