Li Song

BIG surprise from #RECOMB2024 ! What an honor to receive the best paper award! Thanks @RECOMBconf for this wonderful conference with so many interesting talks and posters, and @BenLangmead for many insightful discussions! (Full paper link :D genomebiology.biomedcentral.com/articles/10.11…)

Congrats to Ben Langmead on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational & life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access & use DNA sequencing data. 🧬

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

Excited to share that scPRS is now out @NatureBiotech! We developed a new single-cell-resolved #PRS using deep learning. nature.com/articles/s4158…

Thrilled to announce our paper, "De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells," is officially out in @ScienceMagazine! We used generative AI to build a 'GPS' for immune cells to hunt cancer. Read it here: doi.org/10.1126/scienc…

check out our new @eLife paper, led by @KuanHaoChao along with @alan_mayonnaise, @anqi_liu33, @elapertea: OpenSpliceAI: An efficient, modular implementation of SpliceAI doi.org/10.7554/eLife.…

I am very excited to share our publication, out now in Nature, detailing our developed CRAFTseq methodology for capturing and analysing single cell genomic DNA amplicons alongside the transcriptome and cell surface protein expression. nature.com/articles/s4158…

🚨 Olympiad math + AI: We ran Google’s Gemini 2.5 Pro on the fresh IMO 2025 problems. With careful prompting and pipeline design, it solved 5 out of 6 — remarkable for tasks demanding deep insight and creativity. The model could win gold! 🥇 #AI #Math #LLMs #IMO2025

I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing @divyanshi91! biorxiv.org/content/10.110…

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 @OUCollegeofMed @GeneticsSociety @UofOklahoma

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…

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

My @UCLA_CGSI 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

🚨🚨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…

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…

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

With @giulio_pibiri and @nomad421, we are about to release Fulgor v4.0.0, which is much faster to build and query, without affecting its memory efficiency. You can find all the information in our #WABI2025 paper (bit.ly/3T6TWqw). 🧵 (1/7)

Christina Boucher, an associate professor of computer and information science and engineering @UF, 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…

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