Kashyap Chhatbar
@kashyapchhatbar.bsky.social
PhD Computational Biology and Artificial Intelligence
Bioinformatics Researcher, Adrian Bird Lab
University of Edinburgh
Bioinformatics Researcher, Adrian Bird Lab
University of Edinburgh
Pinned
Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies
Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...
doi.org
🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics
doi.org/10.1371/jour...
Let's break down what we found! 👇
doi.org/10.1371/jour...
Let's break down what we found! 👇
Reposted by Kashyap Chhatbar
1/5 Glad to share our latest work with Ian Chambers’ lab published @embojournal.org in which we investigated the role of TET DNA de-methylases during cell fate transitions.
Great team effort, many thanks to Sara Gonzalez Brito @ebarbieri.bsky.social @edinuni-irr.bsky.social
doi.org/10.1038/s443...
Great team effort, many thanks to Sara Gonzalez Brito @ebarbieri.bsky.social @edinuni-irr.bsky.social
doi.org/10.1038/s443...
TET knockout cells transit between pluripotent states and exhibit precocious germline entry | The EMBO Journal
imageimageThe roles of TET DNA demethylases during early development remain poorly defined.
This work uncovers independence of early mouse embryonic stem cell (ESC) transitions
from TET proteins but a...
www.embopress.org
October 30, 2025 at 4:40 PM
1/5 Glad to share our latest work with Ian Chambers’ lab published @embojournal.org in which we investigated the role of TET DNA de-methylases during cell fate transitions.
Great team effort, many thanks to Sara Gonzalez Brito @ebarbieri.bsky.social @edinuni-irr.bsky.social
doi.org/10.1038/s443...
Great team effort, many thanks to Sara Gonzalez Brito @ebarbieri.bsky.social @edinuni-irr.bsky.social
doi.org/10.1038/s443...
Integrator and Restrictor act sequentially to control transcription!
Great set of experiments to complement some of the Integrator-Restrictor overlap hypotheses proposed here doi.org/10.1371/jour...
Great set of experiments to complement some of the Integrator-Restrictor overlap hypotheses proposed here doi.org/10.1371/jour...
October 24, 2025 at 1:57 PM
Integrator and Restrictor act sequentially to control transcription!
Great set of experiments to complement some of the Integrator-Restrictor overlap hypotheses proposed here doi.org/10.1371/jour...
Great set of experiments to complement some of the Integrator-Restrictor overlap hypotheses proposed here doi.org/10.1371/jour...
🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics
doi.org/10.1371/jour...
Let's break down what we found! 👇
doi.org/10.1371/jour...
Let's break down what we found! 👇
Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies
Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...
doi.org
October 24, 2025 at 11:37 AM
🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics
doi.org/10.1371/jour...
Let's break down what we found! 👇
doi.org/10.1371/jour...
Let's break down what we found! 👇
Excited to share my latest preprint! 🚀
We infer regulatory relationships between chromatin-associated proteins and transcriptional control.
We infer regulatory relationships between chromatin-associated proteins and transcriptional control.
Unravelling epigenetic regulation of gene expression with explainable AI - a case study leveraging degron data https://www.biorxiv.org/content/10.1101/2025.01.30.635704v1
February 5, 2025 at 10:53 PM
Excited to share my latest preprint! 🚀
We infer regulatory relationships between chromatin-associated proteins and transcriptional control.
We infer regulatory relationships between chromatin-associated proteins and transcriptional control.
Reposted by Kashyap Chhatbar
Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)
The PNUTS phosphatase complex controls transcription pause release
Kelley et al. discover that the PNUTS phosphatase complex plays an essential role
in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves
this through its TND, which recog...
www.cell.com
November 26, 2024 at 4:18 PM
Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)
Reposted by Kashyap Chhatbar
Looking forward to sharing a new publication from the lab tomorrow! Something a bit different from us this time around. Stay tuned….
November 25, 2024 at 8:49 PM
Looking forward to sharing a new publication from the lab tomorrow! Something a bit different from us this time around. Stay tuned….
Reposted by Kashyap Chhatbar
Non-native English speakers need 50% more time to write a paper
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
November 24, 2024 at 4:43 AM
Non-native English speakers need 50% more time to write a paper
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
When they do, they face a 2.5 times higher chance of being rejected because of language
journals.plos.org/plosbiology/...
Reposted by Kashyap Chhatbar
Loved being back in Edinburgh. Such a beautiful city, such great science. Great to catch up with Adrian, @cathyabbott.bsky.social @cellysally.bsky.social @hannahlong.bsky.social @kashyapchhatbar.bsky.social @r-pantier.bsky.social et al. Thanks Cath+Adrian for the hospitality and Congrats Sara!
November 23, 2024 at 8:42 AM
Loved being back in Edinburgh. Such a beautiful city, such great science. Great to catch up with Adrian, @cathyabbott.bsky.social @cellysally.bsky.social @hannahlong.bsky.social @kashyapchhatbar.bsky.social @r-pantier.bsky.social et al. Thanks Cath+Adrian for the hospitality and Congrats Sara!