siddhartha jena
@epijenatics.bsky.social
buenrostro lab postdoc @ harvard/broad institute. stoked about chromatin, evolution, and bioengineering.
sidujena.github.io
sidujena.github.io
Pinned
siddhartha jena
@epijenatics.bsky.social
· Sep 11
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
Reposted by siddhartha jena
New Online! Signal control during tissue regeneration in adult animals
Signal control during tissue regeneration in adult animals
Nature Reviews Molecular Cell Biology, Published online: 11 November 2025; doi:10.1038/s41580-025-00917-1The ability to track single cells in vivo, combined with insights into chromatin structure, immune–tissue crosstalk, bioelectric and metabolic cues and quantitative modelling, is changing our understanding of how tissues are repaired and renewed. This Review discusses how signals are regulated during regeneration and future directions for a more quantitative understanding of regenerative biology.
bit.ly
November 11, 2025 at 6:04 PM
New Online! Signal control during tissue regeneration in adult animals
Reposted by siddhartha jena
Ancient amino acid sets enable stable protein folds https://www.biorxiv.org/content/10.1101/2025.10.29.685319v1
October 30, 2025 at 2:47 AM
Ancient amino acid sets enable stable protein folds https://www.biorxiv.org/content/10.1101/2025.10.29.685319v1
As a mammalian-cell bioengineer interested in plants, it was great to connect with Sebastian, and I can assure you you’ll learn a TON from talking to him (if you haven’t already from his posts)
I'd love to connect with more genetic engineers. Let me know if there are folks I should follow or meet. Mostly just need more of that in my timeline, but also I love to see the craft in action. There is always something new to learn. TYIA!
bruce lee is shown with the words always a student written below him
ALT: bruce lee is shown with the words always a student written below him
media.tenor.com
October 16, 2025 at 10:09 AM
As a mammalian-cell bioengineer interested in plants, it was great to connect with Sebastian, and I can assure you you’ll learn a TON from talking to him (if you haven’t already from his posts)
Reposted by siddhartha jena
Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 12, 2025 at 1:22 PM
Algal pyrenoids—condensates that mediate ~1/3 of Earth’s CO2 fixation—change size and number as cells divide. Our data suggest a simple control mechanism: a kinase that continuously ejects material from the condensate! ☀️🌍🔬💧 #Biophysics #Photosynthesis
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by siddhartha jena
Lab’s 1st preprint!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
I’m thrilled to share my postdoc work and the first paper from the McKinley Lab! 🎉
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵
@karalmckinley.bsky.social
We built the first transgenic model of menstruation in mice.
We used it to uncover how the endometrium organizes and sheds during menstruation. 🧪
www.biorxiv.org/content/10.1...
🧵
Induction of menstruation in mice reveals the regulation of menstrual shedding
During menstruation, an inner layer of the endometrium is selectively shed, while an outer, progenitor-containing layer is preserved to support repeated regeneration. Progress in understanding this co...
www.biorxiv.org
October 10, 2025 at 1:26 PM
Lab’s 1st preprint!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Menstruation is understudied due to societal taboos + a biological challenge: mice (a key system for research + drug discovery) don’t menstruate.
@cagricevrim.bsky.social made menstruating mice + used them to discover early events in menstruation.
He is on the job market!
Reposted by siddhartha jena
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
October 8, 2025 at 2:21 PM
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
www.quantamagazine.org/loops-of-dna...
Reposted by siddhartha jena
Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
October 7, 2025 at 9:54 AM
Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
Reposted by siddhartha jena
1. What does a Cold War-era game theory problem known as the silent duel have to do with high-risk research strategies, publication in Cell/Nature/Science glamor journals, and the academic job market?
Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718
Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718
September 14, 2025 at 1:50 PM
1. What does a Cold War-era game theory problem known as the silent duel have to do with high-risk research strategies, publication in Cell/Nature/Science glamor journals, and the academic job market?
Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718
Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718
This is a great initiative, and would be an invaluable resource to learn more about (and maybe borrow from!) the diversity of cellular organization and regulation across evolution!
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 24, 2025 at 8:51 PM
This is a great initiative, and would be an invaluable resource to learn more about (and maybe borrow from!) the diversity of cellular organization and regulation across evolution!
very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!
Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!
An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates https://www.biorxiv.org/content/10.1101/2025.09.21.676939v1
September 23, 2025 at 10:22 PM
very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!
Reposted by siddhartha jena
Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
September 21, 2025 at 6:54 PM
Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
Reposted by siddhartha jena
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
September 19, 2025 at 6:20 AM
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Reposted by siddhartha jena
Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1
September 11, 2025 at 8:04 PM
Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
September 11, 2025 at 7:55 PM
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
Reposted by siddhartha jena
We traveled to DC to talk to Congressional Staffers about the impact of NIH and NIBIB funding. It enables us to develop synthetic biology tools to advance cell & genetic medicines for patients in need. REPOST to deliver the message that SCIENCE saves lives & makes America GREAT!
July 21, 2025 at 12:16 PM
We traveled to DC to talk to Congressional Staffers about the impact of NIH and NIBIB funding. It enables us to develop synthetic biology tools to advance cell & genetic medicines for patients in need. REPOST to deliver the message that SCIENCE saves lives & makes America GREAT!
Reposted by siddhartha jena
What'd you do over the weekend? Public Works began resurfacing the street in front of the Chipotle where Thomas Paine wrote Common Sense
July 14, 2025 at 8:07 PM
What'd you do over the weekend? Public Works began resurfacing the street in front of the Chipotle where Thomas Paine wrote Common Sense
Reposted by siddhartha jena
spending the day watching movies isn’t procrastination, it’s leveling up your cinephile game😎
July 13, 2025 at 3:28 PM
spending the day watching movies isn’t procrastination, it’s leveling up your cinephile game😎
Reposted by siddhartha jena
🎉 Over the moon to share the first paper from my lab!! We discovered an unexpected role for the cytokine OSM in lung epithelial homeostasis and repair. 🧵 1/n www.science.org/doi/10.1126/...
Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage
Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the patho...
www.science.org
July 11, 2025 at 1:03 AM
🎉 Over the moon to share the first paper from my lab!! We discovered an unexpected role for the cytokine OSM in lung epithelial homeostasis and repair. 🧵 1/n www.science.org/doi/10.1126/...
Reposted by siddhartha jena
A must-read for histone afficionados: our new review on 'Histone-mediated chromatin organization in prokaryotes and viruses' www.cell.com/trends/bioch... @samuelschwab.bsky.social @vikramalva.bsky.social
Histone-mediated chromatin organization in prokaryotes and viruses
Histones are fundamental chromatin-organizing proteins in eukaryotes and archaea,
where they assemble into (hyper)nucleosomes that wrap DNA. Recent studies have expanded
the known repertoire of histon...
www.cell.com
June 30, 2025 at 7:35 AM
A must-read for histone afficionados: our new review on 'Histone-mediated chromatin organization in prokaryotes and viruses' www.cell.com/trends/bioch... @samuelschwab.bsky.social @vikramalva.bsky.social
Reposted by siddhartha jena
Check out our latest work on chromatin evolution by @crisnava.bsky.social and @seanamontgomery.bsky.social. Building on our study of histone mark conservation (www.nature.com/articles/s41...), we now explore whether these same marks define similar chromatin states across eukaryotes.
Excited to share this story from the “Chromatin Dream Team” in the @arnausebe.bsky.social lab on chromatin evo across eukaryotes! 12 histone mark profiles from 12 species, including rhizarians, discobans, and cryptomonads. Read on to see what we found! www.biorxiv.org/content/10.1... 1/n
Diversity and evolution of chromatin regulatory states across eukaryotes
Histone post-translational modifications (hPTMs) are key regulators of chromatin states, influencing gene expression, epigenetic memory, and transposable element repression across eukaryotic genomes. ...
www.biorxiv.org
March 19, 2025 at 12:09 PM
Check out our latest work on chromatin evolution by @crisnava.bsky.social and @seanamontgomery.bsky.social. Building on our study of histone mark conservation (www.nature.com/articles/s41...), we now explore whether these same marks define similar chromatin states across eukaryotes.
Reposted by siddhartha jena
born too late to get a two Western blot Nature paper, born too early to be a science TikTokker, born just in time to start a postdoc during a global pandemic and look for faculty positions during a historic hiring freeze
March 10, 2025 at 4:32 PM
born too late to get a two Western blot Nature paper, born too early to be a science TikTokker, born just in time to start a postdoc during a global pandemic and look for faculty positions during a historic hiring freeze
Reposted by siddhartha jena
Our new preprint is out＠bioRxiv: www.biorxiv.org/content/10.1...
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
March 7, 2025 at 12:37 AM
Our new preprint is out＠bioRxiv: www.biorxiv.org/content/10.1...
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
@masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in living cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
Reposted by siddhartha jena
1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genome duplication in a long-term multicellularity evolution experiment - Nature
In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...
www.nature.com
March 5, 2025 at 11:00 PM
1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Check out some awesome new work from my labmate @snaga13.bsky.social on inflammation-induced epigenetic memory!
New to bluesky, but I’m excited to share my work over the last few years with @jbuenrostro.bsky.social! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagar.... Here’s a walkthrough of what we found (🧵)
February 18, 2025 at 1:38 PM
Check out some awesome new work from my labmate @snaga13.bsky.social on inflammation-induced epigenetic memory!
Really sad to hear this. I was fortunate to work with Martin as an undergraduate and learned a great deal of chemistry and physics from him, as I’m sure many others did as well.
Just to add to the sad news on #chemsky right now: I've now had it confirmed to me that Martin Karplus died on Saturday.
December 31, 2024 at 7:19 PM
Really sad to hear this. I was fortunate to work with Martin as an undergraduate and learned a great deal of chemistry and physics from him, as I’m sure many others did as well.