Rohit Thakur
@rohit-thakur.bsky.social
Research fellow at NCI, here to learn about chromatin organization and functional genomics.
Pinned
Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation
Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be es...
www.medrxiv.org
Our recent preprint about using a custom chromatin capture assay, to identify potential target genes for cancer risk variants. For several variants, the target gene for cis regulation was ~ +/- 1Mb away, and we experimentally confirmed this for multiple targets.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Rohit Thakur
Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests.
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 4:08 AM
Excited to share our latest work on the factors that determine what genes we find (and don't find!) in GWAS and burden tests.
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
We describe a critical concept that we call *specificity*.
Led by Jeff Spence and Hakhamanesh Mostafavi:
Reposted by Rohit Thakur
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Rohit Thakur
🎖️Congratulations to Anthony Wynshaw-Boris, MD, PhD, winner of the ASHG 2025 Advocacy Award! Learn more about the award and Dr. Wynshaw-Boris's work: https://www.ashg.org/membership/awards/2025-awardees/ #ASHG #HumanGenetics
August 21, 2025 at 6:55 PM
🎖️Congratulations to Anthony Wynshaw-Boris, MD, PhD, winner of the ASHG 2025 Advocacy Award! Learn more about the award and Dr. Wynshaw-Boris's work: https://www.ashg.org/membership/awards/2025-awardees/ #ASHG #HumanGenetics
Reposted by Rohit Thakur
New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...
Conservation of chromatin states and their association with transcription factors in land plants
The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conse...
www.biorxiv.org
July 21, 2025 at 5:16 PM
New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...
Reposted by Rohit Thakur
Just in time for the holiday weekend--our July issue is online! Check out the latest human #genetics & #genomics research & commentary
www.cell.com/ajhg/current
www.cell.com/ajhg/current
July 3, 2025 at 3:06 PM
Just in time for the holiday weekend--our July issue is online! Check out the latest human #genetics & #genomics research & commentary
www.cell.com/ajhg/current
www.cell.com/ajhg/current
Reposted by Rohit Thakur
It's time to submit abstracts for ASHG 2025! It's going to be a fantastic meeting in Boston. Hope to see you there!
www.ashg.org/meetings/202...
www.ashg.org/meetings/202...
Abstracts
Abstract submission for ASHG 2025. We encourage you to submit your latest research on human genetics and genomics for programming at the ASHG 2025 Annual Meeting.
www.ashg.org
May 22, 2025 at 3:34 AM
It's time to submit abstracts for ASHG 2025! It's going to be a fantastic meeting in Boston. Hope to see you there!
www.ashg.org/meetings/202...
www.ashg.org/meetings/202...
Reposted by Rohit Thakur
🚨New from @rohit-thakur.bsky.social et al!
📄Mapping chromatin interactions at #melanoma susceptibility loci uncovers distant cis-regulatory gene targets
📄Mapping chromatin interactions at #melanoma susceptibility loci uncovers distant cis-regulatory gene targets
Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets
We utilized a custom, GWAS region-focused capture-HiC assay in human melanocytes to
map physical associations between melanoma-risk-associated credible causal variants
to protein-coding gene promoters...
www.cell.com
May 22, 2025 at 2:47 PM
🚨New from @rohit-thakur.bsky.social et al!
📄Mapping chromatin interactions at #melanoma susceptibility loci uncovers distant cis-regulatory gene targets
📄Mapping chromatin interactions at #melanoma susceptibility loci uncovers distant cis-regulatory gene targets
Reposted by Rohit Thakur
Delighted to contribute, along with locally @adwellspenn.bsky.social & @alessandrachesi.bsky.social. "Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets" @chopresearch.bsky.social @penngenetics.bsky.social
authors.elsevier.com/c/1l8KggeXDz0y
authors.elsevier.com/c/1l8KggeXDz0y
May 22, 2025 at 3:09 PM
Delighted to contribute, along with locally @adwellspenn.bsky.social & @alessandrachesi.bsky.social. "Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets" @chopresearch.bsky.social @penngenetics.bsky.social
authors.elsevier.com/c/1l8KggeXDz0y
authors.elsevier.com/c/1l8KggeXDz0y
Reposted by Rohit Thakur
ASHG is deeply troubled by the recent layoffs at a number of agencies. The impact on scientific progress and innovation is profound and alarming.
Read our statement: www.ashg.org/publications...
Read our statement: www.ashg.org/publications...
February 17, 2025 at 7:47 PM
ASHG is deeply troubled by the recent layoffs at a number of agencies. The impact on scientific progress and innovation is profound and alarming.
Read our statement: www.ashg.org/publications...
Read our statement: www.ashg.org/publications...
Reposted by Rohit Thakur
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and...
www.science.org
February 7, 2025 at 2:48 AM
Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
@science.org @ksusztak.bsky.social
www.science.org/doi/10.1126/...
Reposted by Rohit Thakur
We are now accepting applications for scholarships to the @cshlaboratory.bsky.social Biology of Genomes meeting from the @jxtxfoundation.bsky.social. Open to students worldwide in support of open science. Please help spread the word! jxtxfoundation.org/news/2025-2-...
JXTX + CSHL 2025 Biology of Genomes Scholarship
JXTX + CSHL 2025 Biology of Genomes Scholarship
jxtxfoundation.org
February 5, 2025 at 5:05 PM
We are now accepting applications for scholarships to the @cshlaboratory.bsky.social Biology of Genomes meeting from the @jxtxfoundation.bsky.social. Open to students worldwide in support of open science. Please help spread the word! jxtxfoundation.org/news/2025-2-...
Reposted by Rohit Thakur
What the next 🔥hot🔥 path for cellular therapies?
Check out a pan-cancer assessment 👇
You'll be keen to notice the role of 🔎 #microproteins and small ORFs.😜
🧬 💻
🧪
#genomics
#bioinformatics
#CANsky
#ImmunoSky
#RNAsky
www.biorxiv.org/content/10.1...
Check out a pan-cancer assessment 👇
You'll be keen to notice the role of 🔎 #microproteins and small ORFs.😜
🧬 💻
🧪
#genomics
#bioinformatics
#CANsky
#ImmunoSky
#RNAsky
www.biorxiv.org/content/10.1...
A pan-cancer atlas of T cell targets
T-cell-based immunotherapies have revolutionized cancer treatment, yet only a minority of patients respond to these approaches, significantly constrained by the limited knowledge of tumor-specific ant...
www.biorxiv.org
January 26, 2025 at 8:13 PM
What the next 🔥hot🔥 path for cellular therapies?
Check out a pan-cancer assessment 👇
You'll be keen to notice the role of 🔎 #microproteins and small ORFs.😜
🧬 💻
🧪
#genomics
#bioinformatics
#CANsky
#ImmunoSky
#RNAsky
www.biorxiv.org/content/10.1...
Check out a pan-cancer assessment 👇
You'll be keen to notice the role of 🔎 #microproteins and small ORFs.😜
🧬 💻
🧪
#genomics
#bioinformatics
#CANsky
#ImmunoSky
#RNAsky
www.biorxiv.org/content/10.1...
Reposted by Rohit Thakur
Khanh Trang in our @elife.bsky.social paper integrates 3D genomic maps for >50 diverse cell types with pediatric obesity GWAS. Findings implicate a role for pancreatic islet cell types. Our #V2G mapping nominates effector genes. @penngenetics.bsky.social
doi.org/10.7554/eLif...
doi.org/10.7554/eLif...
January 16, 2025 at 12:38 PM
Khanh Trang in our @elife.bsky.social paper integrates 3D genomic maps for >50 diverse cell types with pediatric obesity GWAS. Findings implicate a role for pancreatic islet cell types. Our #V2G mapping nominates effector genes. @penngenetics.bsky.social
doi.org/10.7554/eLif...
doi.org/10.7554/eLif...
Reposted by Rohit Thakur
Data released by the U.S. Department of Agriculture which showed that over 20 million egg-laying chickens in the U.S. were killed by H5N1 bird flu in the last quarter of 2024.
January 16, 2025 at 8:02 PM
Data released by the U.S. Department of Agriculture which showed that over 20 million egg-laying chickens in the U.S. were killed by H5N1 bird flu in the last quarter of 2024.
Reposted by Rohit Thakur
We are recruiting a postdoc to join our team (myself, Boris Bastian, and Iwei Yeh) at UCSF to develop a pre-cancer atlas of skin cancer -- part of the Human Tumor Atlas Network (#HTAN). #CancerEvolution #Bioinformatics. Interested? Email resume and cover letter to me.
December 14, 2024 at 5:43 PM
We are recruiting a postdoc to join our team (myself, Boris Bastian, and Iwei Yeh) at UCSF to develop a pre-cancer atlas of skin cancer -- part of the Human Tumor Atlas Network (#HTAN). #CancerEvolution #Bioinformatics. Interested? Email resume and cover letter to me.
Reposted by Rohit Thakur
We have an update to our preprint, "Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma", which is part of the Human Tumor Atlas Network (HTAN). Also, the first manuscript post from the Shain lab to Blue Sky! www.biorxiv.org/content/10.1...
Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma
We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-ce...
www.biorxiv.org
December 12, 2024 at 3:56 PM
We have an update to our preprint, "Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma", which is part of the Human Tumor Atlas Network (HTAN). Also, the first manuscript post from the Shain lab to Blue Sky! www.biorxiv.org/content/10.1...
Reposted by Rohit Thakur
📢 Calling all future cancer researchers! Adaptmet is offering 16 MSCA PhD positions in cutting-edge metastasis research. Follow this thread & get to know the exciting projects on offer among Europe’s best teams from top host institutions! More details 👉https://adaptmet.eu/recruitment/
December 10, 2024 at 1:52 PM
📢 Calling all future cancer researchers! Adaptmet is offering 16 MSCA PhD positions in cutting-edge metastasis research. Follow this thread & get to know the exciting projects on offer among Europe’s best teams from top host institutions! More details 👉https://adaptmet.eu/recruitment/
Our recent preprint about using a custom chromatin capture assay, to identify potential target genes for cancer risk variants. For several variants, the target gene for cis regulation was ~ +/- 1Mb away, and we experimentally confirmed this for multiple targets.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation
Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be es...
www.medrxiv.org
December 6, 2024 at 7:07 PM
Our recent preprint about using a custom chromatin capture assay, to identify potential target genes for cancer risk variants. For several variants, the target gene for cis regulation was ~ +/- 1Mb away, and we experimentally confirmed this for multiple targets.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...