Genomics Scientist and Engineer; Cooking and Calisthenics Enthusiast
Baltimore, MD
Joined December 2011
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Decades of HIV research. Thousands of RNA-seq studies. No transcriptome annotation.
Announcing HIV Atlas: the first reference annotation of HIV. With @elapertea, @StevenSalzberg1, Diane Bolton, @MykhayloObolon, Sophia Cheng
πbiorxiv.org/content/10.1101/β¦
πccb.jhu.edu/HIV_Atlas
ALT The HIV Atlas web interface provides a simple interface for explore and download transcriptome annotations for any of the currently annotate 2,080 genomes.
ALT The logo for the HIV Atlas
All annotations are available in HIV Atlas - an interactive web portal powered by JBrowse2 for browsing and downloads.
Special thanks to JBrowse2 team (@usejbrowse and Colin Diesh)!
πbiorxiv.org/content/10.1101/β¦
πccb.jhu.edu/HIV_Atlas
Ales Varabyou retweeted
check out the new paper from my PhD student Hayden (Hyun Joo) Ji, in which she uses #AlphaFold, splice site predictors, and other tools to identify hundreds of novel isoforms of human genes. Well done Hayden! biorxiv.org/content/10.1101/β¦
Ales Varabyou retweeted
our new paper led by @IliaMinkin describes how we used a very large multi-genome alignment to discover a striking degree of conservation among most splice sites in protein-coding genes. The paper is now out in @biorxivpreprint
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Ales Varabyou retweeted
The Ph.D. application deadline for the Quantitative Biomedical Sciences program at Dartmouth (geiselmed.dartmouth.edu/qbs/) is this Friday. If you are interested in translational or this type of low-level data structure bioinfos, QBS is a great addition to your application list.
Thrilled to share the first preprint from my lab! We losslessly compressed FM-index using a novel technique called run-block compressed BWT (RBBWT). Building upon it, we implemented the Centrifuger method for taxonomic classification on sequencing data. biorxiv.org/content/10.1101/β¦
Ales Varabyou retweeted
Thrilled to share the first preprint from my lab! We losslessly compressed FM-index using a novel technique called run-block compressed BWT (RBBWT). Building upon it, we implemented the Centrifuger method for taxonomic classification on sequencing data. biorxiv.org/content/10.1101/β¦
Ales Varabyou retweeted
Love to explore how HIV hides in CD4 T cells? Love single-cell multiomics, bioinformatics, genomics, and immunology? Wanna join Michelle and Sam, the freshly minted CROI New Investigator Awardees? About to graduate from PhD? Join our lab as a postdoc now!
jobs.sciencecareers.org/job/β¦
Repeat elements introduce systematic errors during alignment, affecting assembly and introducing artifacts into major gene catalogs. Learn how to detect and greatly improve spliced alignments with EASTR. In @NatureComms from @IdaShinder1 and @elapertea. nature.com/articles/s41467-0β¦
Ales Varabyou retweeted
@ImmunityCP Single-cell epigenetic, transcriptional & protein profile of latent & active HIV+ cells by DOGMAseq identified 4 states of HIV+ cells: IRF, cytotoxic, AP-1 & cell death. IKZF3 helps HIV+ cells proliferate. Congrats to our postdoc @Yulong_Wei!π bitly.ws/ZgNw
Ales Varabyou retweeted
Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With @elapertea @av_sparrow @thesteinegger @markusjsommer @ErdogduBeril @IliaMinkin and others: genomebiology.biomedcentral.β¦
Ales Varabyou retweeted
Our paper debunking the 2020 cancer microbiome results is now published, in @mbiojournal. We'll see if @nature (or the authors) will retract these deeply flawed results. h/t @ProfBootyPhD @EricTopol journals.asm.org/doi/10.1128β¦
Ales Varabyou retweeted
Ales Varabyou, @ErdogduBeril, @StevenSalzberg1 and @elapertea present ORFanage, a method to search for open reading frames in protein-coding transcripts, guided by reference annotation to maximize protein similarity within genes. nature.com/articles/s43588-0β¦
πrdcu.be/dicUB
Ales Varabyou retweeted
A re-analysis of multiple studies that asserted the role of bacteria in cancer raises questions at to the veracity of the findings and the link
biorxiv.org/content/10.1101/β¦ @StevenSalzberg1 @AbrahamGihawi @YuchenGe1 and colleagues
Ales Varabyou retweeted
ORFanage is new system by @av_sparrow @ErdogduBeril and @elapertea that finds protein-coding regions in RNA-seq assemblies, guided by annotation. Just published today in @NatComputSci:
rdcu.be/dibEl