Sudhir Thakurela / सुधीर ठकुरेला

NOFO cancellation struck again! The 3rd R01 was also cancelled 🙄🙄🙄
Prepared for 3 R01 in last 2 months and only able to submit 1. 😡😡😡

1 R01 done !!

2nd NOFO got canceled 😞 !!

So, let's do the 3rd one now !!

Will do.. thanks!

Attempting to submit 3 R01 this cycle !!!

2 new, 1 resubmission.
The next 30 days gonna be interesting!!

Share your strategies on how to organize and stay focused!!

8 Resources to study Transcription factor binding, enhancers and histone modification distribution
 1. ENCODE www.encodeproject.org/

follow the tutorial here https://crazyhottommy.github.io/reproduce_genomics_paper_figures/05_figure1_d_f.htmlIn this video, I walk you through the project an... Let's Replicate Figure 1 of a Genomics Paper TOGETHER NOW

Just finished recording another video for reproducing a genomics paper figure www.youtube.com/watch?v=jLG...

Make sure you subscribe to the chatomics channel!

follow the tutorial here crazyhottommy.github.io/reproduce_g...

Some fantastic news amidst all the negativity! My undergrad intern has been accepted into both Harvard and UC Berkeley's master's programs in Computational & Quantitative Biology. So incredibly proud of this dedicated & sincere young scientist. He absolutely earned it! #ProudMentor #FutureOfScience

Congratulations !! Looking forward to read it!

So proud of Thomas Nguyen and co-authors on the publication of this manuscript. Now out in Genetics!

See full paper here! academic.oup.com/genetics/adv...

Thank you to the editors of Genetics for effiecient handling, and to the peer reviewers for excellent feedback

No matter how dark the night is, it is just the night. The arrival of morning and light is inevitable.
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रात चाहे कितनी भी अंधेरी हो, वह सिर्फ रात ही है। सुबह के उजाले का आना अनिवार्य है।

The footprints are fading, but the path remains unchanged! 🙂

2025 Study section tracking

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

Ummmm.. That's a big one for you 😀

Perception of Temperature Even in the Absence of Actual Change is Sufficient to Drive Transgenerational Epigenetic Inheritance Can processes occurring in one individuals nervous system influence the physiology of the descendants? Here we explored the provocative hypothesis that parents sensation or perception of environmental...

Scared to share this after 10 freaking years of waiting, but here we go: We found that temperature *perception* can change the biology of the next generations, even when “it’s just in the parents' head”. Read how C. elegans neurons control epigenetic inheritance!
www.biorxiv.org/content/10.1...

Congratulations!!

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling - Nature Biotechnology MultiPerturb-seq profiles gene expression and chromatin accessibility in single-cell pooled CRISPR screen.

Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O

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...

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...

Congratulations Dr. Chandrashekar 💐
Using human neurons homozygously-engineered with familial AD mutations, Harshini found a role for miswired promoter-enhancer multi-loops in dysregulated excitatory and inhibitory gene expression programs

doi.org/10.1101/2024...

How do cells remember transient signals? New work reveals that a transient pulse of histone deacetylase inhibition leaves a lasting mark on 3D genome architecture in mESCs, linking chromatin dynamics to cellular memory and gene expression robustness.
www.biorxiv.org/content/10.1...

Please add me as well!!

It's one of my favorites! Unfortunately, dont see many people recommending it. Have also read The Gene, but I would always recommend the 8th Day first.

First post on Bluesky, let’s share some websites offering many free illustrations for scientific figures 🖼️ 🧪 🌍 :

scidraw.io

bioart.niaid.nih.gov

www.phylopic.org

More well known but very nice though: www.freepik.com

Pearl millet bread with ghee, with bottle gourd raita and sabji!

The diversity of food options in India is at another level.

#IndianFood #FoodDiversity

A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping - Nature Communications Brain gene regulation is key for neuropsychiatric disorders. Here, the authors show that profiling gene expression and chromatin states in 25 brain regions enables enhancer-promoter mapping at isoform...

A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping

www.nature.com/articles/s41...

Here is a #compbio starter kit! go.bsky.app/QVPoZXp To all the #Bioinformatics #Genomics #MachineLearning folks: please RP and let’s build this together!

Please add our lab!

It is so disappointing & disheartening to see that the grant was withdrawn stating that it is out of scope 😢. Developmemtal signaling, transcription network and chromosome structure, and epigenetic gene regulation are well within NIGMS stated scope.

Any suggestions from experienced folks here?

I enjoyed meeting Ben and he did a great job running the meeting.

During breaks we had a chance to chat about various topics.

He told me a story about one of the first seminars he gave a Ben. Afterwards, one audience member was overheard saying "His work is so much better than his sister's."

16/n

Intrinsic GATA4 expression sensitizes the aortic root to dilation in a Loeys–Dietz syndrome mouse model - Nature Cardiovascular Research Bramel et al. identify a population of GATA4+ vascular smooth muscle cells enriched in the human and mouse aortic root that is intrinsically more susceptible to Loeys–Dietz-syndrome-causing mutations ...

Beautiful paper out today: “Intrinsic GATA4 expression sensitizes the aortic root to dilation in Loeys–Dietz” points to key developmental TFs specific to vascular segments impacting disease risk, implies a link between developmental programming and genetic disease

www.nature.com/articles/s44...

A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression Using Drosophila S2 cells as a model, Hofbauer et al. identify transcriptional silencers with unique chromatin properties that appear inaccessible and function via three distinct motifs and solitary t...

www.cell.com/molecular-ce...

cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers - Nature Structural & Molecular Biology Here, the authors show that the canonical BRG/BRM-associated factor (SWI/SNF) chromatin remodeler generates subnucleosomes containing 50–80 bp of DNA associated with the four core histones. These hemi...

cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.

www.nature.com/articles/s41...