Jian Ma

Thrilled to launch the AI4BIO Center @CarnegieMellon! Our goal is to tackle grand challenges in understanding how cells work using AI/ML. Excited to help recruit faculty and foster collaboration across @SCSatCMU and campus. There is truly no place like CMU cs.cmu.edu/news/2024/ai4b…

We're hiring! Our lab at the Ragon Institute of MGB, MIT, and Harvard is looking for a motivated postdoc with experience in developing and applying deep learning models. You'll work at the intersection of spatial transcriptomics and structural biology. #postdoc

We introduce EYKTHYR, a computational method that integrates gene expression and chromatin accessibility in a spatially aware model to identify transcription factors shaping spatial gene programs. Led by Lane Fellow @SpencerKrieger #spatialtranscriptomics biorxiv.org/content/10.110…

Thank you Jian for your support! I’m graduating this summer and seeking industry R&D roles in AI/ML for genomics. Looking forward to new opportunities! Please feel free to reach out: [email protected]

My amazing PhD student Wendy Yang @muyu_wendy_yang is graduating this summer & seeking industry R&D roles! She's published in ISMB, Nature Methods, and interned at Genentech. Strong in #AI/#ML for gene regulation. Looking for top AI+bio talent? Contact Wendy: [email protected]

🚨 New to single-cell analysis? Still stuck in a trial-and-error loop? 🚨 Already experienced? Your “optimal” preprocessing pipeline might not actually be optimal. 🚨 Relying on a BioAgent? It likely runs standard procedures that are broadly accepted — but not truly optimal for…

Attending #ISMB2025 and honored to be recognized as a Fellow of the International Society for Computational Biology (@iscb Class of 2025)

Spent some time at #ICML2025 and now heading to #ISMBECCB2025 in Liverpool, UK. Looking forward to seeing many of you there!

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 Humbling to rewatch: some takes are outdated or wrong but many challenges remain.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

Congrats to @muyu_wendy_yang on a successful PhD thesis defense today! Wendy developed a series of ML methods to study genome organization & function, and genome editing - expanding our toolkit for uncovering genome principles. Here is a photo with the happy thesis committee 🎉

Check out the recent preprints in #cellbio, selected by the @prelights community. The featured preLight, from @b_d_maier, highlights STEAMBOAT, a ML framework for delineation of cellular interactions from @jmuiuc @LIANGShaoheng and team. journals.biologists.com/jcs/article/13…

Hannenhalli & Pevzner's legendary STOC-95 paper on sorting by reversals has won the 30-year Test-of-Time Award at STOC! 30 years!! A rare algorithmic gem from #compbio with lasting impact - I still use it to introduce genome rearrangements in my class. sigact.org/prizes/stoc_to…

Enjoyed #CZBiohubCHI Scientific Advisory Board meeting. Incredible science happening under the leadership of @ShanaOKelley @czbiohub - where tech, biology, and AI are being catalyzed under one roof. Photo credit: @Dr_ASingh

We introduce #POPARI, an interpretable, spatially-aware factor-based model for multi-sample #spatialtranscriptomics. Huge kudos to @alam_shahul for his incredible effort (yes, 80+ equations!). In collaboration with @immunoliugy and @insitubiology. biorxiv.org/content/10.110…

The short talk and scholarship deadlines for the @KeystoneSymp AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! keystonesymposia.org/conferences/co…

I got an email that started with "Hi Dr. Massachusetts." For the record, my last name is indeed Ma - not that MA.