Jian Ma (@jmuiuc) / X

Jian Ma

2,125 posts

Jian Ma

@jmuiuc

Ray and Stephanie Lane Professor of Computational Biology at CMU School of Computer Science @CMUCompBio @SCSatCMU @CarnegieMellon

Pittsburgh, PA

Joined February 2011

Pinned
Jian Ma
@jmuiuc
Oct 2, 2024
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 cs.cmu.edu/news/2024/ai4b…
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Jian Ma
@jmuiuc
Jul 3, 2020
Reviewer #3 would say: This paper simply combines rope jumping and soccer ball juggling, neither of which is considered new.
Jian Ma
@jmuiuc
Jul 31, 2024
I'm sharing a public version of my talk slides @UCLA_CGSI two weeks ago - an update from my #LLMs #compbio Primer talk last year - w/ a focus on genomics FMs (DNA, scRNA). As we're exploring related topics, we remain very interested but also skeptical. 1/3 cs.cmu.edu/~jianma/talks/…
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Jian Ma
@jmuiuc
Aug 27, 2022
NIH peer review system is far from perfect, but it's the best I've seen. I just "retired" from the GCAT study section after 4 years' of service, which prompted me to share a few thoughts re computational proposals. These are the points that I also remind myself. Other thoughts?🧵
Jian Ma
@jmuiuc
Jan 31, 2021
I have been promoted to Full Professor @SCSatCMU @CarnegieMellon @CMUCompBio effective on July 1. I am incredibly grateful to my amazing students, and none of this would have been possible without my colleagues, collaborators, and advisors/mentors over the years.
Jian Ma
@jmuiuc
Feb 23, 2022
We're announcing Nucleome Browser, an integrative & multimodal data navigation platform for @4DNucleome & the broad community. This tool is a result of tremendous creativity & herculean effort over the years from @nimezhu @zocean636, in collab. w/ @jrswedlow @belmont_andrew 1/n
bioRxiv
@biorxivpreprint
Feb 23, 2022
Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome biorxiv.org/cgi/content/sh… #bioRxiv
Jian Ma
@jmuiuc
Sep 17, 2021
Every university should do what @CarnegieMellon has done, setting up an outdoor punching bag so that their faculty and students can visit before they start working on their point-by-point rebuttal to Reviewer #3.
Jian Ma
@jmuiuc
Oct 1, 2021
I am honored to be named the Ray and Stephanie Lane Professor of Computational Biology at Carnegie Mellon @SCSatCMU @CMUCompBio
Jian Ma
@jmuiuc
Jan 13, 2023
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! nature.com/ng/volumes/55/…
Jian Ma
@jmuiuc
Jan 9, 2023
Excited to share our paper in @NatureGenet: SPICEMIX, a joint model of spatial info and gene exp from spatial transcriptome data. Advances upon NMF w/ integration of graphical model, resulting in more meaningful latent reps of cells and spatial metagenes. nature.com/articles/s4158…
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Jian Ma
@jmuiuc
May 8, 2025
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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Jian Ma
@jmuiuc
Jan 9, 2023
Excited to share our paper in @NatureGenet: SPICEMIX, a joint model of spatial info and gene exp from spatial transcriptome data. Advances upon NMF w/ integration of graphical model, resulting in more meaningful latent reps of cells and spatial metagenes. nature.com/articles/s4158…
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Jian Ma
@jmuiuc
Jul 25, 2023
We're excited to introduce GAGE-seq, a single-cell co-assay for 3D genome (#scHiC) & transcriptome (#scRNA). We revealed 3D genome--gene expression interplay in mouse cortex (even integrated w/ #spatialtranscriptome) & during human hematopoiesis. Preprint: biorxiv.org/content/10.110…
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Jian Ma
@jmuiuc
Dec 15, 2024
A troubling incident unfolded at #NeurIPS2024, where a keynote speaker used a slide that perpetuated harmful stereotypes and racial biases against Chinese students and researchers. I wasn't attending the conference, but I watched the talk recording and followed this closely. 1/7
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Jian Ma
@jmuiuc
Jul 23, 2023
I'm sharing my @UCLA_CGSI talk slides last week surveying recent #LLM methods in genomics (DNA, scRNA). As exciting as LLM's potential in genomics is, a note of skepticism remains. Hope we maintain vigilance in what we publish. Feedback on slides welcome. cs.cmu.edu/~jianma/talks/…
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