Sergei L. Kosakovsky Pond

According to our database1, Sergei L. Kosakovsky Pond authored at least 24 papers between 2005 and 2020.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

On csauthors.net:

Bibliography

2020
A new method for inferring timetrees from temporally sampled molecular sequences.
PLoS Comput. Biol., 2020

2018
Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.
PLoS Comput. Biol., 2018

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics.
BMC Bioinform., 2018

2017
Lorenzo-Redondo <i>et al</i>. reply.
Nat., 2017

2015
: Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.
PLoS Comput. Biol., 2015

2014
IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.
PLoS Comput. Biol., 2014

2012
Modeling HIV-1 Drug Resistance as Episodic Directional Selection.
PLoS Comput. Biol., 2012

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.
Bioinform., 2012

Workshop: Error correction, noise filtering, and phylogenetic analysis of HIV sequences using the 454 platform.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

2011
Computational analysis of HIV-1 evolution and epidemiology.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010
CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences.
PLoS Comput. Biol., 2010

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.
Bioinform., 2010

2009
An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1.
PLoS Comput. Biol., 2009

2008
Comparison of Immunogen Designs That Optimize Peptide Coverage: Reply to Fischer et al.
PLoS Comput. Biol., 2008

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.
Bioinform., 2008

2007
An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope.
PLoS Comput. Biol., 2007

Evolutionary Interactions between N-Linked Glycosylation Sites in the HIV-1 Envelope.
PLoS Comput. Biol., 2007

Coping with Viral Diversity in HIV Vaccine Design.
PLoS Comput. Biol., 2007

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics.
PLoS Comput. Biol., 2007

A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes.
PLoS Comput. Biol., 2007

2006
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses.
PLoS Comput. Biol., 2006

GARD: a genetic algorithm for recombination detection.
Bioinform., 2006

2005
HyPhy: hypothesis testing using phylogenies.
Bioinform., 2005

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.
Bioinform., 2005


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