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Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes

Microbial ecology, 2018-07, Vol.76 (1), p.272-284

2018

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MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

Systematic biology, 2024-07, Vol.73 (2), p.375-391

2024

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An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

PLoS computational biology, 2021-09, Vol.17 (9), p.e1008949-e1008949

2021

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ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data

IEEE/ACM transactions on computational biology and bioinformatics, 2024-05, Vol.21 (3), p.492-500

2024

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Patterns of gut bacterial colonization in three primate species

PloS one, 2015-05, Vol.10 (5), p.e0124618-e0124618

2015

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Neutral Models of Microbiome Evolution

PLoS computational biology, 2015-07, Vol.11 (7), p.e1004365

2015

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Time‐dependent rates of molecular evolution

Molecular ecology, 2011-08, Vol.20 (15), p.3087-3101

2011

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Models of microbiome evolution incorporating host and microbial selection

Microbiome, 2017-09, Vol.5 (1), p.127-127, Article 127

2017

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Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies

PloS one, 2018-04, Vol.13 (4), p.e0195090-e0195090

2018

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Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

The ISME Journal, 2012-03, Vol.6 (3), p.564-576

2012

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Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution

PloS one, 2016-09, Vol.11 (9), p.e0162454-e0162454

2016

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Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data

Genetics (Austin), 2002-07, Vol.161 (3), p.1307-1320

2002

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Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation

Microbiome, 2018-04, Vol.6 (1), p.80-80, Article 80

2018

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Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

BMC bioinformatics, 2019-12, Vol.20 (1), p.654-654, Article 654

2019

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Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

BMC bioinformatics, 2020-01, Vol.21 (1), p.24-24, Article 24

2020

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pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics

Molecular ecology resources, 2022-02, Vol.22 (2), p.653-663

2022

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HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study

PloS one, 2013-09, Vol.8 (9), p.e71557

2013

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HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations

BMC bioinformatics, 2018-10, Vol.19 (1), p.389-389, Article 389

2018

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Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

PLoS genetics, 2012-02, Vol.8 (2), p.e1002511-e1002511

2012

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Modeling the Site-Specific Variation of Selection Patterns along Lineages

Proceedings of the National Academy of Sciences - PNAS, 2004-08, Vol.101 (35), p.12957-12962

2004

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Likelihood-Based Tests of Topologies in Phylogenetics

Systematic biology, 2000-12, Vol.49 (4), p.652-670

2000

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Time-dependent rates of molecular evolution

Molecular ecology, 2011-08, Vol.20 (15), p.3087-3101

2011

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Measurably evolving populations

Trends in ecology & evolution (Amsterdam), 2003-09, Vol.18 (9), p.481-488

2003

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The perils of plenty: what are we going to do with all these genes?

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2008-12, Vol.363 (1512), p.3893-3902

2008

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Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals

BMC bioinformatics, 2015-11, Vol.16 (1), p.357-357, Article 357

2015

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Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data

Patterns of gut bacterial colonization in three primate species

Neutral Models of Microbiome Evolution

Time‐dependent rates of molecular evolution

Models of microbiome evolution incorporating host and microbial selection

Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution

Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

pgHMA: Application of the heteroduplex mobility assay analysis in phylogenetics and population genetics

HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations

Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

Modeling the Site-Specific Variation of Selection Patterns along Lineages

Likelihood-Based Tests of Topologies in Phylogenetics

Time-dependent rates of molecular evolution

Measurably evolving populations

The perils of plenty: what are we going to do with all these genes?

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals

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