Jacob Schreiber
jmschreiber91.bsky.social
Studying genomics, machine learning, and fruit. My code is like our genomes -- most of it is junk. Assistant Professor UMass Chan Previously IMP Vienna, Stanford Genetics, UW CSE.
👤 Joined on 17 November 2023
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- 17 Kas 2023, 16:39
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Interestingly, tissue-specific accessible regions alone gave performance approaching that of models fine-tuned on VISTA. This suggests a practical route to enhancer design in tissues where experimentally validated enhancer datasets are scarce.
Show PostWhat if no in vivo–validated enhancer dataset is available? We benchmarked inferred enhancer labels based on: • distal accessible regions without CTCF • H3K4me1/H3K27ac-overlapping accessible regions • tissue-specific accessible regions
Show PostIn vivo validation was the critical test: ❤️ heart: 5/5 🦵 limb: 5/5 🧠 midbrain: 5/5
Show PostTo move from prediction to design, we optimized sequences de novo for both accessibility and tissue-specific enhancer activity using Ledidi, a model-guided, gradient-based sequence design method: www.biorxiv.org/content/10.1...
Show PostThe models also captured interpretable regulatory logic, including tissue-specific TF motifs and motif combinations/grammar. This suggests that part of the mammalian cis-regulatory code is sufficiently learnable to support predictive sequence design.
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