Sudhir Thakurela / सुधीर ठकुरेला
@sudhirthakurela.bsky.social
PI @mgh @harvardmed
Interested in developmental neurobiology, genomics/epigenomics, comp bio, neurological disorders, and aging.
TFs are the molecular powerhouse of cells!
Interested in developmental neurobiology, genomics/epigenomics, comp bio, neurological disorders, and aging.
TFs are the molecular powerhouse of cells!
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!!
2 new, 1 resubmission.
The next 30 days gonna be interesting!!
Share your strategies on how to organize and stay focused!!
May 23, 2025 at 10:32 PM
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!!
2 new, 1 resubmission.
The next 30 days gonna be interesting!!
Share your strategies on how to organize and stay focused!!
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
8 Resources to study Transcription factor binding, enhancers and histone modification distribution
1. ENCODE www.encodeproject.org/
1. ENCODE www.encodeproject.org/
April 20, 2025 at 1:45 PM
8 Resources to study Transcription factor binding, enhancers and histone modification distribution
1. ENCODE www.encodeproject.org/
1. ENCODE www.encodeproject.org/
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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...
Make sure you subscribe to the chatomics channel!
follow the tutorial here crazyhottommy.github.io/reproduce_g...
Let's Replicate Figure 1 of a Genomics Paper TOGETHER NOW
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...
www.youtube.com
April 11, 2025 at 3:11 AM
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...
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
April 10, 2025 at 2:45 AM
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
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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
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
April 3, 2025 at 4:12 PM
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
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.
---------------------------------------------------------------
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! 🙂
---------------------------------------------------------------
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! 🙂
March 18, 2025 at 4:32 PM
No matter how dark the night is, it is just the night. The arrival of morning and light is inevitable.
---------------------------------------------------------------
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! 🙂
---------------------------------------------------------------
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! 🙂
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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...
2025 Study section tracking
docs.google.com
February 24, 2025 at 4:17 PM
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...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
December 5, 2024 at 7:32 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O
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.
go.nature.com
November 21, 2024 at 2:26 PM
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling go.nature.com/4hXER5O
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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 Sudhir Thakurela / सुधीर ठकुरेला
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...
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...
November 25, 2024 at 11:05 AM
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...
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...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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...
www.biorxiv.org/content/10.1...
November 24, 2024 at 11:32 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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
scidraw.io
bioart.niaid.nih.gov
www.phylopic.org
More well known but very nice though: www.freepik.com
SciDraw |
Scientific Drawings
SciDraw - an open repository of science drawings
scidraw.io
November 23, 2024 at 6:57 AM
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
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
The diversity of food options in India is at another level.
#IndianFood #FoodDiversity
November 24, 2024 at 6:19 AM
Pearl millet bread with ghee, with bottle gourd raita and sabji!
The diversity of food options in India is at another level.
#IndianFood #FoodDiversity
The diversity of food options in India is at another level.
#IndianFood #FoodDiversity
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
November 23, 2024 at 12:09 PM
A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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!
November 23, 2024 at 4:17 AM
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!
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?
Any suggestions from experienced folks here?
November 23, 2024 at 5:12 AM
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?
Any suggestions from experienced folks here?
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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
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
November 22, 2024 at 1:32 PM
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
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
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
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...
www.nature.com/articles/s44...
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 ...
www.nature.com
November 22, 2024 at 2:28 AM
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...
www.nature.com/articles/s44...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
November 20, 2024 at 6:05 PM
cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
Hey, a question for the genetics community. Does genetic fine-mapping work well? How often does it miss?
We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!
We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!
November 19, 2024 at 7:56 PM
Hey, a question for the genetics community. Does genetic fine-mapping work well? How often does it miss?
We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!
We usually find that most fine-mapped variants do not fall within coding or regulatory regions. Is it a limitation of epigenomics or a limitation of fine-mapping? Please share your thoughts!
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
November 18, 2024 at 6:22 PM
My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
🚨Preprint alert!
tinyurl.com/2zkmynsd
Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays?
Then Spatial-scERA is the method for you!
#spatialOMICs
tinyurl.com/2zkmynsd
Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays?
Then Spatial-scERA is the method for you!
#spatialOMICs
Spatial reconstruction of single-cell enhancer activity in a multicellular organism
Enhancers play an essential role in developmental processes by orchestrating the spatial and temporal regulation of gene expression. However, mapping the location of these regulatory elements in the g...
tinyurl.com
November 18, 2024 at 11:05 AM
🚨Preprint alert!
tinyurl.com/2zkmynsd
Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays?
Then Spatial-scERA is the method for you!
#spatialOMICs
tinyurl.com/2zkmynsd
Did you ever dream of reconstruction #spatial single-cell #enhancer activity in a multicellular organism using massively parallel enhancer-reporter assays?
Then Spatial-scERA is the method for you!
#spatialOMICs
Reposted by Sudhir Thakurela / सुधीर ठकुरेला
💫 Join us! We are looking for an enthusiastic #postdoc! Are you excited about #epigenetics, #neocortex development, neurodevelopmental #disorders, #evolution, #organoids?
Apply until 27 Nov 2024! 4-year fully funded position
tu-dresden.de/vacancy/11767
Apply until 27 Nov 2024! 4-year fully funded position
tu-dresden.de/vacancy/11767
November 18, 2024 at 8:01 PM
💫 Join us! We are looking for an enthusiastic #postdoc! Are you excited about #epigenetics, #neocortex development, neurodevelopmental #disorders, #evolution, #organoids?
Apply until 27 Nov 2024! 4-year fully funded position
tu-dresden.de/vacancy/11767
Apply until 27 Nov 2024! 4-year fully funded position
tu-dresden.de/vacancy/11767