Sign in

Tanmayee Narendra

@tanmayee.bsky.social
452 followers 893 following 16 posts

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 ntanmayee.github.io

PostsRepliesMedia
Reposted by Tanmayee Narendra
Melissa Johnson, PhD @ladyhistorian.bsky.social · 28/09/2026
I am tired of having to pretend that the value of studying my discipline solely rests on the "marketable skills" we teach. Sometimes things are just worth knowing and doing because they make your life bigger and richer.
131223255
Reposted by Tanmayee Narendra
John Stott @jpsastro.bsky.social · 24/09/2026
Had a UKRI funded grant proposal rejected at the "AI triage stage". "This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review." 🧪 #academicsky
I am writing to let you know that, unfortunately, your application was not successful.

Review process

As part of the initial triage of the 179 proposals submitted to this call, each was assessed using an AI-based review. Every proposal was read independently by several different AI models against the same seven criteria used to shape this call (including cyber security relevance, research quality and novelty, importance of the problem addressed, feasibility of the project plan, likely outputs and impact, value for money, and responsible research practice), with each model asked to give a score and a written justification with supporting quotations from the text. To guard against any one model's idiosyncrasies, we also ran a second, independent process in which different AI models debated the merits and weaknesses of each proposal before reaching a judgement, again against the same criteria. Scores from both processes were combined to produce an overall ranking. 

This AI-based triage was used only to identify approximately 50% of the strongest proposals to take forward to full human review.  Projects selected for funding were drawn from those that progressed to the full human review stage. We recognise that AI-assisted assessment is a new and evolving part of the review process, and we are continuing to evaluate how well it aligns with the judgements of human reviewers on this call. We will soon produce a document detailing our method, so that others can build upon it and improve it.

Feedback on your application

Your application was not selected to progress beyond the AI triage stage.  To provide transparency on the outcome of this assessment, we are sharing below the scores (out of 5) from each of the two AI review processes described above, together with the mean score across the two processes.
40430233
Reposted by Tanmayee Narendra
Philip Ball @philipcball.bsky.social · 15/09/2026
In thisa piece for @thenewworldmag.bsky.social I express the wish for a better level of public discourse around AI that doesn't leave us hanging on every word of the alleged tech gurus. www.thenewworld.co.uk/philip-ball-...
thenewworld.co.uk
Apocalyptic AI fantasies are a stupid, annoying distraction from its real problems
The people who work in AI are not gurus and most of their predictions have been wrong. Working in the industry makes them less reliable commentators, not more
713060
Reposted by Tanmayee Narendra
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/
215758
Reposted by Tanmayee Narendra
Jake Grumbach @jakemgrumbach.bsky.social · 09/09/2026
111331209
Tanmayee Narendra @tanmayee.bsky.social · 08/09/2026
This is shocking!
I said that if OpenAI released its result in the way proposed I would go public with what happened. The reply was "Why would you ruin your career?". I replied that I am an academic, and asked why he thought going public would ruin my career. The reply was, "If you don't want me to be nice, then I don't have to be nice."
010
Reposted by Tanmayee Narendra
Quantian @quantian.bsky.social · 08/09/2026
Dancing very very VERY close to saying “OpenAI stole our almost-complete proof of Navier-Stokes from internal access to our ChatGPT sessions because they were desperate to scoop Anthropic” which is absolutely 100% a believable thing OpenAI would do right now cims.nyu.edu/~tristanb/st...
381556449
Reposted by Tanmayee Narendra
Meredith Whittaker @meredithmeredith.bsky.social · 08/09/2026
Appreciating @ciaranm.bsky.social's grounded, pithy rundown of the ghost stories, catastrophizing, and novice security practices dubiously shaping the current cybersecurity + AI landscape 🙏👇 ciaranmartin.substack.com/p/fud-tier-ai
ciaranmartin.substack.com
Welcome to FUD-tier AI!
The not entirely serious weekly (actually one-off) newsletter charting the wild rampage of Frontier AI through the world of cyber security
29217
Reposted by Tanmayee Narendra
Philip Ball @philipcball.bsky.social · 30/08/2026
Earlier in the summer I suggested I’d do a thread on this gnarly paper. Better late than never. (Yes, it's more WTF biology.) 🧵 /1 www.nature.com/articles/s41...
nature.com
Subnuclear genome compartmentalization controls bivalent chromatin activity - Nature
Knowledge of the spatial location of a gene is necessary to understand its epigenomic regulation.
17925
Reposted by Tanmayee Narendra
Philip Ball @philipcball.bsky.social · 10/08/2026
"Restructuring research funding as a choice between discovery and application gets the economics wrong, the evidence wrong and the people wrong." Great piece. I suspect Richard Jones (on Bsky?) will have views. arxiv.org/abs/2608.00172
arxiv.org
Discovery is not the opposite of application
Restructuring research funding as a choice between discovery and application gets the economics wrong, the evidence wrong and the people wrong.
33015
Tanmayee Narendra @tanmayee.bsky.social · 20/02/2026
My ISCB 2025 talk on DecoDen in the HITSeq COSI is now on YouTube! Check it out - youtu.be/-0EOIDzWniU 🧪🧬🖥️
youtu.be
Towards Personalized Epigenomics: Learning Shared... - Tanmayee Narendra - HiTSeq - ISMB/ECCB 2025
YouTube video by ISCB
000
Tanmayee Narendra @tanmayee.bsky.social · 12/02/2026
Thank you to @narjournal.bsky.social for sharing our work! We used NMF and half-sibling regression to build DecoDen: a tool that de-biases chromatin measurements to reveal clearer signals in personal epigenomes. Really happy to see this out as an Editor's Choice! Code: github.com/ntanmayee/de...
020
Reposted by Tanmayee Narendra
Philip Ball @philipcball.bsky.social · 30/01/2026
This was never really the case. We have known since the 1960s that some of our non-coding DNA has a crucial role in gene regulation: turning the expression of coding genes on & off. It’s been clear for decades that the regulatory DNA is at least comparable in proportion to the protein-coding DNA. /5
1398
Tanmayee Narendra @tanmayee.bsky.social · 02/02/2026
Great thread!
010
Tanmayee Narendra @tanmayee.bsky.social · 05/01/2026
Now out in NAR Genomics and Bioinformatics! academic.oup.com/nargab/artic...
academic.oup.com
Towards personalized epigenomics: learning shared chromatin landscapes and joint de-noising of histone modification assays
Abstract. Epigenetic mechanisms enable cellular differentiation and the maintenance of distinct cell types. They enable rapid responses to external signals
030
Tanmayee Narendra @tanmayee.bsky.social · 13/11/2025
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
arxiv.org
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...
130
Reposted by Tanmayee Narendra
Arnaud Krebs @arnaudkr.bsky.social · 18/08/2025
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👇
1011334
Reposted by Tanmayee Narendra
Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025
🤝 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!
131
Tanmayee Narendra @tanmayee.bsky.social · 29/07/2025
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
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...
020
Reposted by Tanmayee Narendra
Anshul Kundaje @anshulkundaje.bsky.social · 28/06/2025
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/
110329
Reposted by Tanmayee Narendra
Niklas Kempynck @niklaskemp.bsky.social · 03/04/2025
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...
17538
Reposted by Tanmayee Narendra
Randall Munroe @xkcd.com · 17/03/2025
Lungfish xkcd.com/3064
95118511304
Tanmayee Narendra @tanmayee.bsky.social · 11/03/2025
🚨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... 🧬 🖥️
github.com
GitHub - ntanmayee/decoden: 🌊 Analyse experimental conditions and replicates jointly to remove cell-type specific bias in multi-condition ChIP-Seq
🌊 Analyse experimental conditions and replicates jointly to remove cell-type specific bias in multi-condition ChIP-Seq - ntanmayee/decoden
040
Reposted by Tanmayee Narendra
AI x Bio Discovery @aixbiobot.bsky.social · 10/03/2025
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.
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification AssaysFigure 1Figure 2Figure 3
001
Reposted by Tanmayee Narendra
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 10/03/2025
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays www.biorxiv.org/content/10.1101/202…
001
Reposted by Tanmayee Narendra
bioRxivpreprint @biorxivpreprint.bsky.social · 10/03/2025
Towards Personalized Epigenomics: Learning Shared Chromatin Landscapes and Joint De-Noising of Histone Modification Assays www.biorxiv.org/content/10.1101/202…
001
Reposted by Tanmayee Narendra
Wolfgang Huber @wkhuber.bsky.social · 08/03/2025
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/...
huber.embl.de
Digital sovereignty – Huber Group @ EMBL
The US is now a mafia-style extortionist you want to stay away from
47632
Reposted by Tanmayee Narendra
Carl T. Bergstrom @carlbergstrom.com · 06/03/2025
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...
nature.com
Three AI-powered steps to faster, smarter peer review
Tired of spending countless hours on peer reviews? An AI-assisted workflow could help.
621622688
Reposted by Tanmayee Narendra
Hajk-Georg Drost @hajkdrost.bsky.social · 03/03/2025
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...
dundee.ac.uk
How do ancient genes regulate animal embryo development at single cell resolution | University of Dundee, UK
A PhD project at the University of Dundee
02522
Reposted by Tanmayee Narendra
Randall Munroe @xkcd.com · 26/02/2025
RNA xkcd.com/3056
154177422542
Reposted by Tanmayee Narendra
Dawid Zyla @dzyla.bsky.social · 16/02/2025
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
mssearch.xyz
Streamlit
33925217
Reposted by Tanmayee Narendra
Vanja @halfacrocodile.bsky.social · 17/02/2025
(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
23113
Reposted by Tanmayee Narendra
Derek Lowe @dereklowe.bsky.social · 04/02/2025
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...
science.org
What's Happening Inside the NIH and NSF
20413291
Reposted by Tanmayee Narendra
Carl T. Bergstrom @carlbergstrom.com · 28/01/2025
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.
pnas.org
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...
11636156
Tanmayee Narendra @tanmayee.bsky.social · 15/01/2025
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 :)
rukhmabai.com
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,...
000
Reposted by Tanmayee Narendra
Geoff Barton @gjbarton.bsky.social · 06/12/2024
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...
scholar.google.com
Gabriele Schweikert
‪PI, University of Dundee, UK and Universität Tübingen, Germany‬ - ‪‪Cited by 2,140‬‬ - ‪Epigenetics‬ - ‪Gene Regulation and Expression‬ - ‪Computational Biology‬ - ‪Bioinformatics‬ - ‪Machine Learnin...
062
Tanmayee Narendra @tanmayee.bsky.social · 06/12/2024
My PhD supervisor Gabriele Schweikert will be presenting two of my projects here! Please check it out 🧬🖥️ #DevBio #GeneReg
040
Reposted by Tanmayee Narendra
Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
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
bmcgenomics.biomedcentral.com
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...
4244126
Reposted by Tanmayee Narendra
Mitch Guttman @mitchguttman.bsky.social · 27/11/2024
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...
nature.com
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...
9382150
Reposted by Tanmayee Narendra
Alejandro Montenegro @aemonten.bsky.social · 21/11/2024
We need Epigenetic Hulk here.
2227
Reposted by Tanmayee Narendra
Wolfgang Huber @wkhuber.bsky.social · 19/11/2024
Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science". Can we have more conceptual thinking, more theory? Asking for what we really want to achieve and what we need to do gets us there.
3322134
Reposted by Tanmayee Narendra
Gabriele Corso @gcorso.bsky.social · 17/11/2024
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
18610204
Reposted by Tanmayee Narendra
Alex de Mendoza @alexdemendoza.bsky.social · 14/11/2024
SOX and POU are crucial Transcription Factors in animal development, believed to be innovations of this group. Here we find them in unicellular relatives of animals. And hold tight, you can use a choanoflagellate 🦠 SOX gene to make a full chimeric 🐁 ! Read more here 🧵: rdcu.be/d0dPN 1/6
rdcu.be
The emergence of Sox and POU transcription factors predates the origins of animal stem cells
Nature Communications - The pluripotency program is maintained by transcription factors from the Sox and POU families. Here they identify SOX and POU factors from unicellular relatives of animals...
1316281
Reposted by Tanmayee Narendra
Anshul Kundaje @anshulkundaje.bsky.social · 13/11/2024
Incredible resource for DNA binding protein specificity from the Codebook consortium. www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1... Am reading these in detail & will have a lot to say. Stay tuned for thoughts.
biorxiv.org
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as "dark matter" DNA. The genome also encodes hundreds of putative and poorly characterized tran...
311947
Reposted by Tanmayee Narendra
Wolfgang Huber @wkhuber.bsky.social · 01/11/2024
Independent GroupLeader / PI position in AI in Genome Biology, Multimodal Omics at European Molecular Biology Lab (EMBL), Heidelberg! www.embl.org/jobs/positio... Looking in particular for researchers with quantitative/ methodological background who want to dive into leading edge biology research.
23449
Tanmayee Narendra @tanmayee.bsky.social · 04/12/2023
This illustration is so cute! I am going to use it to explain my PhD topic to my parents hehe
030
Tanmayee Narendra @tanmayee.bsky.social · 14/11/2023
Hello! So excited to (finally) be here! I am a PhD candidate in computational biology. I work on understanding gene regulation using computational methods, specifically the interplay of chromatin dynamics and transcription. 🧬 🖥️ #HiSciSky #PhDSky #devbio
2283