#Bioinformatics professor, interested in #DataScience, with photography, triathlons & books as hobbies
Yale
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We are excited to announce a tenure-track faculty position in Computational Biophysics and Biochemistry, exploring the intricate molecular and cellular processes and the complex interactions of their macromolecular components!
Apply now at apply.interfolio.com/193444.
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Mark Gerstein retweeted
Our AI framework PASCode w/@panos_roussos @NatureMedicine uses graph neural networks to score phenotypic association of >6M cells #PsychAD and discover unknown cell subtypes & genes in #Alzheimers for pathology, cognitive resilience & psychiatric symptoms nature.com/articles/s41591-0…
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Posting a short talk tomorrow for the #QuantumWorldCongress on using Quantum Computing to achieve Biomedical Privacy lectures.gersteinlab.org/sum… #QWC2026 @QWCevent
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Did my annual triathlon today. Brisk swim; slow bike; fast walk... Overjoyed just to make it to the finish line without any drama. Lots of pictures of a great "Triathlon Sunrise." (More stuff at linkstream2.gerstein.info/ta…)
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Posting my talk today at Oxford CS on AI in Structural Bioinformatics lectures.gersteinlab.org/sum… Modelling Flexibility, Disorder & Interactions. Lots of new slides on World Models for protein folding
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Posting my talk today at University of Montpellier on the changing challenges in genomics lectures.gersteinlab.org/sum… Lots of slides on variant impact models
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Mark Gerstein retweeted
Excited to see our work featured by @YaleMed! We introduce MedicalAgentsBench, a benchmark for evaluating how multi-agent LLMs compare with reasoning models—and how they can complement each other in clinical decision-making: medicine.yale.edu/news-artic…
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Posting my talk today at @CRGenomica in Barcelona (hosted by @beaborsari & @GuigoLab) lectures.gersteinlab.org/sum… Lots of slides on the AI Scientist from @XiangruTang
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Posting my talk today at @UniBarcelona on the 25th anniversary of the human genome (hosted by @beaborsari) lectures.gersteinlab.org/sum… Lots of new slides on variant impact models & pseudogene epigenetics across tissues
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Posting my talk today for tutorial IP2 at @iscb's #ISMB2026: Large Language Models & Agentic AI for Biomedical Informatics (organized by @XiangruTang) lectures.gersteinlab.org/sum… Has lots of slides on case studies for LLMs in brain genomics & comparisons with more classic approaches
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Thought this "re-imagining" of the declaration goes well with a recent @NewYorker piece on the "committee-style" writing of the piece (newyorker.com/magazine/2026/…). Personally, I always find "(re)writing groups" rather taxing.
Love this re-imagining of America’s founding using Docs, Gmail, Calendar and more from @GoogleWorkspace. Really puts the history in version history :)
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Mark Gerstein retweeted
(1/n) Ever wonder why scaling up parameters is effective in LLMs or how to make a small model perform better? Our @icmlconf paper on "Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models" @ChenLiu_1996 and @XingzhiSun, may shed some geometric insight
Paper: arxiv.org/pdf/2602.00217
Code: github.com/KrishnaswamyLab/L…
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Mark Gerstein retweeted
During our recent lab roster meeting, we asked about everyone's AI chatbot preferences (n=69, multi-select):
🥇 Claude — 49 (71%)
🥈 ChatGPT — 43 (62%)
🥉 Gemini — 14 (20%)
Takeaway: Mostly Claude + ChatGPT co-usage, with Gemini as a distant third and a long tail of niche tools.
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Post term, cleaned up my biomed. data sci. course website. gersteinlab.org/courses/3520 Now in its 28th year. New thing this year was #AI integration: the students merged (with color coding) the manual & AI summaries of each lecture. Also, lots of new posted videos & PDFs (esp. on DL)
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Finished @CarlZimmer's genome this year too, doing X & Y. Great thanks to the TFs (Andy Chu, @ZhengSuche29504, @XuezhuYu, @AnnaSu1225, & @RoyZhao15) for putting everything together & the @YaleCBB, @YaleDataScience, @YaleBIDS, @YaleMBB & @YaleCSDept students for participating!!
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🤩 spatial panoramic in vivo CRISPR screen via Perturb-DBiT 🤩 Excited to share our collaborative work with @sidichen lab and many outstanding collaborators, now published in Nature Biotechnology!
nature.com/articles/s41587-0…
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Posting my talk tomorrow at #FOGBoston (#FOG26) lectures.gersteinlab.org/sum… Lots of slides on single-cell multi-omics integration for brain disorders. New slides on a formalism for model interpretation @FLGenomics @FoGenomics
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Mark Gerstein retweeted
New @naturecomms paper by @katerbowie @MarkGerstein @jordan_peccia @H2O_Hannah. We study how disinfection shapes microbes in hospital sink drain biofilms. Biofilms regrew in 4 days, enriched for carbapenem-resistant bacteria and multidrug efflux pump genes nature.com/articles/s41467-0…
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Mark Gerstein retweeted
In our @NatMachIntell paper, we introduce a framework to analyse interpretability in deep learning by drawing on a formal notion of model semantics from the philosophy of science. We illustrate our framework with examples from biomedicine. Read here: rdcu.be/e9uYh
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