Bendall, Matthew

Publications

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selected publications

Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer. Frontiers in cell and developmental biology. 2025 Academic Article GET IT
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
Oncogenic Transformation Drives DNA Methylation Loss and Transcriptional Activation at Transposable Element Loci. Cancer research. 2023 Academic Article GET IT
Times cited: 11
Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation. mBio. 2023 Academic Article GET IT
Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19. Frontiers in microbiology. 2023 Academic Article GET IT
Times cited: 2
A field guide to endogenous retrovirus regulatory networks. Molecular cell. 2022 Article GET IT
Specific human endogenous retroviruses predict metastatic potential in uveal melanoma. JCI insight. 2022 Academic Article GET IT
Times cited: 10
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
Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression. Frontiers in immunology. 2021 Academic Article GET IT
Times cited: 23
HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intrahost Viral Populations. Molecular biology and evolution. 2021 Academic Article GET IT
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 GET IT
Times cited: 14
Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival. Viruses. 2020 Academic Article GET IT
Times cited: 26
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses. Viruses. 2020 Academic Article GET IT
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
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 GET IT
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 GET IT
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 GET IT
Times cited: 11
Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression. PLoS computational biology. 2019 Academic Article GET IT
Times cited: 109
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 GET IT
Times cited: 39
Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature methods. 2018 Letter GET IT
Times cited: 819
Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity. Frontiers in microbiology. 2018 Academic Article GET IT
Times cited: 8
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. The ISME journal. 2016 Academic Article GET IT
Times cited: 165
Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PeerJ. 2015 Academic Article GET IT
Times cited: 208
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PloS one. 2015 Academic Article GET IT
Times cited: 86
Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS chemical biology. 2014 Academic Article GET IT
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 GET IT
Times cited: 146
Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1. Journal of bacteriology. 2013 Academic Article GET IT
Times cited: 34
Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome research. 2013 Academic Article GET IT
Times cited: 110
Phylogenetics applied to genotype/phenotype association and selection analyses with sequence data from angptl4 in humans. International journal of molecular sciences. 2010 Academic Article GET IT
Times cited: 4
Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses. Molecular biology and evolution. 2009 Academic Article GET IT
Times cited: 30

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Research

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Co-investigator Network

Funding awarded

Single cell dark matter in the context of HIV and substance use awarded by National Institute on Drug Abuse Co-Investigator 2025 - 2030
HOPE - HIV Obstruction by Programmed Epigenetics awarded by National Institute of Allergy & Infectious Diseases Co-Investigator 2021 - 2026

The Role of Transposable Elements in Healthy Aging and in Alzheimer''s Disease awarded by National Institute on Drug Abuse Principal Investigator Subaward 2025 - 2025

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Background

education and training

Ph.D., George Washington University 2019
M.S., Brigham Young University 2012
B.S., Brigham Young University 2009

Contact

full name

Matthew Bendall

primary email

mlb4001@med.cornell.edu

VIVO Weill Cornell Medical College

Matthew Bendall Assistant Professor of Computational Biology Research in Medicine

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email