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Olivier Lichtarge
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Journal Articles
- 2023
- [j22]Chen Wang
, Harikumar Govindarajan, Panagiotis Katsonis, Olivier Lichtarge:
ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis. Bioinform. 39(8) (2023) - 2021
- [j21]Chih-Hsu Lin
, Olivier Lichtarge:
Using interpretable deep learning to model cancer dependencies. Bioinform. 37(17): 2675-2681 (2021) - [j20]Chen Wang
, Daniel M. Konecki
, David C. Marciano, Harikumar Govindarajan, Amanda M. Williams, Brigitta Wastuwidyaningtyas, Thomas Bourquard, Panagiotis Katsonis, Olivier Lichtarge:
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family. Bioinform. 37(22): 4033-4040 (2021) - 2020
- [j19]Minh Pham
, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge:
Discovery of disease- and drug-specific pathways through community structures of a literature network. Bioinform. 36(6): 1881-1888 (2020) - [j18]Minh Pham, Stephen J. Wilson, Harikumar Govindarajan, Chih-Hsu Lin, Olivier Lichtarge:
Discovery of disease- and drug-specific pathways through community structures of a literature network. Bioinform. 36(11): 3623 (2020) - [j17]Ilya B. Novikov
, Angela D. Wilkins, Olivier Lichtarge
:
An Evolutionary Trace method defines functionally important bases and sites common to RNA families. PLoS Comput. Biol. 16(3) (2020) - 2019
- [j16]Chih-Hsu Lin
, Daniel M. Konecki
, Meng Liu, Stephen J. Wilson, Huda Nassar, Angela D. Wilkins, David F. Gleich
, Olivier Lichtarge:
Multimodal network diffusion predicts future disease-gene-chemical associations. Bioinform. 35(9): 1536-1543 (2019) - 2016
- [j15]Rhonald C. Lua, Stephen J. Wilson
, Daniel M. Konecki
, Angela D. Wilkins, Eric Venner, Daniel H. Morgan, Olivier Lichtarge:
UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. Nucleic Acids Res. 44(Database-Issue): 308-312 (2016) - 2013
- [j14]Angela D. Wilkins, Eric Venner, David C. Marciano
, Serkan Erdin
, Benu Atri
, Rhonald C. Lua, Olivier Lichtarge:
Accounting for epistatic interactions improves the functional analysis of protein structures. Bioinform. 29(21): 2714-2721 (2013) - [j13]Serkan Erdin
, Eric Venner, Andreas Martin Lisewski, Olivier Lichtarge:
Function prediction from networks of local evolutionary similarity in protein structure. BMC Bioinform. 14(S-3): S6 (2013) - 2012
- [j12]Benjamin J. Bachman, Eric Venner, Rhonald C. Lua, Serkan Erdin
, Olivier Lichtarge:
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape. Bioinform. 28(16): 2186-2188 (2012) - 2010
- [j11]Rhonald C. Lua, Olivier Lichtarge:
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes. Bioinform. 26(23): 2981-2982 (2010) - 2009
- [j10]R. Matthew Ward, Eric Venner, Bryce Daines, Stephen Murray, Serkan Erdin
, David M. Kristensen, Olivier Lichtarge:
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. Bioinform. 25(11): 1426-1427 (2009) - 2008
- [j9]David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin
, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki
, Olivier Lichtarge:
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinform. 9 (2008) - 2007
- [j8]Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge:
Graph sharpening plus graph integration: a synergy that improves protein functional classification. Bioinform. 23(23): 3217-3224 (2007) - [j7]I. Mihalek, I. Res, Olivier Lichtarge:
Background frequencies for residue variability estimates: BLOSUM revisited. BMC Bioinform. 8 (2007) - [j6]Brian Y. Chen, Drew H. Bryant, Viacheslav Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
:
Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. J. Bioinform. Comput. Biol. 5(2a): 353-382 (2007) - [j5]Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki
:
The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. J. Comput. Biol. 14(6): 791-816 (2007) - 2006
- [j4]I. Mihalek, I. Res, Olivier Lichtarge:
A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins. Bioinform. 22(2): 149-156 (2006) - [j3]I. Mihalek, I. Res, Olivier Lichtarge:
Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinform. 22(13): 1656-1657 (2006) - [j2]Daniel H. Morgan, David M. Kristensen, David Mittelman, Olivier Lichtarge:
ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinform. 22(16): 2049-2050 (2006) - 2005
- [j1]I. Res, I. Mihalek, Olivier Lichtarge:
An evolution based classifier for prediction of protein interfaces without using protein structures. Bioinform. 21(10): 2496-2501 (2005)
Conference and Workshop Papers
- 2020
- [c11]Minh Pham, Olivier Lichtarge:
Graph-Based Information Diffusion Method for Prioritizing Functionally Related Genes in Protein-Protein Interaction Networks. PSB 2020: 439-450 - 2017
- [c10]Stephen J. Wilson, Angela D. Wilkins, Chih-Hsu Lin, Rhonald C. Lua, Olivier Lichtarge:
Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks. PSB 2017: 336-347 - [c9]Jonathan Gallion, Angela D. Wilkins, Olivier Lichtarge:
Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer. PSB 2017: 414-425 - 2016
- [c8]Sam Regenbogen, Angela D. Wilkins, Olivier Lichtarge:
Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions. PSB 2016: 21-32 - [c7]Amanda Koire, Panagiotis Katsonis, Olivier Lichtarge:
Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering. PSB 2016: 207-218 - 2015
- [c6]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, Curtis R. Pickering, Linda Kato, Andreas Martin Lisewski, Ana Lelescu, Houyin Zhang, Stephen Boyer, Griff Weber, Ying Chen, Lawrence A. Donehower, W. Scott Spangler, Olivier Lichtarge:
Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature. KDD 2015: 2019-2028 - 2014
- [c5]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, Ana Lelescu, Jacques J. Labrie, Neha Parikh, Andreas Martin Lisewski, Lawrence A. Donehower, Ying Chen, Olivier Lichtarge:
Automated hypothesis generation based on mining scientific literature. KDD 2014: 1877-1886 - 2007
- [c4]Hyunjung Shin, Andreas Martin Lisewski, Olivier Lichtarge:
Graph-Based Protein Functional Classification. BIOCOMP 2007: 738-744 - 2006
- [c3]Brian Y. Chen, Viacheslav Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. RECOMB 2006: 500-515 - 2005
- [c2]Brian Y. Chen, Viacheslav Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki:
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. Pacific Symposium on Biocomputing 2005 - 1986
- [c1]Barbara Hayes-Roth, Bruce G. Buchanan, Olivier Lichtarge, Mike Hewitt, Russ B. Altman, James F. Brinkley, Craig Cornelius, Bruce S. Duncan, Oleg Jardetzky:
PROTEAN: Deriving Protein Structure from Constraints. AAAI 1986: 904-909
Coauthor Index
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