José Garzón

Overview

José Garzón

Titles

Postdoctoral Research Scientist

Phone
+1 212-851-4656
Email
jig2114@columbia.edu

Lab

Barry Honig

José I. Garzón is an associate research scientist in the laboratory of Barry Honig. His current research is related to the design and implementation of methods for the prediction of protein-protein interactions on a genome-wide scale and their integration with systems biology approaches. The goal of this approach is to integrate structural evidence with functional, evolutionary, and expression data to produce wide and highly reliable predictions. Finally, the predicted set of interactions in the human genome produced by this approximation will be employed to understand disease mechanisms through the structure-enabled annotation of disease mechanisms through the structure-enabled annotation of disease-related SNPs and determination of cancer protein-protein interactions.

Prior to his recruitment for Honig's group, José was a member of  Pablo Chacón's group at the Centro Superior de Investigaciones Cientificas (CSIC) in Spain, where he earned his PhD in computer sciences. In the Chacón Group he implemented new, efficient applications for the resolution of a variety of structural bioinformatics docking problems. He also designed strategies for running these applications on grid computing platforms, improving their execution with cache mechanics.

Education History

PhD, Universidad Computense, Madrid, Spain

Bsc, Universidad de Granada, Spain
Computer Sciences

Publications

Garzón JI, Deng L, Murray D, Shapira S, Petrey D, Honig B. A computational interactome and functional annotation for the human proteome. Elife. 2016 Oct 22;5. pii: e18715.

Soner S., Ozbek P., Garzon J. I., Ben-Tal N., Haliloglu T. DynaFace: discrimination between obligatory and non-obligatory protein-protein interactions based on the complex’s dynamics. PLoS Computational Biology . 2015;11(10)

Chen TS, Petrey D, Garzon JI, Honig B. Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput Biol. 2015 May 4;11(5):e1004248.

Petrey D, Chen TS, Deng L, Garzon JI, Hwang H, Lasso G, Lee H, Silkov A, Honig B. Template-based prediction of protein function. Curr Opin Struct Biol. 2015 Feb 9;32C:33-38.

Krüger DM, Ignacio Garzón J, Chacón P, Gohlke H. DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking. PLoS One. 2014 Feb 21;9(2):e89466.

Garcia S, Ramirez-Aportela E, Garzón JI, Chacón P, Montemayor AS, Cabido R. FRODRUG: A Virtual Screening GPU Accelerated Approach for Drug Discovery. 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP). 2014: 594-600

Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Res. 2013 Jan;41(Database issue):D828-33.

Lopéz-Blanco JR, Garzón JI, Chacón P. iMod: multipurpose normal mode analysis in internal coordinates. Bioinformatics. 2011 Oct 15;27(20):2843-50.

Krüger DM, Garzón JI, Montes PC, Gohlke H. Predicting protein-protein interactions with DrugScorePPI: fully-flexible docking, scoring, and in silico alanine-scanning. J. Cheminform. 2011;3(Suppl 1):P36.

Garzón JI, Huedo E, Montero RS, Llorente IM, Chacón P. End-to-end cache system for grid computing: design and efficiency analysis of a high-throughput bioinformatic docking application. Int J. High Perform C. 2010;24(3):243-64.

Garzon JI, Lopéz-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P. FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics. 2009 Oct 1;25(19):2544-51.

Garzón JI, Kovacs J, Abagyan R, Chacón P. ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 2007 Feb 15;23(4):427-33.

Garzón JI, Kovacs J, Abagyan R, Chacón P. DFprot: a webtool for predicting local chain deformability. Bioinformatics. 2007 Apr 1;23(7):901-2.

Garzón JI, Huedo E, Montero RS, Llorente IM, Chacón P. Adaptation of a multi-resolution docking bioinformatics application to the grid. J Software. 2007;2(2):1-10. (2007)

Garzón JI, Huedo E, Montero RS, Llorente IM, Chacón P. Grid multi-resolution docking. 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP). 2007: 3-10