Shenzhi Chen
shenzhichen1999.bsky.social
Shenzhi Chen
@shenzhichen1999.bsky.social
PhD student in Stark group@IMP Vienna, Machine Learning, Gene Regulation
We use compact CNNs and transfer learning (pre‑trained on genome‑wide ATAC‑seq and fine‑tuned on validated enhancers from VISTA enhancer browser) to program tissue‑specific enhancers. (2/6)
December 24, 2025 at 5:52 PM
Transfer learning reveals clear shifts in motif importance between sequence‑to‑accessibility and sequence‑to‑activity models, highlighting the specific features that drive enhancer function. (3/6)
December 24, 2025 at 5:52 PM
100% (15/15) of designed enhancers for heart, limb, and CNS are active in their intended tissues in mouse embryos. 🎯 (4/6)
December 24, 2025 at 5:51 PM
We hope this approach will help enable the design of more versatile and precise synthetic enhancers across mammalian tissues, cell types, and dynamic cell states. (5/6)
December 24, 2025 at 5:50 PM
Grateful for the amazing guidance from @alex-stark.bsky.social and Vincent Loubiere to help me make my first PhD project come ture!
Huge thanks to all co-authors and collaborators, especially Evgeny @evgenykvon.bsky.social and Jacob @jmschreiber91.bsky.social, for making this work possible. 🙏 (6/6)
December 24, 2025 at 5:50 PM
We use compact CNNs and transfer learning (pre‑trained on genome‑wide ATAC‑seq and fine‑tuned on validated enhancers from VISTA enhancer browser) to program tissue‑specific enhancers. (2/5)
December 24, 2025 at 5:42 PM
Transfer learning reveals clear shifts in motif importance between sequence‑to‑accessibility and sequence‑to‑activity models, highlighting the specific features that drive enhancer function. (2/5)
December 24, 2025 at 5:42 PM
100% (15/15) of designed enhancers for heart, limb, and CNS are active in their intended tissues in mouse embryos. 🎯 (3/5)
December 24, 2025 at 5:41 PM
We hope this approach will help enable the design of more versatile and precise synthetic enhancers across mammalian tissues, cell types, and dynamic cell states. (4/5)
December 24, 2025 at 5:40 PM
Grateful for the amazing guidance from @alex-stark.bsky.social and Vincent Loubiere to help me make my first PhD project come ture!

Huge thanks to all co-authors and collaborators, especially Evgeny @evgenykvon.bsky.social and Jacob @jmschreiber91.bsky.social, for making this work possible. 🙏 (5/5)
December 24, 2025 at 5:39 PM