PROTEAN: Deriving Protein Structure from Constraints. - Barbara Hayes-Roth; Bruce G. Buchanan; Olivier Lichtarge; Mike Hewitt; Russ B. Altman; James F. Brinkley; Craig Cornelius; Bruce S. Duncan; Oleg Jardetzky (AAAI, 1986)

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. - Brian Y. Chen; Viacheslav Fofanov; David M. Kristensen; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (Pacific Symposium on Biocomputing, 2005)

An evolution based classifier for prediction of protein interfaces without using protein structures. - I. Res; I. Mihalek; Olivier Lichtarge (Bioinform., 2005)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (RECOMB, 2006)

A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins. - I. Mihalek; I. Res; Olivier Lichtarge (Bioinform., 2006)

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. - I. Mihalek; I. Res; Olivier Lichtarge (Bioinform., 2006)

ET viewer: an application for predicting and visualizing functional sites in protein structures. - Daniel H. Morgan; David M. Kristensen; David Mittelman; Olivier Lichtarge (Bioinform., 2006)

Graph-Based Protein Functional Classification. - Hyunjung Shin; Andreas Martin Lisewski; Olivier Lichtarge (BIOCOMP, 2007)

Graph sharpening plus graph integration: a synergy that improves protein functional classification. - Hyunjung Shin; Andreas Martin Lisewski; Olivier Lichtarge (Bioinform., 2007)

Background frequencies for residue variability estimates: BLOSUM revisited. - I. Mihalek; I. Res; Olivier Lichtarge (BMC Bioinform., 2007)

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. - Brian Y. Chen; Drew H. Bryant; Viacheslav Fofanov; David M. Kristensen; Amanda E. Cruess; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Bioinform. Comput. Biol., 2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Comput. Biol., 2007)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. - David M. Kristensen; R. Matthew Ward; Andreas Martin Lisewski; Serkan Erdin; Brian Y. Chen; Viacheslav Fofanov; Marek Kimmel; Lydia E. Kavraki; Olivier Lichtarge (BMC Bioinform., 2008)

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. - R. Matthew Ward; Eric Venner; Bryce Daines; Stephen Murray; Serkan Erdin; David M. Kristensen; Olivier Lichtarge (Bioinform., 2009)

PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. - Rhonald C. Lua; Olivier Lichtarge (Bioinform., 2010)

ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. - Benjamin J. Bachman; Eric Venner; Rhonald C. Lua; Serkan Erdin; Olivier Lichtarge (Bioinform., 2012)

Accounting for epistatic interactions improves the functional analysis of protein structures. - Angela D. Wilkins; Eric Venner; David C. Marciano; Serkan Erdin; Benu Atri; Rhonald C. Lua; Olivier Lichtarge (Bioinform., 2013)

Function prediction from networks of local evolutionary similarity in protein structure. - Serkan Erdin; Eric Venner; Andreas Martin Lisewski; Olivier Lichtarge (BMC Bioinform., 2013)

Automated hypothesis generation based on mining scientific literature. - W. Scott Spangler; Angela D. Wilkins; Benjamin J. Bachman; Meena Nagarajan; Tajhal Dayaram; Peter J. Haas; Sam Regenbogen; Curtis R. Pickering; Austin Comer; Jeffrey N. Myers; Ioana Stanoi; Linda Kato; et al. (KDD, 2014)

Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature. - Meenakshi Nagarajan; Angela D. Wilkins; Benjamin J. Bachman; Ilya B. Novikov; Shenghua Bao; Peter J. Haas; María E. Terrón-Díaz; Sumit Bhatia; Anbu K. Adikesavan; Jacques J. Labrie; Sam Regenbogen; Christie M. Buchovecky; et al. (KDD, 2015)

Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering. - Amanda Koire; Panagiotis Katsonis; Olivier Lichtarge (PSB, 2016)

Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions. - Sam Regenbogen; Angela D. Wilkins; Olivier Lichtarge (PSB, 2016)

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. - Rhonald C. Lua; Stephen J. Wilson; Daniel M. Konecki; Angela D. Wilkins; Eric Venner; Daniel H. Morgan; Olivier Lichtarge (Nucleic Acids Res., 2016)

Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer. - Jonathan Gallion; Angela D. Wilkins; Olivier Lichtarge (PSB, 2017)

Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks. - Stephen J. Wilson; Angela D. Wilkins; Chih-Hsu Lin; Rhonald C. Lua; Olivier Lichtarge (PSB, 2017)

Multimodal network diffusion predicts future disease-gene-chemical associations. - Chih-Hsu Lin; Daniel M. Konecki; Meng Liu 027; Stephen J. Wilson; Huda Nassar; Angela D. Wilkins; David F. Gleich; Olivier Lichtarge (Bioinform., 2019)

Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein-Protein Interaction Networks. - Minh Pham; Olivier Lichtarge (PSB, 2020)

Discovery of disease- and drug-specific pathways through community structures of a literature network. - Minh Pham; Stephen J. Wilson; Harikumar Govindarajan; Chih-Hsu Lin; Olivier Lichtarge (Bioinform., 2020)

An Evolutionary Trace method defines functionally important bases and sites common to RNA families. - Ilya B. Novikov; Angela D. Wilkins; Olivier Lichtarge (PLoS Comput. Biol., 2020)

Using interpretable deep learning to model cancer dependencies. - Chih-Hsu Lin; Olivier Lichtarge (Bioinform., 2021)

Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family. - Chen Wang 073; Daniel M. Konecki; David C. Marciano; Harikumar Govindarajan; Amanda M. Williams; Brigitta Wastuwidyaningtyas; Thomas Bourquard; Panagiotis Katsonis; Olivier Lichtarge (Bioinform., 2021)

ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. - Chen Wang 073; Harikumar Govindarajan; Panagiotis Katsonis; Olivier Lichtarge (Bioinform., 2023)