🔥The 9th Round of Easy Loan, Earn $40 Reward is in progress❗️ ⏰ Promotion Period: January 15th - Feburary 15th, 2025 👉 Register now and check more details at gate.io/campaigns/358

The 17 fired members of ACIP, including me, have written an article in JAMA about our experience and our concerns. jamanetwork.com/journals/jama/…

Excited to introduce LiftOn – an open-source tool for accurate liftover of genome annotations (GFF) across assemblies. 🚀 👉 Code &community: github.com/Kuanhao-Chao/L… It’s been incredibly rewarding building this for the genomics community. Thank you to all collaborators/friends!

Sara Mostafavi (Genentech ) & I (Stanford University) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/

FastGA: Fast Genome Alignment biorxiv.org/content/10.110… 🧬🖥️🧪 github.com/thegenemyers/F…

The keynote speakers for the 2025 Wonderful Algorithms in Bioinformatics (WABI) conference have been announced! Ben Langmead, an associate professor of computer science Johns Hopkins University, will present "We Are What We Index; A Primer for the Wheeler Graph Era." wabiconf.github.io/2025/talks/tal…

Christina Boucher, an associate professor of computer and information science and engineering FLORIDA, will give the talk "Recursive Parsing and Grammar Compression in the Era of Pangenomics" as the second keynote at #WABI2025. wabiconf.github.io/2025/talks/tal…

🧵1/n Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome? In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.

Just mind-bendingly awesome work by Alessio here! You can now query md-Fulgor, the most compressed variant, FASTER than you could previously query basic (uncompressed) Fulgor! And the speedup increases with reference size! Also... 1/2

1st paper out as the senior author, fittingly it is the revamped scRepertoire: building a more comprehensive and efficient single-cell immune profiling ecosystem!! Large thanks to my co-authors KelvinTuong and others Paper: journals.plos.org/ploscompbiol/a… Repo: github.com/BorchLab/scRep…

🚨🚨New paper out!!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉nature.com/articles/s4146…

My CGSI-The Computational Genomics Summer Institute 2024 talk is on YouTube -an update to my 2023 talk on #LLMs in #compbio. Humbling to rewatch: some takes are outdated or wrong but many challenges remain. Short on time? Watch the last 10 min of 2024 talk. 2023: youtu.be/tRTVxlakJCw 2024: youtu.be/aBWJomCzkok

My lab’s 5-year NIH R01 grant, awarded to study gene therapy for hearing loss, was abruptly terminated. I want to share how this action has been incredibly harmful and disruptive, not just to my lab, but to the scientific process itself. 1/15

In this blog post, I use #RStats to analyze public ICE detention data. #Dataviz highlight record numbers of detainees without criminal records. More/bigger ICE facilities are popping up far from the border. Code along + take a look yourself: jef.works/blog/2025/07/1… 🧵1/2

Part of the IGVF single-cell analysis workflow - the IGVF-chromap tool offers a command-line interface for indexing and aligning single-cell ATAC-seq data using the Chromap pipeline. Explore the tool: github.com/IGVF/atomic-wo…

Tenure-track faculty positions in Molecular Genetics and Genome Sciences in the University of Oklahoma College of Medicine. Come Join us! medicine.ouhsc.edu/academic-depar… #OUHSC OU College of Medicine ASHG University of Oklahoma