Jian Ma
@jmuiuc
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Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science @CMUCompBio @SCSatCMU @CarnegieMellon
Pittsburgh, PA
Joined February 2011
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
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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 Humbling to rewatch: some takes are outdated or wrong but many challenges remain.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: 2024:
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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 🎉
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RT @J_Cell_Sci: Check out the recent preprints in #cellbio, selected by the @prelights community. The featured preLight, from @b_d_maier, h….
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RT @immunoliugy: We're hiring! Our lab at the Ragon Institute of MGB, MIT, and Harvard is looking for a motivated postdoc with experience i….
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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
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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
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POPARI (a variant of potpourri):
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.
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LLOKI (a variant of Loki):
Integrating spatial transcriptomics across platforms is hard - different gene panels, sparse data. We introduce LLOKI, using optimal transport + single-cell FMs for unified ST integration. Work led by @ellie_haber (@mldcmu) & Lane Fellow @SpencerKrieger
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Cellular interactions span scales and shape cell states & tissue function. We introduce STEAMBOAT, a multiscale attention model for spatial omics that reveals how cells interact - from local contact to long-range signals. Led by Lane Fellow @LIANGShaoheng.
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We are overjoyed! Our SPICEMIX paper is being featured on the cover of @NatureGenet! Does it resemble a spatial transcriptome? It looks just like a spice mix!
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In our lab, we take developing computational methods seriously - and we name them well ! Here are some of our #spatialtranscriptomics ML methods so far 👇More to come . .
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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.
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RT @drklly: The short talk and scholarship deadlines for the @KeystoneSymp AI in Molecular Biology meeting in September are coming up fast,….
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I got an email that started with "Hi Dr. Massachusetts." For the record, my last name is indeed Ma - not that MA.
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RT @razoralign: STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues https://t.co/….
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Had a wonderful time in Seoul for #RECOMB2025 @RECOMBconf. Proud of @LIANGShaoheng and @ellie_haber from my group — both delivered fantastic presentation !
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Final version of our paper @eLife (led by @belmont_andrew): Major nuclear locales define nuclear genome organization and function beyond A and B compartments.
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