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All talks from the main #RECOMB2023 meeting are now available at: youtube.com/playlist?list=… Also: Day 1: youtube.com/playlist?list=… Day 2: youtube.com/playlist?list=… Day 3: youtube.com/playlist?list=… Day 4: youtube.com/playlist?list=…

The final version of our #ISMB2023 Proceedings paper UNADON, a transformer-based model to predict chromosome spatial positioning relative to nuclear bodies, is now online. Muyu "Wendy" Yang will present her work in Lyon during #ISMB2023. academic.oup.com/bioinformatics…

I'm sharing my CGSI-The Computational Genomics Summer Institute 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/…

If you’re at #ISMBECCB2023 in Lyon this year, I highly recommend attending my student Muyu "Wendy" Yang’s proceedings paper talk. Wendy will impress you! I unfortunately will miss ISMB this year

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…

Grateful for everyone who joined me at #ISMBECCB2023 today for my first in-person conference presentation! The past four days have been truly inspiring, filled with so many incredible talks that sparked new ideas. Thank you all for making it memorable!

In Nature Reviews Genetics today, we discuss recent advances in computational methods for #3Dgenome analysis, pointing to an integrative future. Apologies for any missed refs. Joint w/ @NCITomMisteli Frank Alber Yang Zhang Lorenzo Boninsegna Muyu "Wendy" Yang. 4DNucleome nature.com/articles/s4157…

Computational methods for analysing multiscale 3D genome organization go.nature.com/3Lhb4Xb #Review by Yang Zhang, Lorenzo Boninsegna, Muyu "Wendy" Yang, @NCITomMisteli, Frank Alber & Jian Ma 4DNucleome Ray and Stephanie Lane Computational Biology Dept. CMU School of Computer Science UCLA UCLA QCBio National Cancer Institute

This is a massive effort from many, enabled by the leadership of Dr. Tijana Milenkovic. I am glad to have contributed a bit.

Pleased to share our TSA-seq mapping of human genome localization relative to nucleoli and pericentric heterochromatin (PCH) which provides new insights into nuclear genome organization. doi.org/10.1101/2023.1…

Carnegie Mellon University Trustee Ray Lane and his wife, Stephanie, have invested $25 million in support of the university’s boundary-breaking Computational Biology Department. cmu.is/Lane-gift-comp…

When the Richard King Mellon Hall of Sciences is completed, Ray and Stephanie Lane Computational Biology Dept. Machine Learning Dept. at Carnegie Mellon Language Technologies Institute | Carnegie Mellon University from CMU School of Computer Science, along with CMU Biological Sciences CMU Chemistry and @cmuneurosci, will all share the same space. This proximity will undoubtedly usher in a vibrant new era of AI + sciences @CarnegieMellon.

My star PhD student Tianming Zhou is graduating this summer & seeking industry R&D roles. He made outstanding contributions to ML methods for single-cell spatial epigenomics. Seeking top talent at the intersection of #AI and #biomedicine? Contact Tianming tianmingzhou.github.io

Excited to share new results from our 4DN collaboration between the Gilbert, Ma, van Steensel, and Belmont research groups. Joint analysis, led by our trainees, compared chromosome positioning relative to multiple nuclear locales across 4 cell types doi.org/10.1101/2024.0…

How has the AI boom impacted algorithmic biology? Voices piece Cell Systems from Mona Singh Cenk Sahinalp & Team Jianyang (Michael) Zeng Wei Vivian Li Carl Kingsford Qiangfeng Zhang Teresa przytycka Josh Welch Bonnie Berger Lab and myself

Excited to share our @NatureMethods paper on pitfalls & opportunities of using #interpretable #AI in comp bio in the #LLM era. Great collab w/ Ameet Talwalkar's lab. Huge kudos to Valerie Chen & Muyu "Wendy" Yang! Ray and Stephanie Lane Computational Biology Dept. Machine Learning Dept. at Carnegie Mellon CMU School of Computer Science Carnegie Mellon University nature.com/articles/s4159…

Protein Language Models: Is Scaling Necessary? - This paper challenges the prevailing belief that scaling up protein language models (pLMs) is essential for better performance, proposing that careful data curation can achieve comparable results at a fraction of the cost. - The

Genome-wide analyses correlate nuclear speckle proximity with gene expression. We share our minireview discussing possible functional relationships between nuclear speckles and gene expression in both health and disease: authors.elsevier.com/sd/article/S09…

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 Q. Tsai yong cheng and their teams. The ML component, CHANGE-net, was developed by Muyu "Wendy" Yang in the lab!

Thank you so much! I’m really grateful for all the support and guidance throughout this journey. It’s been such a privilege to work on these exciting problems in genome structure and function, and I’m lucky to have had such a wonderful committee!