Jian Ma

Check out the recent preprints in #cellbio, selected by the @prelights.bsky.social community.

The featured preLight, from @bdmaier.bsky.social,‬ highlights STEAMBOAT, a ML framework for delineation of cellular interactions from @jianma.bsky.social & team.

journals.biologists.com/jcs/article/...

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_...

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.

We introduce POPARI -- an interpretable, spatially-aware factor-based model for multi-sample spatial transcriptomics, capturing spatial patterns of gene programs and how they vary across samples and conditions.

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

Major nuclear locales define nuclear genome organization and function beyond A and B compartments New insights into nuclear genome organization were generated by comparing genome localization relative to three major nuclear locales- nuclear lamina, nuclear speckles, and nucleoli- across several hu...

Final version of our paper @elife.bsky.social: Major nuclear locales define nuclear genome organization and function beyond A and B compartments. elifesciences.org/articles/99116

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, uncovering previously unrecognized patterns. Led by Lane Fellow Shaoheng Liang

Integrating spatial transcriptomics across platforms is hard - different gene panels, sparse data. We introduce LLOKI, using optimal transport + single-cell FM for unified ST integration. Work led by Ellie Haber @mldcmu.bsky.social & Lane Fellow Spencer Krieger.

Congratulations Xian!

Honored to be elected as a Fellow of ISCB @iscb.bsky.social ! Grateful to the community, colleagues, and students who have shaped my journey. Look forward to contributing to the next wave of advances in comp bio!

How does genetic variation affect the cellular genome-wide activity of CRISPR-Cas9 at a population scale? Excited to have contributed to this work in collab w/ Shengdar Tsai, Yong Cheng and their teams @stjuderesearch.bsky.social. The ML component, CHANGE-net, was developed by Wendy Yang in the lab

It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.

PQG Seminar | Program in Quantitative Genomics | Harvard T.H. Chan School of Public Health The goal of the PQG Seminar Series seeks to further the development and application of quantitative methods, especially for high dimensional data, as well as focus on the training of quantitative geno...

Boston friends: I'm giving a PQG seminar next Tuesday (2/11) at @harvardchanschool.bsky.social. Hope to see some of you there! hsph.harvard.edu/research/qua...

Delighted to be hosting @jianma.bsky.social as a Distinguished Speaker (Lecturer?) at Duke Cell Biology.

Great talk on a variety of foods, from Higashi and SpiceMix to Steamboat!

Also, some stuff on 3D genome.

Was asked to contribute brief commentary about my views on the present and future of AI models for regulatory genomics. Wud love for others to add their comments to this thread.

Also check out commentaries from @jianma.bsky.social, Katie Pollard, Remo Rohs & others

www.cell.com/molecular-ce...

DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks https://www.biorxiv.org/content/10.1101/2025.01.06.631595v1

bsky.app/profile/jian...

Fred A. Kummerow, an Early Opponent of Trans Fats, Dies at 102 (Published 2017) Artificial trans fats were ruled unsafe by the Food and Drug Administration partly in response to a lawsuit that Professor Kummerow filed against the agency.

This is so inspiring! I know Fred Kummerow (www.nytimes.com/2017/06/01/s...) published a paper when he was 100 years old: pubmed.ncbi.nlm.nih.gov/28955814/

a black background with fireworks and the words happy new year 2025 ALT: a black background with fireworks and the words happy new year 2025

Happy New Year 2025! 新年快乐~ 🎉

We’re thrilled to announce the keynote speakers for #RECOMB2025! Don’t miss the opportunity to gain insights from leading experts in the field: Peer Bork, Evan Eichler, Narry Kim, Sang Yup Lee, Lior Pachter, Olga Troyanskaya, and Leslie Valiant.

📢 Stay tuned for more updates 📢

Excited about L2G, led by Wenduo Cheng. We leverage LLMs to beat genomic FMs and strong supervised baselines on a wide range of benchmarks. L2G uses cross-modal transfer (rather than vanilla fine-tuning), and neural architecture search to learn a genomic-specific embedder model.

Can we bypass the resource bottleneck of pretraining genomic Foundation Models? Our work L2G repurposes language LLMs for genomics via cross-modal transfer, matching fine-tuned genomic FMs. Kudos to Wenduo & fantastic collab w/ @atalwalkar.bsky.social. L2G, language to genome; L2G, life’s too good!

Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/

I am so, so sorry, Rita. My deepest condolences

People at CZ Biohub Chicago Meet the people of Chan Zuckerberg Biohub Chicago.

I've recently joined the Scientific Advisory Board of
@czbiohub.bsky.social Chicago. CZ Biohub Chicago is tackling major challenges in understanding tissue inflammation. Look forward to the new technologies, including AI/ML solutions, emerging from this Biohub. www.czbiohub.org/chi/people/#...

Looking forward to my seminar trip to Princeton Computer Science next week! www.cs.princeton.edu/events/26752

Mostly agree, but this is also because many colleagues in the field claim every one of their students is the best in the universe :-) Supporting students is great, but I think this tendency contributes to the issue you are pointing out. Is this a US-specific problem (over-the-top effusive letters)?

Best of luck starting your group Jacob

How Bluesky, Alternative to X and Facebook, Is Handling Growth The fledgling social media site has been flooded with new users since the election. It hasn’t all been easy.

The New York Times reported on the rapid growth of @bsky.app. Today I also learned that Jay Graber, the CEO of Bluesky, is half Chinese, and her Chinese first name, Lantian (蓝天), literally means "blue sky."

www.nytimes.com/2024/11/17/t...

CMU Launches Center for AI-Driven Biomedical Research The new Center for AI-Driven Biomedical Research (AI4BIO) will use novel artificial intelligence and machine learning methods to illuminate fundamental aspects of gene regulation, cellular function, t...

We recently launched the AI4BIO Center at Carnegie Mellon. Our goal is to tackle grand challenges in decoding the molecular language governing cellular behavior. Look forward to collaborating with the broad community!

www.cmu.edu/news/stories...