Our paper describing our new, greatly improved human genome annotation is just out in preprint form, by Ales Varabyou Mihaela Pertea Markus Sommer Beril Erdogdu @IliaMinkin Kuan-Hao Chao Jakob Heinz Alaina Shumate, PhD @thesteinegger Sukhwan Park et al. biorxiv.org/content/10.110…

We still don't know exactly what genes our genome contains, but we had a great workshop at @cshlbanbury to discuss a path forward, described in our arXiv.org preprint: arxiv.org/abs/2303.13996

ORFanage is new system by Ales Varabyou Beril Erdogdu and Mihaela Pertea that finds protein-coding regions in gene annotation, esp. in RNA-seq assemblies. See what it can do in our new preprint biorxiv.org/content/10.110…

Accurate DTU detection in complex diseases with SPIT by Beril Erdogdu,Stephanie Hicks, PhD,Steven Salzberg 💙💛,Mihaela Pertea! Findings include previously unreported DTU events in 6 genes associated with schizophrenia. Also available on Google Colab -> Learn more at biorxiv.org/content/10.110…

check out SPIT, a new method by Beril Erdogdu that detects genes that switch from one transcript to another, with new findings in 6 genes associated with schizophrenia. Co-authors include Stephanie Hicks, PhD Ales Varabyou and senior author Mihaela Pertea biorxiv.org/content/10.110…

Congratulations to Beril Erdogdu who developed a tool to detect #differential #transcript usage (DTU) in #complex diseases (eg #schizophrenia) where lots of #heterogeneity / subgroups exist! Wonderful collaboration w/ Ales Varabyou Steven Salzberg 💙💛 Mihaela Pertea! 🎉

ORFanage is new system by Ales Varabyou Beril Erdogdu and Mihaela Pertea that finds protein-coding regions in RNA-seq assemblies, guided by annotation. Just published today in Nature Computational Science: rdcu.be/dibEl

Ales Varabyou, Beril Erdogdu, Steven Salzberg 💙💛 and Mihaela Pertea 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/s4358… 👉rdcu.be/dicUB

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/10.110… Steven Salzberg 💙💛 Abraham Yuchen Ge and colleagues

Our paper debunking the 2020 cancer microbiome results is now published, in mBio. We'll see if @nature (or the authors) will retract these deeply flawed results. h/t Professor Booty PhD Eric Topol journals.asm.org/doi/10.1128/mb…

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 Mihaela Pertea Ales Varabyou @thesteinegger Markus Sommer Beril Erdogdu @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…

Immunity 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!🎊 bitly.ws/ZgNw

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 Nature Communications from Ida Shinder and Mihaela Pertea. nature.com/articles/s4146…

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/652233/pos…

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/10.110…

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.

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 bioRxiv

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/10.110…