Olivier Lichtarge

发表

Automated hypothesis generation based on mining scientific literature

Peter J. Haas, Ioana Stanoi, W. Scott Spangler, 2014, KDD.

PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes

Olivier Lichtarge, Rhonald C. Lua, O. Lichtarge, 2010, Bioinform..

Discovery of disease a literature network.

Olivier Lichtarge, Minh Pham, Stephen J. Wilson, 2020 .

Graph sharpening plus graph integration: a synergy that improves protein functional classification

Andreas Martin Lisewski, Olivier Lichtarge, Hyunjung Shin, 2007, Bioinform..

PROTEAN: A New Method for Deriving Solution Structures of Proteins

Russ B. Altman, Olivier Lichtarge, Craig Cornelius, 2007 .

Geometry-inspired Optimization Methods for Structural Motifs for Protein Function Prediction

Lydia E. Kavraki, Mark Moll, Olivier Lichtarge, 2007 .

Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states.

Andreas Martin Lisewski, Olivier Lichtarge, A. M. Lisewski, 2010, Physica A.

An Evolutionary Trace method defines functionally important bases and sites common to RNA families

Olivier Lichtarge, Ilya B Novikov, Angela D Wilkins, 2020, PLoS Comput. Biol..

Function prediction from networks of local evolutionary similarity in protein structure

Andreas Martin Lisewski, Olivier Lichtarge, Serkan Erdin, 2013, BMC Bioinformatics.

Computational Approaches to Studying Molecular Phylogenetics

Olivier Lichtarge, Benu Atri, O. Lichtarge, 2018 .

Author Correction: Exploring use of unsupervised clustering to associate signaling profiles of GPCR ligands to clinical response

Olivier Lichtarge, Michel Bouvier, Besma Benredjem, 2020, Nature Communications.

Human Kinases Display Mutational Hotspots at Cognate Positions Within Cancer

Angela D. Wilkins, Olivier Lichtarge, Jonathan Gallion, 2017, PSB.

Background frequencies for residue variability estimates: BLOSUM revisited

Olivier Lichtarge, I. Mihalek, I. Res, 2007, BMC Bioinformatics.

BIOINFORMATICS ORIGINAL PAPER Systems biology

Olivier Lichtarge, I. Mihalek, I. Res, 2004 .

Discovery of Functional and Disease Pathways by Community Detection in Protein-Protein Interaction Networks

Angela D. Wilkins, Olivier Lichtarge, Rhonald C. Lua, 2017, PSB.

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Olivier Lichtarge, Lydia E Kavraki, Marek Kimmel, 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2006, RECOMB.

A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins

Olivier Lichtarge, I. Mihalek, I. Res, 2006, Bioinform..

Evolutionary trace report_maker: a new type of service for comparative analysis of proteins

Olivier Lichtarge, I. Mihalek, I. Res, 2006, Bioinform..

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2007, J. Bioinform. Comput. Biol..

Discovery of disease- and drug-specific pathways through community structures of a literature network

Olivier Lichtarge, Stephen J. Wilson, Harikumar Govindarajan, 2019, Bioinform..

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2007, J. Comput. Biol..

Cavity-aware motifs reduce false positives in protein function prediction.

Olivier Lichtarge, Lydia E Kavraki, Marek Kimmel, 2006, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs

Lydia E. Kavraki, Olivier Lichtarge, Marek Kimmel, 2004, Pacific Symposium on Biocomputing.

Accounting for epistatic interactions improves the functional analysis of protein structures

Angela D. Wilkins, Olivier Lichtarge, Rhonald C. Lua, 2013, Bioinform..

Protein function prediction: towards integration of similarity metrics.

Andreas Martin Lisewski, Olivier Lichtarge, Serkan Erdin, 2011, Current opinion in structural biology.

Getting past appearances: the many-fold consequences of remote homology

Olivier Lichtarge, O. Lichtarge, 2001, Nature Structural Biology.

Graph-Based Protein Functional Classification

Andreas Martin Lisewski, Olivier Lichtarge, Hyunjung Shin, 2007, BIOCOMP.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

Lydia E. Kavraki, Andreas Martin Lisewski, Olivier Lichtarge, 2008, BMC Bioinformatics.

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

Olivier Lichtarge, David M. Kristensen, Stephen Murray, 2009, Bioinform..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

ET viewer: an application for predicting and visualizing functional sites in protein structures

Olivier Lichtarge, David M. Kristensen, David Mittelman, 2006, Bioinform..

Automated literature mining and hypothesis generation through a network of Medical Subject Headings

Angela D. Wilkins, Lawrence A. Donehower, Olivier Lichtarge, 2018, bioRxiv.

Predicting Future Scientific Discoveries Based on a Networked Analysis of the Past Literature

Peter J. Haas, W. Scott Spangler, Angela D. Wilkins, 2015, KDD.

Network Analytics: Evolutionary Compression, Diffusion and the Action Equation for Mutations

Olivier Lichtarge, 2016 .

Repurposing Germline Exomes of the Cancer Genome Atlas Demands a Cautious Approach and Sample-Specific Variant Filtering

Olivier Lichtarge, Amanda Koire, Panagiotis Katsonis, 2016, PSB.

Multimodal network diffusion predicts future disease-gene-chemical associations

Meng Liu, Angela D. Wilkins, Olivier Lichtarge, 2018, Bioinform..

Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-entity Interactions

Angela D. Wilkins, Sam Regenbogen, Olivier Lichtarge, 2016, PSB.

UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures

Angela D. Wilkins, Olivier Lichtarge, Rhonald C. Lua, 2015, Nucleic Acids Res..

ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape

Benjamin J. Bachman, Olivier Lichtarge, Rhonald C. Lua, 2012, Bioinform..

Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks

Olivier Lichtarge, Minh Pham, 2020, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Using interpretable deep learning to model cancer dependencies

Olivier Lichtarge, Chih-Hsu Lin, O. Lichtarge, 2021, Bioinform..

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

Yuedong Yang, Olivier Lichtarge, Giovanni Minervini, 2017, Human mutation.

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Olivier Lichtarge, Predrag Radivojac, Emidio Capriotti, 2019, Human mutation.

Mamun Repair of DNA Breaks Identity and Function of a Large Gene Network Underlying Mutagenic

Olivier Lichtarge, Janet L. Gibson, Abu Amar M. Al Mamun, 2012 .

Separation of Recombination and SOS Response in Escherichia coli RecA Suggests LexA Interaction Sites

Olivier Lichtarge, Rhonald Lua, Anbu K. Adikesavan, 2011, PLoS genetics.

Receptor and βγ Binding Sites in the α Subunit of the Retinal G Protein Transducin

Olivier Lichtarge, Paul Herzmark, Henry R. Bourne, 1997, Science.

Determinants of Endogenous Ligand Specificity Divergence among Metabotropic Glutamate Receptors*

Angela D. Wilkins, Olivier Lichtarge, Angela D Wilkins, 2014, The Journal of Biological Chemistry.

Evolutionary trace for prediction and redesign of protein functional sites.

Angela D. Wilkins, Olivier Lichtarge, Rhonald Lua, 2012, Methods in molecular biology.

Literature-based automated discovery of tumor suppressor p53 phosphorylation and inhibition by NEK2

Peter J. Haas, Angela D. Wilkins, Benjamin J. Bachman, 2018, Proceedings of the National Academy of Sciences.

Olivier Lichtarge, O. Lichtarge, A. Cooney, 2005, Journal of molecular biology.

Prediction and experimental validation of enzyme substrate specificity in protein structures

Olivier Lichtarge, Shivas R. Amin, S. Erdin, 2013, Proceedings of the National Academy of Sciences.

Prediction and confirmation of a site critical for effector regulation of RGS domain activity

Olivier Lichtarge, Theodore G. Wensel, Wei He, 2001, Nature Structural Biology.

Accurate Protein Structure Annotation through Competitive Diffusion of Enzymatic Functions over a Network of Local Evolutionary Similarities

Andreas Martin Lisewski, Olivier Lichtarge, Eric Venner, 2010, PloS one.

Accurate and scalable identification of functional sites by evolutionary tracing

Olivier Lichtarge, David M. Kristensen, Srinivasan Madabushi, 2004, Journal of Structural and Functional Genomics.

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Olivier Lichtarge, Marek Kimmel, L. Kavraki, 2006, Protein science : a publication of the Protein Society.

Determination of Macromolecular Structure and Dynamics by NMR

Olivier Lichtarge, Bruce G. Buchanan, Barbara Hayes-Roth, 1986 .

Evolution: a guide to perturb protein function and networks.

Angela D. Wilkins, Olivier Lichtarge, O. Lichtarge, 2010, Current opinion in structural biology.

beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor.

Olivier Lichtarge, Eric Reiter, Srinivasan Madabushi, 2006, The Journal of biological chemistry.

Rank information: A structure‐independent measure of evolutionary trace quality that improves identification of protein functional sites

Olivier Lichtarge, O. Lichtarge, H. Yao, 2006, Proteins.

Evolutionary identification of a subtype specific functional site in the ligand binding domain of steroid receptors

Olivier Lichtarge, O. Lichtarge, Carolyn L. Smith, 2006, Proteins.

Elucidation of G-protein and β-arrestin functional selectivity at the dopamine D2 receptor

Angela D. Wilkins, Olivier Lichtarge, Marc G. Caron, 2015, Proceedings of the National Academy of Sciences.

Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness

Olivier Lichtarge, Rhonald C. Lua, O. Lichtarge, 2016, Physical review letters.

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4

Olivier Lichtarge, Roland L Dunbrack, Qifang Xu, 2017, Human mutation.

The Maternal-to-Zygotic Transition Targets Actin to Promote Robustness during Morphogenesis

Olivier Lichtarge, Rhonald C. Lua, Ido Golding, 2013, PLoS genetics.

Evolutionary traces of functional surfaces along G protein signaling pathway.

Olivier Lichtarge, O. Lichtarge, M. Sowa, 2002, Methods in enzymology.

Single nucleotide variations: Biological impact and theoretical interpretation

Angela D. Wilkins, Olivier Lichtarge, Stephen J. Wilson, 2014, Protein science : a publication of the Protein Society.

Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

Olivier Lichtarge, O. Lichtarge, T. Wensel, 2010, Proceedings of the National Academy of Sciences.

Evolutionary action and structural basis of the allosteric switch controlling β2AR functional selectivity

Angela D. Wilkins, Olivier Lichtarge, Michel Bouvier, 2017, Nature Communications.

De-Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features

Andreas Martin Lisewski, Olivier Lichtarge, David M. Kristensen, 2008, PloS one.

The use of evolutionary patterns in protein annotation.

Angela D. Wilkins, Benjamin J. Bachman, Olivier Lichtarge, 2012, Current opinion in structural biology.

Evolutionary Action Score of TP53 Coding Variants Is Predictive of Platinum Response in Head and Neck Cancer Patients.

Olivier Lichtarge, Marek Kimmel, Thomas O McDonald, 2015, Cancer research.

Role of transmembrane domain/transmembrane domain interfaces of P-glycoprotein (ABCB1) in solute transport. Convergent information from photoaffinity labeling, site directed mutagenesis and in silico importance prediction.

Olivier Lichtarge, Stephan Kopp, Peter Chiba, 2006, Current medicinal chemistry.

Supergenomic Network Compression and the Discovery of EXP1 as a Glutathione Transferase Inhibited by Artesunate

Manuel Llinás, Andreas Martin Lisewski, Olivier Lichtarge, 2014, Cell.

Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer.

Olivier Lichtarge, Marek Kimmel, Beth M Beadle, 2015, Cancer research.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

Distinct faces of the Ku heterodimer mediate DNA repair and telomeric functions

Olivier Lichtarge, Albert Ribes-Zamora, O. Lichtarge, 2007, Nature Structural &Molecular Biology.

Evolutionary Trace-based Peptides Identify a Novel Asymmetric Interaction That Mediates Oligomerization in Nuclear Receptors*

Olivier Lichtarge, Xueping Xu, O. Lichtarge, 2005, Journal of Biological Chemistry.

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI‐5

Olivier Lichtarge, Emidio Capriotti, Kivilcim Ozturk, 2019, Human mutation.

Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI‐blinded contests

Olivier Lichtarge, Panagiotis Katsonis, O. Lichtarge, 2017, Human mutation.

Essential Helix Interactions in the Anion Transporter Domain of Prestin Revealed by Evolutionary Trace Analysis

Olivier Lichtarge, Srinivasan Madabushi, O. Lichtarge, 2006, The Journal of Neuroscience.

β-Arrestin-dependent, G Protein-independent ERK1/2 Activation by the β2 Adrenergic Receptor*

Olivier Lichtarge, Eric Reiter, Srinivasan Madabushi, 2006, Journal of Biological Chemistry.