selected publications
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Locus specific human endogenous retroviruses reveal new lymphoma subtypes.
bioRxiv : the preprint server for biology.
2023
Article
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Times cited: 3855 - Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci. Cancer research. 2023 Academic Article GET IT
- 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: 1031 -
A field guide to endogenous retrovirus regulatory networks.
Molecular cell.
2022
Academic Article
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Times cited: 1 -
How human endogenous retroviruses interact with the microbiota in health and disease.
Trends in microbiology.
2022
Academic Article
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Times cited: 4 -
Specific human endogenous retroviruses predict metastatic potential in uveal melanoma.
JCI insight.
2022
Academic Article
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Times cited: 2 -
SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements.
JCI insight.
2021
Academic Article
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Times cited: 16 -
Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers.
Cancer research.
2021
Academic Article
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Times cited: 14 -
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: 8 -
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: 3 -
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: 6 -
Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival.
Viruses.
2020
Academic Article
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Times cited: 11 -
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.
Viruses.
2020
Academic Article
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Times cited: 2 - Author Correction: A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing. Scientific reports. 2020 Article 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: 21 -
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: 9 -
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: 8 -
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.
PLoS computational biology.
2019
Academic Article
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Times cited: 53 -
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: 33 -
Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nature methods.
2018
Letter
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Times cited: 398 -
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: 461 -
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.
The ISME journal.
2016
Academic Article
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Times cited: 130 -
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: 92 -
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: 72 -
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: 47 -
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: 115 -
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: 31 -
Pathoscope: species identification and strain attribution with unassembled sequencing data.
Genome research.
2013
Academic Article
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Times cited: 98 -
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: 29