Jian Ma
@jianma.bsky.social
Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science. https://www.cs.cmu.edu/~jianma/
Pinned
Jian Ma
@jianma.bsky.social
· Nov 16
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...
www.cmu.edu
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...
www.cmu.edu/news/stories...
Reposted by Jian Ma
HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models https://www.biorxiv.org/content/10.1101/2025.11.09.687403v1
November 10, 2025 at 5:49 PM
HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models https://www.biorxiv.org/content/10.1101/2025.11.09.687403v1
that was me scienc'ing the other day
Carnegie Mellon researchers shared their transformative work during an Innovation Exhibit with attendees at Forging the Future: The Intersection of Health, AI and Tech, organized in partnership with the Council on Competitiveness and the Global Federation of Competitiveness Councils (GFCC).
October 23, 2025 at 3:33 AM
that was me scienc'ing the other day
Reposted by 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/...
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
June 20, 2025 at 9:51 AM
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/...
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_...
June 7, 2025 at 4:10 AM
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.
EYKTHYR reveals transcriptional regulators of spatial gene programs https://www.biorxiv.org/content/10.1101/2025.05.19.654884v1
May 24, 2025 at 5:02 AM
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.
POPARI: Modeling multisample variation in spatial transcriptomics https://www.biorxiv.org/content/10.1101/2025.05.08.652741v1
May 14, 2025 at 6:13 AM
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.
Reposted by Jian Ma
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/...
May 11, 2025 at 9:29 PM
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/...
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
April 26, 2025 at 6:26 PM
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
STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues https://www.biorxiv.org/content/10.1101/2025.04.06.647437v1
April 10, 2025 at 3:18 PM
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.
Unified integration of spatial transcriptomics across platforms https://www.biorxiv.org/content/10.1101/2025.03.31.646238v1
April 10, 2025 at 3:13 PM
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.
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!
🌟 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
March 11, 2025 at 3:34 PM
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
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
February 14, 2025 at 7:00 PM
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
Reposted by Jian Ma
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.
February 8, 2025 at 9:21 PM
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.
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
February 4, 2025 at 2:54 AM
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...
Reposted by Jian Ma
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.
Great talk on a variety of foods, from Higashi and SpiceMix to Steamboat!
Also, some stuff on 3D genome.
January 27, 2025 at 7:18 PM
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.
Great talk on a variety of foods, from Higashi and SpiceMix to Steamboat!
Also, some stuff on 3D genome.
Reposted by Jian Ma
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...
Also check out commentaries from @jianma.bsky.social, Katie Pollard, Remo Rohs & others
www.cell.com/molecular-ce...
January 19, 2025 at 5:20 AM
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...
Also check out commentaries from @jianma.bsky.social, Katie Pollard, Remo Rohs & others
www.cell.com/molecular-ce...
Reposted by Jian Ma
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks https://www.biorxiv.org/content/10.1101/2025.01.06.631595v1
January 8, 2025 at 6:47 PM
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks https://www.biorxiv.org/content/10.1101/2025.01.06.631595v1
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
December 31, 2024 at 7:00 PM
Happy New Year 2025! 新年快乐~ 🎉
Reposted by Jian Ma
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 📢
📢 Stay tuned for more updates 📢
December 20, 2024 at 11:14 AM
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 📢
📢 Stay tuned for more updates 📢
Reposted by Jian Ma
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!
L2G: Repurposing Language Models for Genomics Tasks https://www.biorxiv.org/content/10.1101/2024.12.09.627422v1
December 11, 2024 at 7:36 PM
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!
L2G: Repurposing Language Models for Genomics Tasks https://www.biorxiv.org/content/10.1101/2024.12.09.627422v1
December 11, 2024 at 1:41 PM
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!
Reposted by Jian Ma
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
(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
December 11, 2024 at 2:54 AM
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'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/#...
@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
December 6, 2024 at 12:17 AM
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/#...
@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
Learning Multiscale Genome and Cellular Organization | Computer Science Department at Princeton University
www.cs.princeton.edu
November 30, 2024 at 2:26 AM
Looking forward to my seminar trip to Princeton Computer Science next week! www.cs.princeton.edu/events/26752
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...
www.nytimes.com/2024/11/17/t...
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.
www.nytimes.com
November 17, 2024 at 11:55 PM
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...
www.nytimes.com/2024/11/17/t...