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Ales Varabyou
Researcher at Johns Hopkins University
Publications - 15
Citations - 456
Ales Varabyou is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 5, co-authored 9 publications receiving 271 citations. Previous affiliations of Ales Varabyou include Johns Hopkins University School of Medicine.
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Journal ArticleDOI
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
Mihaela Pertea,Mihaela Pertea,Alaina Shumate,Alaina Shumate,Geo Pertea,Ales Varabyou,Ales Varabyou,Florian P. Breitwieser,Yu Chi Chang,Anil K. Madugundu,Akhilesh Pandey,Akhilesh Pandey,Steven L. Salzberg +12 more
TL;DR: The sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project are assembled to create a new catalog of human genes and transcripts, called CHESS, revealing a heretofore unappreciated amount of transcriptional noise in human cells.
Journal ArticleDOI
Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target
Runxia Liu,Yang Hui Jimmy Yeh,Ales Varabyou,Jack A. Collora,Scott Sherrill-Mix,C. Conover Talbot,Sameet Mehta,Kristen Albrecht,Haiping Hao,Hao Zhang,Ross A. Pollack,Subul A. Beg,Rachela M. Calvi,Jianfei Hu,Christine M. Durand,Richard F. Ambinder,Rebecca Hoh,Steven G. Deeks,Jennifer Chiarella,Serena Spudich,Daniel C. Douek,Frederic D. Bushman,Mihaela Pertea,Ya Chi Ho +23 more
TL;DR: Analysis of the isolated single cells showed that the 5′ long terminal repeat of HIV-1 was capable of driving the transcription of host genes downstream of the integration site, which may contribute to HIV persistence.
Journal ArticleDOI
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie.
TL;DR: Salzberg et al. as mentioned in this paper identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population.
Posted ContentDOI
Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise
Mihaela Pertea,Alaina Shumate,Geo Pertea,Ales Varabyou,Yu Chi Chang,Anil K. Madugundu,Anil K. Madugundu,Akhilesh Pandey,Steven L. Salzberg +8 more
TL;DR: Over 30 million additional transcripts are detected at more than 650,000 sites, nearly all of which are likely to be nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells.
Posted ContentDOI
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
TL;DR: Bolotie is presented, an efficient method designed to detect recombination and reassortment events between clades of viral genomes that applied to a large collection of SARS-CoV-2 genomes and discovered hundreds of isolates that are likely of a recombinant origin.