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Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model

Oikos, 2014-10, Vol.123 (10), p.1250-1260

2014

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Detection of Mammalian Virulence Determinants in Highly Pathogenic Avian Influenza H5N1 Viruses: Multivariate Analysis of Published Data

Journal of Virology, 2009-10, Vol.83 (19), p.9901-9910

2009

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FUBAR: a fast, unconstrained bayesian approximation for inferring selection

Molecular biology and evolution, 2013-05, Vol.30 (5), p.1196-1205

2013

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Maintenance of Nef-Mediated Modulation of Major Histocompatibility Complex Class I and CD4 after Sexual Transmission of Human Immunodeficiency Virus Type 1

Journal of Virology, 2007-05, Vol.81 (9), p.4776-4786

2007

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Estimating selection pressures on HIV-1 using phylogenetic likelihood models

Statistics in medicine, 2008-10, Vol.27 (23), p.4779-4789

2008

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Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy

Molecular biology and evolution, 2012-02, Vol.29 (2), p.451-456

2012

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A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus

Molecular biology and evolution, 2008-09, Vol.25 (9), p.1809-1824

2008

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Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1

Molecular biology and evolution, 2010-04, Vol.27 (4), p.819-832

2010

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Statistics and Truth in Phylogenomics

Molecular biology and evolution, 2012-02, Vol.29 (2), p.457-472

2012

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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Molecular biology and evolution, 2022, Vol.39 (4)

2022

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Evolutionary Fingerprinting of Genes

Molecular biology and evolution, 2010-03, Vol.27 (3), p.520-536

2010

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Conserved recombination patterns across coronavirus subgenera

Virus evolution, 2022, Vol.8 (2), p.veac054

2022

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Efficient pedigree recording for fast population genetics simulation

PLoS computational biology, 2018-11, Vol.14 (11), p.e1006581-e1006581

2018

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Evolution of the interferon alpha gene family in eutherian mammals

Gene, 2007-08, Vol.397 (1), p.38-50

2007

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Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009347-e1009347

2021

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Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

PLoS computational biology, 2021-01, Vol.17 (1), p.e1008561-e1008561

2021

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An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009334-e1009334

2021

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Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution

PLoS pathogens, 2023-12, Vol.19 (12), p.e1011901-e1011901

2023

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Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin

PLoS computational biology, 2014-11, Vol.10 (11), p.e1003935-e1003935

2014

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Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

PLoS computational biology, 2022-02, Vol.18 (2), p.e1009269-e1009269

2022

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Bayesian inference of ancestral recombination graphs

PLoS computational biology, 2022-03, Vol.18 (3), p.e1009960-e1009960

2022

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Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics

PLoS computational biology, 2021-10, Vol.17 (10), p.e1008874-e1008874

2021

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Building blocks and blueprints for bacterial autolysins

PLoS computational biology, 2021-04, Vol.17 (4), p.e1008889-e1008889

2021

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Estimating effective population size changes from preferentially sampled genetic sequences

PLoS computational biology, 2020-10, Vol.16 (10), p.e1007774-e1007774

2020

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A deep learning approach to real-time HIV outbreak detection using genetic data

PLoS computational biology, 2022-10, Vol.18 (10), p.e1010598-e1010598

2022

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Detecting phylogenetic signal in mutualistic interaction networks using a Markov process model

Detection of Mammalian Virulence Determinants in Highly Pathogenic Avian Influenza H5N1 Viruses: Multivariate Analysis of Published Data

FUBAR: a fast, unconstrained bayesian approximation for inferring selection

Maintenance of Nef-Mediated Modulation of Major Histocompatibility Complex Class I and CD4 after Sexual Transmission of Human Immunodeficiency Virus Type 1

Estimating selection pressures on HIV-1 using phylogenetic likelihood models

Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy

A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and Its Application to Influenza A Virus

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1

Statistics and Truth in Phylogenomics

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

Evolutionary Fingerprinting of Genes

Conserved recombination patterns across coronavirus subgenera

Efficient pedigree recording for fast population genetics simulation

Evolution of the interferon alpha gene family in eutherian mammals

Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City

Deep mutational scans of XBB.1.5 and BQ.1.1 reveal ongoing epistatic drift during SARS-CoV-2 evolution

Phosphorylation by PINK1 releases the UBL domain and initializes the conformational opening of the E3 ubiquitin ligase Parkin

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

Bayesian inference of ancestral recombination graphs

Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics

Building blocks and blueprints for bacterial autolysins

Estimating effective population size changes from preferentially sampled genetic sequences

A deep learning approach to real-time HIV outbreak detection using genetic data

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