Transposable elements may enhance antiviral resistance in HIV-1 elite controllers

Authors: Manvendra Singh, Sabrina M. Leddy, Luis Pedro Iñiguez, Matthew L. Bendall, Douglas F. Nixon, Cédric Feschotte

Source: Genome Biology, Vol 26, Iss 1, Pp 1-29 (2025)

Subject Terms: Genomics, HIV, Retroviruses, Immunology, Gene regulation, Transposable elements, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/4652d1ca25fd4b56bd2d915a2f64159b

Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions

Authors: Rodrigo R. R. Duarte, Oliver Pain, Matthew L. Bendall, Miguel de Mulder Rougvie, Jez L. Marston, Sashika Selvackadunco, Claire Troakes, Szi Kay Leung, Rosemary A. Bamford, Jonathan Mill, Paul F. O’Reilly, Deepak P. Srivastava, Douglas F. Nixon, Timothy R. Powell

Source: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b450345af2824456a3a8a93c234cbf75

Ribosomal profiling of human endogenous retroviruses in healthy tissues

Authors: Nicholas Dopkins, Bhavya Singh, Stephanie Michael, Panpan Zhang, Jez L. Marston, Tongyi Fei, Manvendra Singh, Cedric Feschotte, Nicholas Collins, Matthew L. Bendall, Douglas F. Nixon

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-8 (2024)

Subject Terms: Human endogenous retrovirus (HERV), Ribosomal profiling (RiboSeq), Protein translation, Dark genome, Endoretrotranslatome (ERT), Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/b795fcd1fa0147f6a7b6d5bddd81345f

Endogenous retroelement expression in the gut microenvironment of people living with HIV-1Research in context

Authors: Nicholas Dopkins, Tongyi Fei, Stephanie Michael, Nicholas Liotta, Kejun Guo, Kaylee L. Mickens, Brad S. Barrett, Matthew L. Bendall, Stephanie M. Dillon, Cara C. Wilson, Mario L. Santiago, Douglas F. Nixon

Source: EBioMedicine, Vol 103, Iss , Pp 105133- (2024)

Subject Terms: Human endogenous retrovirus (HERV), Interferons, Human immunodeficiency virus type I (HIV-I), Endogenous retroelement (ERE), Long interspersed nuclear element (LINE), Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396424001683; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/77bd4000351b463188eba2fb539d30cc

Endogenous Reverse Transcriptase Inhibition Attenuates TLR5-Mediated Inflammation

Authors: Nicholas Dopkins, Bhavya Singh, Stephanie Michael, Morgan M. O’Mara, Jez L. Marston, Tongyi Fei, Matthew L. Bendall, Douglas F. Nixon

Source: mBio, Vol 14, Iss 1 (2023)

Subject Terms: human endogenous retrovirus (HERV), long interspersed nuclear element (LINE), toll-like receptors (TLRs), innate immunity, flagella, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/2a8e87ef15604f50b84d1e0755b27d0d

Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19

Authors: Maria Carolina Viana, Gislaine Curty, Carolina Furtado, Bhavya Singh, Matthew L. Bendall, João P. B. Viola, Andreia Cristina de Melo, Marcelo A. Soares, Miguel A. M. Moreira

Source: Frontiers in Microbiology, Vol 13 (2023)

Subject Terms: Breast cancer, COVID-19, SARS-CoV-2, microbiome, amplicon sequence variants, 16S-rDNA analysis, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.1074382/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/35ade85c1dd547fbb707629b7c95bc67

Specific human endogenous retroviruses predict metastatic potential in uveal melanoma

Authors: Matthew L. Bendall, Jasmine H. Francis, Alexander N. Shoushtari, Douglas F. Nixon

Source: JCI Insight, Vol 7, Iss 9 (2022)

Subject Terms: Microbiology, Oncology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/af98cb7c69c24e40a048e82b7ed96b0f

SARS-CoV-2 infection mediates differential expression of human endogenous retroviruses and long interspersed nuclear elements

Authors: Jez L. Marston, Matthew Greenig, Manvendra Singh, Matthew L. Bendall, Rodrigo R.R. Duarte, Cédric Feschotte, Luis P. Iñiguez, Douglas F. Nixon

Source: JCI Insight, Vol 6, Iss 24 (2021)

Subject Terms: COVID-19, Infectious disease, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/5f450c2df1094712aae65226d29bf52d

Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression

Authors: Nathaniel Stearrett, Tyson Dawson, Ali Rahnavard, Prathyusha Bachali, Matthew L. Bendall, Chen Zeng, Roberto Caricchio, Marcos Pérez-Losada, Amrie C. Grammer, Peter E. Lipsky, Keith A. Crandall

Source: Frontiers in Immunology, Vol 12 (2021)

Subject Terms: HERV human endogenous retroviruses, lupus (SLE), RNA-Seq, deep learning - artificial neural network (DL-ANN), retrovirus < virus classification, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2021.661437/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/1764a61a79264ac2944a875bd12c909c

Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study

Authors: Gislaine Curty, Greta A. Beckerle, Luis P. Iñiguez, Robert L. Furler, Pedro S. de Carvalho, Jez L. Marston, Stephane Champiat, Jonas J. Heymann, Christopher E. Ormsby, Gustavo Reyes-Terán, Marcelo A. Soares, Douglas F. Nixon, Matthew L. Bendall, Fabio E. Leal, Miguel de Mulder Rougvie

Source: Frontiers in Oncology, Vol 10 (2020)

Subject Terms: breast cancer, HIV, human endogenous retrovirus, retrotranscriptome, microenvironment, formalin-fixed paraffin-embedded, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2020.553983/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/2f536d9c9808435bbb6863b2acbf1212

Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival

Authors: Allison R. Kolbe, Matthew L. Bendall, Alexander T. Pearson, Doru Paul, Douglas F. Nixon, Marcos Pérez-Losada, Keith A. Crandall

Source: Viruses, Vol 12, Iss 9, p 956 (2020)

Subject Terms: RNA-seq, transposable element, endogenous retrovirus, cancer, TCGA, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/12/9/956; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/1f2bff19db004143879ae68348aba4e1

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Authors: Keylie M. Gibson, Margaret C. Steiner, Uzma Rentia, Matthew L. Bendall, Marcos Pérez-Losada, Keith A. Crandall

Source: Viruses, Vol 12, Iss 7, p 758 (2020)

Subject Terms: bioinformatics, validation, simulation, viruses, consensus, haplotypes, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/12/7/758; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/dd026e8a641f4d6ba8619e10a9db6b02

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity

Authors: Andrea Hahn, Matthew L. Bendall, Keylie M. Gibson, Hollis Chaney, Iman Sami, Geovanny F. Perez, Anastassios C. Koumbourlis, Timothy A. McCaffrey, Robert J. Freishtat, Keith A. Crandall

Source: Frontiers in Microbiology, Vol 9 (2018)

Subject Terms: cystic fibrosis, antibiotics, microbiome, metagenomics, true single molecule DNA sequencing, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmicb.2018.01069/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/a4684307258d42c18c76177177e4c1c8

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls

Authors: Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez-Losada, Sarven Sabuncyan, Emily G. Severance, Faith B. Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall

Source: PeerJ, Vol 3, p e1140 (2015)

Subject Terms: Metagenomics, Microbiome, Shotgun sequencing, Schizophrenia, Microbial diversity, Lactic acid bacteria, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/1140.pdf; https://peerj.com/articles/1140/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/0753dfc1e1ba42e7a4e63d36c5960354

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression.

Authors: Matthew L Bendall, Miguel de Mulder, Luis Pedro Iñiguez, Aarón Lecanda-Sánchez, Marcos Pérez-Losada, Mario A Ostrowski, R Brad Jones, Lubbertus C F Mulder, Gustavo Reyes-Terán, Keith A Crandall, Christopher E Ormsby, Douglas F Nixon

Source: PLoS Computational Biology, Vol 15, Iss 9, p e1006453 (2019)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/8960a0b0df054048b5a274ad3c967189

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

Authors: Marcos Pérez-Losada, Eduardo Castro-Nallar, Matthew L Bendall, Robert J Freishtat, Keith A Crandall

Source: PLoS ONE, Vol 10, Iss 6, p e0131819 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4488395?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/819781b1328f4f63b19b5b3e0b5d863a