selected publications
- A single-cell transposable element atlas of human cell identity. Cell reports methods. 2025 Academic Article GET IT
- Locus-specific human endogenous retroviruses reveal lymphoma subtypes. iScience. 2025 Academic Article GET IT
- Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. Genome biology. 2025 Academic Article GET IT
- Endogenous Retroelement Expression in Modeled Airway Epithelial Repair. Microbes and infection. 2024 Academic Article GET IT
- Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging cell. 2024 Academic Article GET IT
- Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nature communications. 2024 Academic Article GET IT
- Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine. 2024 Academic Article GET IT
- Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC genomics. 2024 Review GET IT
- A single-cell transposable element atlas of human cell identity. 2023 GET IT
- Transposable elements may enhance antiviral resistance in HIV-1 elite controllers. 2023 GET IT
- Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. 2023 GET IT
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Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci.
Cancer research.
2023
Academic Article
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Times cited: 10 - Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation. mBio. 2023 Academic Article GET IT
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Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19.
Frontiers in microbiology.
2023
Academic Article
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Times cited: 2 - A field guide to endogenous retrovirus regulatory networks. Molecular cell. 2022 Article GET IT
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Specific human endogenous retroviruses predict metastatic potential in uveal melanoma.
JCI insight.
2022
Academic Article
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Times cited: 9 - SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements. JCI insight. 2021 Academic Article GET IT
- Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers. Cancer research. 2021 Academic Article GET IT
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Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression.
Frontiers in immunology.
2021
Academic Article
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Times cited: 23 -
HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations.
Molecular biology and evolution.
2021
Academic Article
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Times cited: 7 -
Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study.
Frontiers in oncology.
2020
Academic Article
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Times cited: 13 -
Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival.
Viruses.
2020
Academic Article
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Times cited: 25 -
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
Viruses.
2020
Academic Article
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Times cited: 4 - Author Correction: A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. 2020 GET IT
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Evaluation of haplotype callers for next-generation sequencing of viruses.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.
2020
Academic Article
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Times cited: 29 -
A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing.
Scientific reports.
2020
Academic Article
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Times cited: 12 -
Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus.
Proceedings of the National Academy of Sciences of the United States of America.
2019
Letter
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Times cited: 11 -
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.
PLoS computational biology.
2019
Academic Article
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Times cited: 106 -
Transcriptome patterns in hidradenitis suppurativa: support for the role of antimicrobial peptides and interferon pathways in disease pathogenesis.
Clinical and experimental dermatology.
2019
Academic Article
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Times cited: 39 -
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nature methods.
2018
Letter
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Times cited: 771 -
Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity.
Frontiers in microbiology.
2018
Academic Article
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Times cited: 8 -
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
The ISME journal.
2016
Academic Article
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Times cited: 163 -
Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.
PeerJ.
2015
Academic Article
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Times cited: 208 -
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.
PloS one.
2015
Academic Article
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Times cited: 85 -
Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.
ACS chemical biology.
2014
Academic Article
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Times cited: 55 -
The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida).
Systematic biology.
2014
Academic Article
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Times cited: 146 -
Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.
Journal of bacteriology.
2013
Academic Article
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Times cited: 34 -
Pathoscope: species identification and strain attribution with unassembled sequencing data.
Genome research.
2013
Academic Article
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Times cited: 108 -
Phylogenetics applied to genotype/phenotype association and selection analyses with sequence data from angptl4 in humans.
International journal of molecular sciences.
2010
Academic Article
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Times cited: 4 -
Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses.
Molecular biology and evolution.
2009
Academic Article
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Times cited: 30