Carles Corbi-Verge

Carles Corbi-Verge

Scientist, Computational Biologist, Data Analyst, Machine Learning Engineer, and geek

Publications

For an overview of citations of my papers, please view my Google Scholar profile.

High-Troughput experiments analysis.

Keywords: Data integration, Data Visualization, Molecular Biology, Peptides, Protein-Protein Interactions, Systems Biology, Math and Statistics, Supervised models, Computational Biology

• The geometric influence on the Cys2His2 zinc finger domain and functional plasticity. Nucleic Acids Res. 2020. Mueller AL, Corbi-Verge C*, Giganti DO, Ichikawa DM, Spencer JM, MacRae M, Garton M, Kim PM, Noyes MB. [PMID], [CODE]

• A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions. ACS Synth Biol. 2019. Ichikawa DM, Corbi-Verge C*, Shen MJ, Snider J, Wong V, Stagljar I, Kim PM, Noyes MB. [PMID], [CODE]

• A PxL motif conveys timely cell cycle substrate dephosphorylation by the Cdc14 phosphatase. Nat Struct Mol Biol 2018. Kataria M, Mouilleron S, Moon-Hyeong Seo, Corbi-Verge C , Kim PM, Uhlmann F.
[PMID], [CODE]

• Protein engineering by highly parallel screening of computationally designed variants. Sci Adv. 2016. Sun MG, Seo MH, Nim S, Corbi-Verge C, Kim PM. [PMID]

• Pooled screening for antiproliferative inhibitors of protein-protein interactions. Nat Chem Biol. 2016. Nim S, Jeon J, Corbi-Verge C, Seo MH, Ivarsson Y, Moffat J, Tarasova N, Kim PM. [PMID]

• Strategies to develop inhibitors of motif-mediated protein-protein interactions as drug leads. Annu Rev Pharmacol Toxicol. 2017. Corbi-Verge C*, Garton M, Nim S, Kim PM. [PMID]

• Motif mediated protein-protein interactions as drug targets. Cell Commun Signal. 2016. Corbi-Verge C*, Kim PM. [PMID]

Building and design of predictive models.

Keywords: Data engineering, Structural Biology, Proteins, Protein-Protein Interactions, Data Science, Supervised and Unsupervised models, Structural Computational Biology, Math and Statistics.

• Predicting changes in protein stability caused by mutation using sequence- and structure-based methods in a CAGI5 blind challenge. Human Mutation. 2019. Strokach A, Corbi-Verge C, Teyra J, Kim PM. [PMID]

• Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Human Mutation. 2019. Castrense Savojardo, Maria Petrosino, Giulia Babbi, Samuele Bovo, Carles Corbi‐Verge, Rita Casadio, Piero Fariselli, Lukas Folkman, Aditi Garg, Mostafa Karimi, Panagiotis Katsonis, Philip M Kim, Olivier Lichtarge, Pier Luigi Martelli, Alessandra Pasquo, Debnath Pal, Yang Shen, Alexey V Strokach, Paola Turina, Yaoqi Zhou, Gaia Andreoletti, Steven E Brenner, Roberta Chiaraluce, Valerio Consalvi, Emidio Capriotti. [PMID]

• Predicting the effect of mutations on protein folding and protein-protein interaction. Methods Mol Biol. 2019. Strokach A, Corbi-Verge C, Teyra J, Kim PM. [PMID]

• Rapid and Accurate Structure‐Based Therapeutic Peptide Design using GPU Accelerated Thermodynamic Integration. Proteins 2018. Garton M, Corbi-Verge C*, Hu Y, Nim S, Sherborne B, Kim PM. [PMID], [CODE]

• Semi-supervised Learning Predicts Approximately One-Third of the Alternative Splicing Isoforms as Functional Proteins. Cell Rep. 2015. Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM. [PMID], [CODE]

• RNApulse, A pipeline for identification of novel isoforms. (In preparation) Corbi-Verge C, Kim PM. [CODE]

Protein structure and conformation analysis.

Keywords: Structural Biology, Proteins, Protein-Protein Interactions, Molecular Biology, Data analytics, Biophysics, Structural Computational Biology, Math and Statistics.

• Binding Site Plasticity in Viral PPxY Late Domain Recognition by the Third WW Domain of Human NEDD4 Sci Rep. 2019. Iglesias-Bexiga M, Palencia A, Corbi-Verge C, Martin-Malpartida P, Blanco FJ, Macias MJ, Cobos ES, Luque I. [PMID]

• Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores. J Mol biol 2018. Ben-David M, Huang H, Sun MGF, Corbi-Verge C, Petsalaki E, Liu K, Gfeller D, Garg P, Tempel W, Sochirca I, Shifman JM, Davidson A, Min J, Kim PM, Sidhu SS. [PMID]

• Post-Translational modifications modulate ligand recognition by the third PDZ domain of the MAGUK protein PSD-95. PLoS One. 2014. Murciano-Calles J, Corbi-Verge C*, Candel AM, Luque I, Martinez JC. [PMID]

• Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap. Proc Natl Acad Sci U S A. 2013. Corbi-Verge C*, Marinelli F, Zafra-Ruano A, Ruiz-Sanz J, Luque I, Faraldo-Gómez JD. [PMID]

• The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. Proteins. 2006. Bonet J, Caltabiano G, Khan AK, Johnston MA, Corbí C, Gómez A, Rovira X, Teyra J, Villà-Freixa J. [PMID]

Conferences.

• Designing novel proteins with high accuracy using deep graph neural networks. 14th Machine Learning in Computational Biology (MLCB) meeting. Alexey Strokach, David Becerra, Carles Corbi-Verge, Albert Perez-Riba and Philip M. Kim. 2019 Vancouver, Canada. [POSTER]

• C2H2 Zinc Finger DNA Binding Motif Prediction combining High-throughput experiments and Deep Learning. 14th Machine Learning in Computational Biology (MLCB) meeting Carles Corbi-Verge, April Muller, Marcus Noyes and Philip Kim. 2019. Vancouver, Canada. [POSTER]

• De Novo Crystallization Condition Prediction with Deep Learning. 14th Machine Learning in Computational Biology (MLCB) meeting. Hyunmin Lee, Zhen Hao Wu, Carles Corbi-Verge, Mac Mok, Sidney Kang, Shun Liao, Zhaolei Zhang and Michael Garton. 2019. Vancouver, Canada. [POSTER]

• RNAseq pipeline for the identification and classification of aberrant isoforms on cancer. Donelly Center for Cellular and Biomolecular Research Retreat. Corbi-Verge C, Kim PM. 2017. Ontario, Canada. [POSTER]

• Conformational Distribution of the SH3-SH2 Tandem of the ABL kinase and its Modulation by Intramolecular interactions. XXXVII Congreso de la Sociedad Española de Bioquímica y Biología Molecular. Corbi-Verge C, Marinelli F, Zafra-Ruano A, Ruiz-Sanz J, Luque I, Faraldo-Gómez JD. 2014 Granada, Spain. [POSTER]

• Long Range Cooperative effects in SH3 Domains From The Src Family. VIII European Symposium of the Protein Society. Corbi-Verge C, Martin-Garcia JM, Martinez, JC, Sanz JR, Luque I. 2009 Zurich, Switzerland. [POSTER]

• Specificity on SH3 interactions: long-range effects on the binding energetics of proline-rich ligands to SH3 domains from the SRC family. 2nd International Conference on molecular Perspectives on Protein-protein interactions. Corbi-Verge C, Martin-Garcia JM, Martinez, JC, Sanz JR, Luque I. 2008. Dubrovnik, Croatia. [POSTER]