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Jeremy Parker Yang

@jeremyparkeryang.bsky.social
69 followers 176 following 1 posts

PhD Student @ UCSD ML/Bio, genomic language models, epigenetics

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Reposted by Jeremy Parker Yang
Jeff Spence @jeffspence.github.io · 30/05/2025
How well can deep learning models predict the effect of modifying chromatin on gene expression??? Our work -- led by Sanjit Batra and Alan Cabrera when they were in @yun-s-song.bsky.social ’s and Isaac Hilton’s labs -- tries to answer this. 🧵🧬🧪 elifesciences.org/reviewed-pre...
elifesciences.org
Predicting the effect of CRISPR-Cas9-based epigenome editing
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Reposted by Jeremy Parker Yang
Philip Romero @philromero.bsky.social · 08/05/2025
Congrats to Nathaniel and Sri for their exciting work teaching protein language models to generate beyond what evolution has explored. They introduce Reinforcement Learning from eXperimental Feedback (RLXF) to steer generation toward enhanced and non-natural functions www.biorxiv.org/content/10.1...
biorxiv.org
Functional alignment of protein language models via reinforcement learning
Protein language models (pLMs) enable generative design of novel protein sequences but remain fundamentally misaligned with protein engineering goals, as they lack explicit understanding of function a...
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Reposted by Jeremy Parker Yang
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 30/04/2025
Protein language model likelihood are better zero shot mutation effect predictions when they have perplexity 3-6 on the wildtype sequence. www.biorxiv.org/content/10.1...
Relationship between perplexity and zero shot performance.
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Reposted by Jeremy Parker Yang
Vikram Agarwal @vagar.bsky.social · 22/04/2025
One of the toughest parts of the field of massively parallel reporter assays to measure >~thousands of elements is that there are hundreds of pubs using them, but no central repo to easily locate the results....until now! Great collab w/ Jingjing Zhao, Ilias G-S, and @nadavahituv.bsky.social!!
genome.cshlp.org
MPRAbase a Massively Parallel Reporter Assay database
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Reposted by Jeremy Parker Yang
Hani Goodarzi @genophoria.bsky.social · 25/02/2025
@thejohnnyyu.bsky.social, @therealnima.bsky.social, and I, are excited to tell you about Tahoe-100M! The largest publicly available single-cell dataset that measures the effect of 1200 genes on 50 cell line models. The Vevo team has outdone itself. #Tahoe100M www.biorxiv.org/content/10.1...
biorxiv.org
Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling
Building predictive models of the cell requires systematically mapping how perturbations reshape each cell's state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas ...
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Jeremy Parker Yang @jeremyparkeryang.bsky.social · 19/12/2024
Really enjoyed this creative paper using "DNA prompts" to guide Evo in designing genomic sequences. Curious to see how this research evolves. www.biorxiv.org/content/10.1...
biorxiv.org
Semantic mining of functional de novo genes from a genomic language model
Generative genomics models can design increasingly complex biological systems. However, effectively controlling these models to generate novel sequences with desired functions remains a major challeng...
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Reposted by Jeremy Parker Yang
Judith Kribelbauer @jk-swietek.bsky.social · 16/12/2024
Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale! www.biorxiv.org/content/10.1... A 🧵about what it can do: #SynBio #DeepLearning #GeneRegulation
biorxiv.org
EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication
Precise control of gene expression is essential for cellular function, but the mechanisms by which enhancers communicate with promoters to coordinate this process are not fully understood. While seque...
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Reposted by Jeremy Parker Yang
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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Reposted by Jeremy Parker Yang
Christoph Molnar @christophmolnar.bsky.social · 20/11/2024
Even as an interpretable ML researcher, I wasn't sure what to make of Mechanistic Interpretability, which seemed to come out of nowhere not too long ago. But then I found the paper "Mechanistic?" by @nsaphra.bsky.social and @sarah-nlp.bsky.social, which clarified things.
Screenshot of the paper.
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Reposted by Jeremy Parker Yang
Pooja Kathail @poojakathail.bsky.social · 20/11/2024
Super excited to share our review on genomic deep learning models for non-coding variant effect prediction, with Ayesha Bajwa and Nilah Ioannidis. We’d like this review to be a useful resource, and welcome any feedback, comments, or questions! 1/4 arxiv.org/abs/2411.11158
arxiv.org
Leveraging genomic deep learning models for non-coding variant effect prediction
The majority of genetic variants identified in genome-wide association studies of complex traits are non-coding, and characterizing their function remains an important challenge in human genetics. Gen...
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