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Revising transcriptome assemblies with phylogenetic information

PloS one, 2021-01, Vol.16 (1), p.e0244202-e0244202

2021

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Phylogenomic Analyses Support Traditional Relationships within Cnidaria

PloS one, 2015-10, Vol.10 (10), p.e0139068-e0139068

2015

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An Integrated Perspective on Phylogenetic Workflows

Trends in ecology & evolution (Amsterdam), 2016-02, Vol.31 (2), p.116-126

2016

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Toward a statistically explicit understanding of de novo sequence assembly

Bioinformatics, 2013-12, Vol.29 (23), p.2959-2963

2013

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Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth

Viruses, 2023-06, Vol.15 (7), p.1416

2023

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Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

Frontiers in microbiology, 2022-02, Vol.12, p.803190-803190

2022

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An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic

Viruses, 2023-03, Vol.15 (3), p.737

2023

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Bayesian genome assembly and assessment by markov chain monte carlo sampling

PloS one, 2014-06, Vol.9 (6), p.e99497-e99497

2014

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Measurement error and variant-calling in deep Illumina sequencing of HIV

Bioinformatics (Oxford, England), 2019-06, Vol.35 (12), p.2029-2035

2019

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High-Throughput Compression of FASTQ Data with SeqDB

IEEE/ACM transactions on computational biology and bioinformatics, 2013-01, Vol.10 (1), p.213-218

Howison, Mark

2013

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Agalma: an automated phylogenomics workflow

BMC bioinformatics, 2013-11, Vol.14 (1), p.330-330, Article 330

2013

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SIRAD: Secure Infrastructure for Research with Administrative Data

Software impacts, 2022-05, Vol.12, p.100245, Article 100245

2022

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Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora

Molecular biology and evolution, 2022-02, Vol.39 (2)

2022

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Predicting high-risk opioid prescriptions before they are given

Proceedings of the National Academy of Sciences - PNAS, 2020-01, Vol.117 (4), p.1917-1923

2020

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Predicting Divertible Medicaid Emergency Department Costs

Digital government (New York, N.Y. Online), 2022-10, Vol.3 (3), p.1-19, Article 19

2022

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Recommending Career Transitions to Job Seekers Using Earnings Estimates, Skills Similarity, and Occupational Demand

Digital government (New York, N.Y. Online), 2024-09, Vol.5 (3), p.1-19, Article 31

2024

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Protecting Sensitive Data with Secure Data Enclaves

Digital government (New York, N.Y. Online), 2024-06, Vol.5 (2), p.1-11, Article 14

2024

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Acquired Human Immunodeficiency Virus Type 1 Drug Resistance in Rhode Island, USA, 2004-2021

The Journal of infectious diseases, 2024-07

2024

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Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

Proceedings of the Royal Society. B, Biological sciences, 2014-11, Vol.281 (1794), p.20141739-20141739

2014

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Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic

AIDS (London), 2023-03, Vol.37 (3), p.389-399

2023

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Longitudinal typing of molecular HIV clusters in a statewide epidemic

AIDS (London), 2021-09, Vol.35 (11), p.1711-1722

2021

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Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing

Scientific reports, 2020-01, Vol.10 (1), p.1634-1634, Article 1634

2020

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HIV Drug Resistance and Transmission Networks Among a Justice-Involved Population at the Time of Community Reentry in Washington, D.C

AIDS research and human retroviruses, 2021-12, Vol.37 (12), p.903-912

2021

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Revising transcriptome assemblies with phylogenetic information

Phylogenomic Analyses Support Traditional Relationships within Cnidaria

An Integrated Perspective on Phylogenetic Workflows

Toward a statistically explicit understanding of de novo sequence assembly

Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic

Beyond HIV outbreaks: protocol, rationale and implementation of a prospective study quantifying the benefit of incorporating viral sequence clustering analysis into routine public health interventions

Bayesian genome assembly and assessment by markov chain monte carlo sampling

Measurement error and variant-calling in deep Illumina sequencing of HIV

High-Throughput Compression of FASTQ Data with SeqDB

Agalma: an automated phylogenomics workflow

SIRAD: Secure Infrastructure for Research with Administrative Data

Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora

Predicting high-risk opioid prescriptions before they are given

Predicting Divertible Medicaid Emergency Department Costs

Recommending Career Transitions to Job Seekers Using Earnings Estimates, Skills Similarity, and Occupational Demand

Protecting Sensitive Data with Secure Data Enclaves

Acquired Human Immunodeficiency Virus Type 1 Drug Resistance in Rhode Island, USA, 2004-2021

Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

Not all clusters are equal: dynamics of molecular HIV-1 clusters in a statewide Rhode Island epidemic

Longitudinal typing of molecular HIV clusters in a statewide epidemic

Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing

HIV Drug Resistance and Transmission Networks Among a Justice-Involved Population at the Time of Community Reentry in Washington, D.C

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