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Jian Ma

@jianma.bsky.social
3.9K followers 789 following 25 posts

Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science. www.cs.cmu.edu/~jianma

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Reposted by Jian Ma
CMU Griffin School of Computer Science @scsatcmu.bsky.social · 31/07/2026
In a paper published in Science, computational biology researchers at Carnegie Mellon University shed new light on Alzheimer's disease that could lead to improved treatment options.
cs.cmu.edu
AI, Single-Cell Technology Reveal How 3D Genome Differs in People With Alzheimer's Disease
About
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Giulio Maria Pasinetti, MD, PhD @giuliompasinetti.bsky.social · 24/07/2026
Jian Ma, et al. generated multiscale view connecting genome structure, gene expression, & tissue organization in #Alzheimers. They linked alterations in genome folding to disrupted gene regulation, providing a new layer of insight into biology of #Neurodegeneration. 👉 www.science.org/doi/10.1126/...
science.org
Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer’s disease
Alzheimer’s disease (AD) disrupts brain function through cell type–specific transcriptomic and epigenomic alterations, yet the contribution of three-dimensional (3D) genome organization to AD remains ...
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Waggoner Lab @labwaggoner.bsky.social · 23/07/2026
Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer’s disease www.science.org/doi/10.1126/... @science.org @zocean636.bsky.social
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Science Magazine @science.org · 23/07/2026
A new special issue, with papers in Science and #ScienceAdvances, features single-cell and multiomic studies from the National Institutes of Health Common Fund's 4D Nucleome Program, which examines a fourth dimension of nuclear organization. Learn more: scim.ag/4wc4SF8
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Moffitt Lab @moffittlab.bsky.social · 13/07/2026
Genome Research has just announced an exciting call for spatial 'omics related papers! I am thrilled to be co-editing this special issue with Jian Ma (@jianma.bsky.social) and Christina Leslie!
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CMU Griffin School of Computer Science @scsatcmu.bsky.social · 08/04/2026
CMU ranks first for overall graduate computer science programs, tied with MIT and Stanford. Among CS programs, CMU also earned No. 1 rankings in Programming Language, Artificial Intelligence, and Systems, along with a No. 2 ranking in Theory. live-cmu-news.pantheonsite.io/stories/arch...
live-cmu-news.pantheonsite.io
CMU Ranks No. 1 in 2026 U.S. News Graduate Rankings
Carnegie Mellon University secured six No. 1 rankings in the newly released 2026 Best Graduate Schools rankings from the U.S. News & World Report.
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CMU Griffin School of Computer Science @scsatcmu.bsky.social · 22/03/2026
CMU's Center for AI-Driven Biomedical Research chose its first research projects that will use AI and machine learning to unlock the complex information inside genomes and cells, paired with automated laboratory platforms that can run and refine experiments at scale.
cmu.edu
AI4BIO Selects Inaugural Projects for Biomedical Discovery - Center for AI-Driven Biomedical Research - School of Computer Science - Carnegie Mellon University
Carnegie Mellon University's Center for AI-Driven Biomedical Research (AI4BIO) chose its first research projects that will use artificial intelligence and machine learning to unlock the complex information inside genomes and cells, paired with automated laboratory platforms that can run and refine experiments at scale.
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bioRxivpreprint @biorxivpreprint.bsky.social · 27/02/2026
Uncertainty-aware synthetic lethality prediction with pretrained foundation models www.biorxiv.org/content/10.64898/20…
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Association for Computing Machinery @acm.org · 21/01/2026
Meet the 2025 ACM Fellows! Hailing from 14 countries and chosen from among ACM's global membership of over 100,000 computing professionals, these 72 honorees are cited for contributions in a wide range of computing research areas. Please join us in congratulating the new inductees! buff.ly/Pga16R8
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bioRxivpreprint @biorxivpreprint.bsky.social · 27/11/2025
MIMYR: Generative modeling of missing tissue in spatial transcriptomics www.biorxiv.org/content/10.1101/202…
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bioRxivpreprint @biorxivpreprint.bsky.social · 27/11/2025
TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models www.biorxiv.org/content/10.1101/202…
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bioRxivpreprint @biorxivpreprint.bsky.social · 10/11/2025
HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models www.biorxiv.org/content/10.1101/202…
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Jian Ma @jianma.bsky.social · 23/10/2025
that was me scienc'ing the other day
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Journal of Cell Science @jcellsci.bsky.social · 20/06/2025
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/...
journals.biologists.com
preLights in cell biology (June 2025) | Journal of Cell Science | The Company of Biologists
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Jian Ma @jianma.bsky.social · 07/06/2025
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 · 24/05/2025
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.
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Jian Ma @jianma.bsky.social · 14/05/2025
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.
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David Kelley @drkbio.bsky.social · 11/05/2025
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 · 26/04/2025
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
elifesciences.org
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...
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Jian Ma @jianma.bsky.social · 10/04/2025
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
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Jian Ma @jianma.bsky.social · 10/04/2025
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.
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Jian Ma @jianma.bsky.social · 11/03/2025
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!
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Jian Ma @jianma.bsky.social · 14/02/2025
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
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Sri Kosuri @srikosuri.bsky.social · 08/02/2025
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 · 04/02/2025
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...
hsph.harvard.edu
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...
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Rohit Singh @rohitsingh8080.bsky.social · 27/01/2025
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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Anshul Kundaje @anshulkundaje.bsky.social · 19/01/2025
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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bioRxivpreprint @biorxivpreprint.bsky.social · 08/01/2025
DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks www.biorxiv.org/content/10.1101/202…
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Jian Ma @jianma.bsky.social · 31/12/2024
Happy New Year 2025! 新年快乐~ 🎉
media.tenor.com
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
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RECOMB Conference Series @recombconf.bsky.social · 20/12/2024
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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Ameet Talwalkar @atalwalkar.bsky.social · 11/12/2024
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.
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Jian Ma @jianma.bsky.social · 11/12/2024
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!
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Anshul Kundaje @anshulkundaje.bsky.social · 11/12/2024
Check out this systematic benchmark of genome-wide, annotation agnostic DNALMs & strong baseline ab-initio models for biologically meaningful tasks in regulatory genomics 1/
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Jian Ma @jianma.bsky.social · 06/12/2024
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.org
People at CZ Biohub Chicago
Meet the people of Chan Zuckerberg Biohub Chicago.
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Jian Ma @jianma.bsky.social · 30/11/2024
Looking forward to my seminar trip to Princeton Computer Science next week! www.cs.princeton.edu/events/26752
cs.princeton.edu
Learning Multiscale Genome and Cellular Organization | Computer Science Department at Princeton University
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Jian Ma @jianma.bsky.social · 17/11/2024
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...
nytimes.com
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.
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Jian Ma @jianma.bsky.social · 16/11/2024
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...
cmu.edu
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...
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Jian Ma @jianma.bsky.social · 16/11/2024
Hi everyone, loving the vibe here !
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