rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024Finally, there is so much gratitude for support from @NIMHgov, @NIH_NINDS, @cziscience, @4DNucleome, and our community in the 4DN that empowered me to do this work.(8/8) 010
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024This has been a team effort across the Cremins lab! Special shoutout to Kenneth Pham for helping in crafting and iterating FISHnet, and Harshini Chandrashekar for helping with genomic analyses. (7/8) 110
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024Raw pairwise distances from sequential Oligopaints DNA FISH data have limited ability to separate chromatin traces from different cell types. Using FISHnet boundary calls, we can segregate chromatin traces based on cell type. (6/8) 110
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024We ensemble sequential Oligopaints DNA FISH data where we mask individual allele data based on FISHnet domain calls and aggregate the masks. We envision that FISHnet will empower studies into how single-allele chromatin conformations results in ensemble features. (5/8) 120
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024FISHnet found chromatin domains on published data in human cells (Bintu, Mateo … Boettiger, Zhuang, 2018). When we line up the frequency of single-allele boundary calls we find they line up with bulk Hi-C TADs/subTADs and CTCF/Cohesin peaks. (4/8) 120
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024With simulated data, we showed that FISHnet is robust in calling domains in sequential Oligopaints DNA FISH data including when we create datasets with missing signal like real-world data. We also show linear interpolation as an effective tool to deal with missing signal. (3/8) 110
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024FISHnet is a graph theory method that capture hierarchical chromatin domains using 4 key steps. (2/8) 110
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024Howdy! I'm thrilled to showcase FISHnet, a computational tool designed to identify chromatin domains within sequential Oligopaints DNA FISH data. Check it out on BioRxiv: www.biorxiv.org/content/10.1... 🧵 ⬇️ ⬇️ ⬇️ (1/8). 120
rohaniopatel.bsky.social @rohaniopatel.bsky.social · 05/12/2024Thank you @creminslab.bsky.social!! I am super excited for the work to come, and extremely grateful to the NIH, NHGRI, and the reviewers for believing in my work! 041
Reposted by @rohaniopatel.bsky.socialJenn Cremins @creminslab.bsky.social · 05/12/2024Congratulations to PhD student Rohan Patel @rohaniopatel.bsky.social: Awarded a new NIH F31 fellowship for his work to computationally explore chromatin patterns and mechanisms of loop extrusion in sequential oligopaints imaging data. doi.org/10.1101/2024... x.com/PatelRohanD/... 1142
