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Reposted by Jian Ma

Journal of Cell Science @jcellsci.bsky.social · Jun 20

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/...

preLights in cell biology (June 2025) | Journal of Cell Science | The Company of Biologists

journals.biologists.com

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Jian Ma @jianma.bsky.social · Jun 7

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_...

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Jian Ma @jianma.bsky.social · May 24

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.

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · May 24

EYKTHYR reveals transcriptional regulators of spatial gene programs https://www.biorxiv.org/content/10.1101/2025.05.19.654884v1

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Jian Ma @jianma.bsky.social · May 14

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.

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · May 14

POPARI: Modeling multisample variation in spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.05.08.652741v1

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Reposted by Jian Ma

David Kelley @drkbio.bsky.social · May 11

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/...

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Jian Ma @jianma.bsky.social · Apr 26

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

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...

elifesciences.org

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Jian Ma @jianma.bsky.social · Apr 10

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

bioRxivpreprint @biorxivpreprint.bsky.social · Apr 10

STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues https://www.biorxiv.org/content/10.1101/2025.04.06.647437v1

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Jian Ma @jianma.bsky.social · Apr 10

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.

bioRxivpreprint @biorxivpreprint.bsky.social · Apr 6

Unified integration of spatial transcriptomics across platforms https://www.biorxiv.org/content/10.1101/2025.03.31.646238v1

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Jian Ma @jianma.bsky.social · Mar 22

Congratulations Xian!

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Jian Ma @jianma.bsky.social · Mar 11

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!

ISCB News @iscb.bsky.social · Mar 11

🌟 Congrats to the 2025 ISCB Fellows! 🌟 Honoring leaders in #computationalbiology for outstanding research, innovation and service. See this year's Fellows and their contributions here: https://t.ly/VYfLk

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Jian Ma @jianma.bsky.social · Feb 14

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

bioRxivpreprint @biorxivpreprint.bsky.social · Feb 13

Population-scale cellular GUIDE-seq-2 and biochemical CHANGE-seq-R profiles reveal human genetic variation frequently affects Cas9 off-target activity https://www.biorxiv.org/content/10.1101/2025.02.10.637517v1

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Reposted by Jian Ma

Sri Kosuri @srikosuri.bsky.social · Feb 8

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.

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Jian Ma @jianma.bsky.social · Feb 4

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...

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...

hsph.harvard.edu

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Reposted by Jian Ma

Rohit Singh @rohitsingh8080.bsky.social · Jan 27

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.

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Reposted by Jian Ma

Anshul Kundaje @anshulkundaje.bsky.social · Jan 19

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...

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Reposted by Jian Ma

bioRxivpreprint @biorxivpreprint.bsky.social · Jan 8

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

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Jian Ma @jianma.bsky.social · Jan 1

bsky.app/profile/jian...

Jian Ma @jianma.bsky.social · Jan 1

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/

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.

www.nytimes.com

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Jian Ma @jianma.bsky.social · Jan 1

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/

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.

www.nytimes.com

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Jian Ma @jianma.bsky.social · Dec 31

Happy New Year 2025! 新年快乐~ 🎉

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

media.tenor.com

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Reposted by Jian Ma

RECOMB Conference Series @recombconf.bsky.social · Dec 20

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 📢

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Reposted by Jian Ma

Ameet Talwalkar @atalwalkar.bsky.social · Dec 11

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.

Jian Ma @jianma.bsky.social · Dec 11

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!

bioRxivpreprint @biorxivpreprint.bsky.social · Dec 11

L2G: Repurposing Language Models for Genomics Tasks https://www.biorxiv.org/content/10.1101/2024.12.09.627422v1

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Jian Ma @jianma.bsky.social · Dec 11

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!

bioRxivpreprint @biorxivpreprint.bsky.social · Dec 11

L2G: Repurposing Language Models for Genomics Tasks https://www.biorxiv.org/content/10.1101/2024.12.09.627422v1

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Reposted by Jian Ma

Anshul Kundaje @anshulkundaje.bsky.social · Dec 11

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

Austin Wang @austintwang.bsky.social · Dec 11

(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430

DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...

arxiv.org

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Jian Ma @jianma.bsky.social · Dec 10

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

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Jian Ma @jianma.bsky.social · Dec 6

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/#...

People at CZ Biohub Chicago

Meet the people of Chan Zuckerberg Biohub Chicago.

www.czbiohub.org

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