Gonzalo Lopez

Gonzalo Lopez

Titles

Research Associate, Jon Maris Lab, Children's Hospital of Philadelphia

Phone

(212) 851-5456

Gonzalo Lopez is an associate research scientist in the laboratory of Andrea Califano. The aim of his work is to gain a better understanding of tumor heterogeneity in order to contribute to the design of future personalized medicine strategies. Specifically, he works on the integration of multiple types of genomic data derived from neuroblastoma patients to identify novel molecular subtypes and subsequently describe their specific genetic/epigenetic alterations and associated phenotypic effects.

Prior to arriving at Columbia University Gonzalo worked in Alfonso Valencia’s lab at Spanish National Cancer Research Center (CNIO), where he obtained his PhD. His thesis focused on understanding the evolutionary basis of protein-small molecule binding and its applications for protein function annotation and functional genomics.


Education History

PhD, Autonoma University of Madrid (UAM)
Molecular Biology

MS, Complutense University of Madrid (UCM)
Bioinformatics and Computational Biology

BS/MS, Autonoma University of Madrid (UAM)
Biological Sciences


Publications

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 Jan 1;42(1):D267-72.

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 Jan;41:D110-7.

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

Tendulkar AV, Krallinger M, de la Torre V, López G, Wangikar PP, Valencia A. FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PLoS One. 2010 Mar 18;5(3):e9679.  

López G, Ezkurdia I, Tress ML. Assessment of ligand binding residue predictions in CASP8. Proteins. 2009;77 Suppl 9:138-46.

Tress ML, Wesselink JJ, Frankish A, Lopez G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics. 2008 Jan 1;24(1):11-7.

López G, Rojas A, Tress M, Valencia A. Assessment of predictions submitted for the CASP7 function prediction category. Proteins. 2007;69 Suppl 8:165-74.

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, et al. The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500.

López G, Valencia A, Tress ML. Firestar - Prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res. 2007 Jul;35:W573-7.

Lopez G, Valencia A, Tress M. FireDB - a database of functionally important residues from proteins of known structure. Nucleic Acids Res. 2007 Jan;35:D219-23. 

Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins. 2005;61 Suppl 7:27-45.

Tress M, Tai CH, Wang G, Ezkurdia I, Lopez G, Valencia A, Lee B, Dunbrack RL Jr. Domain definition and target classification for CASP6. Proteins. 2005;61 Suppl 7:8-18.     

Tress M, de Juan D, Grana O, Gomez MJ, Gomez-Puertas P, Gonzalez JM, Lopez G, Valencia A. Scoring docking models with evolutionary information. Proteins. 2005 Aug 1;60(2):275-80.

Book Chapters

Tress M, Bujniki JM, López G, Valencia A. Integrating pediction of structure, function and interactions. In Prediction of Protein Structure, Function and Interactions, Janusz M. Bujnicki, ed.  Hoboken: John Wiley & Sons. 2009.

Watson JD, Thornton JM, Tress ML, López G, Valencia A, Redfern O, Orengo CA, Sommer I, Domingues FS. Structure to function. In Modern Genome Annotation (The Biosapiens Network). Dmitrij Frishman, Alfonso Valencia, eds. New York: Springer. 2008.


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