Carles Pons

Previous working experience

2011 - 15 Postdoctoral associate at the Computational Biology and Functional Genomics Lab of the University of Minnesota. Advisor: Prof. Chad Myers

2005 - 11 Ph.D. student at the Protein Interactions and Docking Group of the Barcelona Supercomputing Center. Advisor: Dr. Juan Fernandez-Recio

2004 - 11 Research assistant/supercomputing support at the Life Sciences Department of the Barcelona Supercomputing Center in partnership with the Spanish National Bioinformatics Institute. Supervisors: Prof. Alfonso Valenc

Publications

Becker JR, Pons C, Nguyen HD, Costanzo M, Boone C, Myers CL, Bielinsky AK. 5’ Flap-dependent activation of postreplicative repair MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM. A gene-centered in vivo regulatory network reveals complex transcription factor hierarchies

Pons C, Costanzo M, Boone C, Myers CL. Computational paradigms for analyzing genetic interaction networks. Book chapter in Systems genetics. Cambridge University Press (in press) Carles Pons, Ph.D. 1/424. Jimenez-Garcia B, Pons C, Svergun DI, Bernado P, Fernandez-Recio J. pyDockSAXS: protein–protein complex structure by SAXS and computational docking. Nucleic Acids Res doi: 10.1093/nar/gkv368 (2015)

DiPrima S, Haarer B, Viggiano S, Pons C, Myers CL, Amberg DC. Linking genetics to structural biology: Complex heterozygosity screening with actin alanine scan alleles identifies functionally related surfaces on yeast actin. G3 (Bethesda) 4:1491 (2014)

Pallara C, Jimenez‐Garcia B, Perez‐Cano L, Romero‐Durana M, Solernou M, Grosdidier S, Pons C, Moal IH, Fernandez‐Recio J. Expanding the frontiers of protein–protein modeling: From docking and scoring to binding affinity predictions and other challenges. Proteins 81:2192 (2013)

Reece-Hoyes JS*, Pons C*, Diallo A, Mori A, Shrestha S, Kadreppa S, Nelson J, DiPrima S, Dricot A, Lajoie BR, Moraes Ribeiro PS, Weirauch MT, Hill DE, Hughes TR, Myers CL, Walhout AJM. Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network. Molecular Cell 51:116

Jimenez-Garcia B, Pons C, Fernandez-Recio J. pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring. Bioinformatics 29:1698

Pons C, Fenwick RB, Salvatella X, Fernandez-Recio J. Validated conformational ensembles are key for the successful prediction of protein complexes. J Chem Theory Comput 9:1830

Emperador A, Solernou A, Sfriso P, Pons C, Gelpi JL, Fernandez-Recio J, Orozco M. Efficient relaxation of protein–protein interfaces by discrete molecular dynamics simulations. J Chem Theory Comput 9:1222 (2012)

Pons C, Jimenez-Gonzalez D, Gonzalez-Alvarez C, Servat H, Cabrera-Benitez D, Aguilar X, Fernandez-Recio J. Cell-Dock: high-performance protein-protein docking. Bioinformatics 28:2394

Masone D, Cabeza de Vaca I, Pons C, Fernandez-Recio J, Guallar V. H-bond network optimization in protein-protein complexes: Are all-atom force field scores enough? Proteins 80:818 (2011)

Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. J Mol Biol 414:289

Pons C, Glaser F, Fernandez-Recio J. Prediction of protein-binding areas by small-world residue networks and application to docking. BMC Bioinformatics 12:378 13. Wass MN, Fuentes G, Pons C, Pazos F, Valencia A. Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol 7:469

Pons C, Talavera D, de la Cruz X, Orozco M, Fernandez-Recio J. Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A new efficient potential for protein-protein docking. J Chem Inf Model 51:370

Pons C, D’Abramo M, Svergun DI, Orozco M, Bernado P, Fernandez-Recio J. Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J Mol Biol 403:217 (2010)

Gonzalez-Alvarez C, Servat H, Cabrera-Benitez D, Aguilar X, Pons C, Fernandez-Recio J, Jimenez-Gonzalez D. Drug design on the Cell BE. Book chapter in Scientific computing with multicore and accelerators. Computational Science Series, Chapman & Hall / CRC

Pons C, Solernou A, Perez-Cano L, Grosdidier S, Fernandez-Recio J. Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding. Proteins 78:3182

Perez-Cano L, Solernou A, Pons C, Fernandez-Recio J. Structural prediction of protein-RNA interaction by computational docking with propensity-based statistical potentials. Pac Symp Biocomput 2010:293 Carles Pons, Ph.D.

Pons C, Grosdidier S, Solernou A, Perez-Cano L, Fernandez-Recio J. Present and future challenges and limitations in protein-protein docking. Proteins 78:95 2009

D'Abramo M, Meyer T, Bernado P, Pons C, Fernandez-Recio J, Orozco M. On the use of low-resolution data to improve structure prediction of proteins and protein complexes. J Chem Theory Comput 5:3129

Mosca R, Pons C, Fernandez-Recio J, Aloy P. Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PLoS Comput Biol 5:e1000490

Garzon JI, Lopez-Blanco JR, Pons C, Kovacs J, Abagyan R, Fernandez-Recio J, Chacon P. FRODOCK: a new approach for fast rotational protein-protein docking. Bioinformatics 25:2544

Izarzugaza JM, Juan D, Pons C, Pazos F, Valencia A. Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics 9:35 (2008)

Grosdidier S, Pons C, Solernou A, Fernandez-Recio J. Prediction and scoring of docking poses with pyDock. Proteins 69:852 (2007)

Izarzugaza JM, Juan D, Pons C, Ranea JA, Valencia A, Pazos F. TSEMA: interactive prediction of protein pairings between interacting families. Nucleic Acids Res 34:315 (2006)