Tanmayee Narendra
@tanmayee.bsky.social
Postdoc in Computational Biology at University of Dundee, PhD from University of Tübingen and IMPRS-IS
My interests are epigenomics, chromatin biology, gene regulation, machine learning and causal inference
https://ntanmayee.github.io/
My interests are epigenomics, chromatin biology, gene regulation, machine learning and causal inference
https://ntanmayee.github.io/
Pinned
Tanmayee Narendra
@tanmayee.bsky.social
· Mar 11
🚨New pre-print on Biorxiv! 🚨
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
I was at the Symposium on Causality in Biology & AI in Barcelona. I presented a flash talk on inferring time-varying gene regulatory networks from time series scRNA-Seq data.
Some results here - arxiv.org/abs/2110.06257
Some results here - arxiv.org/abs/2110.06257
Causal Discovery from Conditionally Stationary Time Series
Causal discovery, i.e., inferring underlying causal relationships from observational data, is highly challenging for AI systems. In a time series modeling context, traditional causal discovery methods...
arxiv.org
November 13, 2025 at 2:29 PM
I was at the Symposium on Causality in Biology & AI in Barcelona. I presented a flash talk on inferring time-varying gene regulatory networks from time series scRNA-Seq data.
Some results here - arxiv.org/abs/2110.06257
Some results here - arxiv.org/abs/2110.06257
Reposted by Tanmayee Narendra
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
August 18, 2025 at 1:00 PM
This is not a HiC map! Ever wondered if multiple enhancers get activated simultaneously? We measured chromatin accessibility on thousands of molecules by nanopore to create genome-wide co-accessibility maps. Proud of @mathias-boulanger.bsky.social @kasitc.bsky.social Biology in the thread👇
Reposted by Tanmayee Narendra
🤝 It was a real joy to reconnect with my PhD supervisor and mentor @gjbarton.bsky.social, as well as former colleagues
@stuartmac44.bsky.social, @foreveremain.bsky.social, @mitsenkov.bsky.social, Vanessza Fentor, Douglas Freeburn,
@tanmayee.bsky.social and @rosiegallagher.bsky.social!
@stuartmac44.bsky.social, @foreveremain.bsky.social, @mitsenkov.bsky.social, Vanessza Fentor, Douglas Freeburn,
@tanmayee.bsky.social and @rosiegallagher.bsky.social!
August 6, 2025 at 12:30 PM
🤝 It was a real joy to reconnect with my PhD supervisor and mentor @gjbarton.bsky.social, as well as former colleagues
@stuartmac44.bsky.social, @foreveremain.bsky.social, @mitsenkov.bsky.social, Vanessza Fentor, Douglas Freeburn,
@tanmayee.bsky.social and @rosiegallagher.bsky.social!
@stuartmac44.bsky.social, @foreveremain.bsky.social, @mitsenkov.bsky.social, Vanessza Fentor, Douglas Freeburn,
@tanmayee.bsky.social and @rosiegallagher.bsky.social!
Update: Our paper on "Causal Discovery from Conditionally Stationary Time Series" was presented two weeks ago at ICML 2025!
arxiv.org/abs/2110.06257
arxiv.org/abs/2110.06257
Causal Discovery from Conditionally Stationary Time Series
Causal discovery, i.e., inferring underlying causal relationships from observational data, is highly challenging for AI systems. In a time series modeling context, traditional causal discovery methods...
arxiv.org
July 29, 2025 at 10:22 AM
Update: Our paper on "Causal Discovery from Conditionally Stationary Time Series" was presented two weeks ago at ICML 2025!
arxiv.org/abs/2110.06257
arxiv.org/abs/2110.06257
Reposted by Tanmayee Narendra
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
June 28, 2025 at 10:38 AM
One thing that really bothers me with the new "virtual cell" terminology is that it is currently largely focused on a very narrow definition of models that can predict effects of trans perturbations (gene dosage, drugs etc) on gene expression. 1/
Reposted by Tanmayee Narendra
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
Reposted by Tanmayee Narendra
🚨New pre-print on Biorxiv! 🚨
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
March 11, 2025 at 12:52 PM
🚨New pre-print on Biorxiv! 🚨
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
Histone modifications are measured with ChIP-Seq, but the chromatin landscape introduces biases. We introduce DecoDen to simultaneously learn shared chromatin landscapes while de-biasing individual measurement tracks.
Check it out: github.com/ntanmayee/de...
🧬 🖥️
Reposted by Tanmayee Narendra
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays [new]
Learns shared chromatin structure, correcting histone modification biases across epigenomes.
Learns shared chromatin structure, correcting histone modification biases across epigenomes.
March 10, 2025 at 6:02 PM
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays [new]
Learns shared chromatin structure, correcting histone modification biases across epigenomes.
Learns shared chromatin structure, correcting histone modification biases across epigenomes.
Reposted by Tanmayee Narendra
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays https://www.biorxiv.org/content/10.1101/2025.03.04.641154v1
March 10, 2025 at 5:47 PM
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays https://www.biorxiv.org/content/10.1101/2025.03.04.641154v1
Reposted by Tanmayee Narendra
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays https://www.biorxiv.org/content/10.1101/2025.03.04.641154v1
March 10, 2025 at 5:47 PM
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays https://www.biorxiv.org/content/10.1101/2025.03.04.641154v1
Reposted by Tanmayee Narendra
It's time for individuals and organizations in Europe and other democratic countries to move mission- or life-critical IT services and infrastructure outside the reach of the US government; noting that US tech companies have already largely subordinated themselves.
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
Digital sovereignty – Huber Group @ EMBL
The US is now a mafia-style extortionist you want to stay away from
www.huber.embl.de
March 8, 2025 at 9:15 AM
It's time for individuals and organizations in Europe and other democratic countries to move mission- or life-critical IT services and infrastructure outside the reach of the US government; noting that US tech companies have already largely subordinated themselves.
www.huber.embl.de/group/posts/...
www.huber.embl.de/group/posts/...
Reposted by Tanmayee Narendra
Let's talk about this Nature piece in more detail.
I've rarely read something so anti-scientific anywhere short of the National Review.
www.nature.com/articles/d41...
I've rarely read something so anti-scientific anywhere short of the National Review.
www.nature.com/articles/d41...
Three AI-powered steps to faster, smarter peer review
Tired of spending countless hours on peer reviews? An AI-assisted workflow could help.
www.nature.com
March 6, 2025 at 5:34 AM
Let's talk about this Nature piece in more detail.
I've rarely read something so anti-scientific anywhere short of the National Review.
www.nature.com/articles/d41...
I've rarely read something so anti-scientific anywhere short of the National Review.
www.nature.com/articles/d41...
Reposted by Tanmayee Narendra
Please spread the word🙏:
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
How do ancient genes regulate animal embryo development at single cell resolution | University of Dundee, UK
A PhD project at the University of Dundee
www.dundee.ac.uk
March 3, 2025 at 11:44 AM
Please spread the word🙏:
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
[PhD Position in Computational Evolutionary Transcriptomics]
If you are interested in doing a PhD in gorgeous Scotland on 'Why embryo development goes wrong sometimes?', please consider applying and join our wonderful team in Dundee!
www.dundee.ac.uk/phds/opportu...
Reposted by Tanmayee Narendra
Reposted by Tanmayee Narendra
I've been developing a semantic search tool that covers not just bioRxiv and medRxiv, but the entire PubMed database. This means you can search across a massive collection of biomedical research using keywords, questions, hypotheses, or even full abstracts. Try it out: mssearch.xyz
Streamlit
mssearch.xyz
February 16, 2025 at 7:02 PM
I've been developing a semantic search tool that covers not just bioRxiv and medRxiv, but the entire PubMed database. This means you can search across a massive collection of biomedical research using keywords, questions, hypotheses, or even full abstracts. Try it out: mssearch.xyz
Reposted by Tanmayee Narendra
(1/4) Thrilled to announce another major release of the HOCOMOCO motif collection, well-known for its silly name and rigorous approach to constructing and benchmarking DNA sequence motifs recognized by human and mouse transcription factors.
hocomoco.autosome.org
hocomoco.autosome.org
February 17, 2025 at 11:38 AM
(1/4) Thrilled to announce another major release of the HOCOMOCO motif collection, well-known for its silly name and rigorous approach to constructing and benchmarking DNA sequence motifs recognized by human and mouse transcription factors.
hocomoco.autosome.org
hocomoco.autosome.org
Reposted by Tanmayee Narendra
A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it.
www.science.org/content/blog...
www.science.org/content/blog...
What's Happening Inside the NIH and NSF
www.science.org
February 4, 2025 at 4:40 PM
A long post about what’s happening to the science funding agencies in the US and why. As mentioned, this one just kept getting longer even as I kept stripping curse words from it.
www.science.org/content/blog...
www.science.org/content/blog...
Reposted by Tanmayee Narendra
An LLM "creates textual claims, and then predicts the citations that might be associated with similar text. Obviously, this practice violates all norms of scholarly citation.
At best, LLMs gesticulate toward the shoulders of giants."
Bender, West, and I contributed to this pro/con piece in PNAS.
At best, LLMs gesticulate toward the shoulders of giants."
Bender, West, and I contributed to this pro/con piece in PNAS.
How should the advancement of large language models affect the practice of science? | PNAS
Large language models (LLMs) are being increasingly incorporated into scientific workflows.
However, we have yet to fully grasp the implications of...
www.pnas.org
January 28, 2025 at 1:13 AM
An LLM "creates textual claims, and then predicts the citations that might be associated with similar text. Obviously, this practice violates all norms of scholarly citation.
At best, LLMs gesticulate toward the shoulders of giants."
Bender, West, and I contributed to this pro/con piece in PNAS.
At best, LLMs gesticulate toward the shoulders of giants."
Bender, West, and I contributed to this pro/con piece in PNAS.
Anagha Pavithran interviewed me and Janani about mentorship programs for Indian women interested STEM research. The article is finally out - rukhmabai.com/stem-collect...
Thank you for your kind words about WISR!
Glad to see other organisations like WoAA also mentioned :)
Thank you for your kind words about WISR!
Glad to see other organisations like WoAA also mentioned :)
STEM Collectives: Sisters are doin’ it for themselves - Rukhmabai Initiatives
In the uneven playing field of academia and research, women are now empowering women through mentoring collectives that connect experienced people with those seeking guidance and support in education,...
rukhmabai.com
January 15, 2025 at 11:38 PM
Anagha Pavithran interviewed me and Janani about mentorship programs for Indian women interested STEM research. The article is finally out - rukhmabai.com/stem-collect...
Thank you for your kind words about WISR!
Glad to see other organisations like WoAA also mentioned :)
Thank you for your kind words about WISR!
Glad to see other organisations like WoAA also mentioned :)
Reposted by Tanmayee Narendra
Great work from our colleagues in the Division of Computational Biology! Gabriele Schweikert's group work on machine learning techniques in epigenomics. scholar.google.com/citations?hl...
December 6, 2024 at 12:07 PM
Great work from our colleagues in the Division of Computational Biology! Gabriele Schweikert's group work on machine learning techniques in epigenomics. scholar.google.com/citations?hl...
My PhD supervisor Gabriele Schweikert will be presenting two of my projects here! Please check it out 🧬🖥️
#DevBio #GeneReg
#DevBio #GeneReg
We are super excited. Tomorrow starts the 7th Max Planck Epigenetics Meeting in #Freiburg. We have an exciting line-up. Who is already in Freiburg or on its way? Raise your hands? 🙋♂️🙋♀️
December 6, 2024 at 12:02 PM
Reposted by Tanmayee Narendra
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
bmcgenomics.biomedcentral.com
December 3, 2024 at 8:38 AM
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
1/8
Reposted by Tanmayee Narendra
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Tanmayee Narendra
We need Epigenetic Hulk here.
November 21, 2024 at 7:29 PM
We need Epigenetic Hulk here.