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siddhartha jena

@epijenatics.bsky.social
247 followers 668 following 25 posts

buenrostro lab postdoc @ harvard/broad institute. stoked about chromatin, evolution, and bioengineering. sidujena.github.io

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siddhartha jena @epijenatics.bsky.social · 05/10/2026
Awesome work from my talented labmate!
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Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 28/09/2026
Today at #ASTRO26: MSK radiation oncologist Dr. Alexander Goglia will present five-year outcomes from a trial of MR-guided SBRT with a focal DIL boost for intermediate-risk prostate cancer. 🗓️ Monday, September 28 | 3:10 p.m. ET Learn more: bit.ly/47lXHPT
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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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Mo Khalil @mokhalil.bsky.social · 17/07/2026
🌱🚨 Very proud and excited to share our PREPRINT, unveiling an advance for plant science, biotech, & synthetic biology in the first (of many) Khalil <> Gehring collaborations! www.biorxiv.org/content/10.6...
biorxiv.org
Rational design of T-DNA vectors enables predictable, single-copy integration in Arabidopsis thaliana
Agrobacterium -mediated transformation is the dominant method for plant transgenesis, yet it frequently produces multi-copy, structurally complex T-DNA insertions associated with transgene silencing, ...
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Deepa Rajan, PhD @deeparajan.bsky.social · 23/04/2026
How can a single cell learn without a brain? We explore this in my paper with @wallaceucsf.bsky.social! We discovered that single cells may learn using molecules similar to those that animal brains use to learn, like CaMKII. Cells can also propagate memory states to their progeny!
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 08/04/2026
Our H1 paper is out #ScienceAdvances: www.science.org/doi/10.1126/... @masaashimazoe.bsky.social et al. reveal that linker histone H1 acts as a liquid-like glue to organize chromatin in live cells. 🎉 Fantastic collab with @rcollepardo.bsky.social @janhuemar.bsky.social and others—huge thanks! 🙌 1/
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VIZCIE | SCIENTIFIC VISUALS @vizcie.bsky.social · 27/02/2026
February's PDB Molecule of the Month is for "Histones Across the Tree of Life". I wanted to focus on the histones of archaea Methanothermus fervidus which thrives at 83°C in sulfur pools in Iceland. I call the image: "Compacting DNA at nearly boiling water."
The image shows DNA nucleosomes arranged from histones in archaea. DNA is portrayed as an incandescent metal in a heated environment.
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Alex Holehouse @alexholehouse.bsky.social · 19/02/2026
Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...
nature.com
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only&nbsp;protein sequence as input.
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FragileNucleosome @fnucleosome.bsky.social · 06/02/2026
We've got two exciting chromatin talks coming up on Wednesday next week: @epijenatics.bsky.social from @jbuenrostro.bsky.social's lab and @ambystoma22.bsky.social! register and join us: us06web.zoom.us/webinar/regi...
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siddhartha jena @epijenatics.bsky.social · 02/02/2026
😍
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siddhartha jena @epijenatics.bsky.social · 13/12/2025
Had a great time at #EMBOevoChromo25 learning about some really cool work at the interface of chromatin and evolution. Really an amazing community of scientists! Thank you to all the organizers :) and can't wait for the next one!
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Will Ratcliff @wcratcliff.bsky.social · 09/12/2025
1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size! www.biorxiv.org/content/10.6...
biorxiv.org
The fitness costs of reproductive specialization scale inversely with organismal size
The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 09/12/2025
A little reading before the Christmas break by the one and only @nucleosomepolice.bsky.social in @annualreviews.bsky.social The expanding Histone universe: Histone-Based DNA organization in noneukaryotic organisms www.annualreviews.org/content/jour...
annualreviews.org
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms
Histones are small basic proteins that form the proteinaceous core of the nucleosome, the repeating building block of chromatin in all eukaryotes. Long thought to be exclusive to eukaryotes, histones ...
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siddhartha jena @epijenatics.bsky.social · 25/11/2025
Phenomenal work!
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Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 11/11/2025
New Online! Signal control during tissue regeneration in adult animals
bit.ly
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.
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bioRxivpreprint @biorxivpreprint.bsky.social · 30/10/2025
Ancient amino acid sets enable stable protein folds www.biorxiv.org/content/10.1101/202…
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siddhartha jena @epijenatics.bsky.social · 16/10/2025
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)
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Martin Jonikas @mjonikas.bsky.social · 12/10/2025
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...
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Kara McKinley @karalmckinley.bsky.social · 10/10/2025
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!
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Philip Ball @philipcball.bsky.social · 08/10/2025
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...
quantamagazine.org
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.
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 07/10/2025
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/...
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Carl T. Bergstrom @carlbergstrom.com · 14/09/2025
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
How competition propels scientific risk-taking
Kevin Gross∗
Department of Statistics
North Carolina State University
Raleigh, NC USA
Carl T. Bergstrom†
Department of Biology
University of Washington
Seattle, WA USA
(Dated: September 9, 2025)
In science as elsewhere, attention is a limited resource and scientists compete with one another
to produce the most exciting, novel and impactful results. We develop a game-theoretic model to
explore how such competition influences the degree of risk that scientists are willing to embrace in
their research endeavors. We find that competition for scarce resources—for example, publications
in elite journals, prestigious prizes, and faculty jobs—motivates scientific risk-taking and may be
important in counterbalancing other incentives that favor cautious, incremental science. Even small
amounts of competition induce substantial risk-taking. Moreover, we find that in an “opt-in” contest,
increasing the stakes induces increased participation—which crowds the contest and further impels
entrants to pursue higher-risk, higher-return investigations. The model also illuminates a source of
tension in academic training and collaboration. Researchers at different career stages differ in their
need to amass accomplishments that distinguish them from their peers, and therefore may not agree
on what degree of risk to accept.
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siddhartha jena @epijenatics.bsky.social · 24/09/2025
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!
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siddhartha jena @epijenatics.bsky.social · 23/09/2025
very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!
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Anders Sejr Hansen @andersshansen.bsky.social · 21/09/2025
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...
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Dr. Sedona Murphy @sedonamurphy.bsky.social · 19/09/2025
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/...
science.org
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...
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bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 11/09/2025
Engineered histones reshape chromatin in human cells www.biorxiv.org/content/10.1101/202…
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siddhartha jena @epijenatics.bsky.social · 12/09/2025
Thank you Kaushik!
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siddhartha jena @epijenatics.bsky.social · 12/09/2025
It’d be so cool to screen evolutionarily divergent CENP-A and map effects on centromere organization!
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siddhartha jena @epijenatics.bsky.social · 12/09/2025
Thank you!
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siddhartha jena @epijenatics.bsky.social · 12/09/2025
Thank you so much!
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
One last thing - I am on the job market! My lab will extend this approach to decode resilient chromatin: adaptations in proteins/DNA that allow for survival in harsh environments. These hold the 🔑 to designing cells that thrive under stress, esp. as we push the limits of where we take them ❄️🚀🪐🌱9/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9
biorxiv.org
Engineered histones reshape chromatin in human cells
Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
This work is a proof of concept towards fully programmable chromatin, something I think will become very common. By combining evolutionary insights, high-throughput assays and predictive/generative modeling, we should be able to uncover some true “superpowers” of chromatin (more on this soon!) 7/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
Finally, we set out to achieve what I’d always wanted. Using screen data and sequence embeddings, we trained a classifier to predict heterochromatin repression, and used it to design totally synthetic histones we called synH4s that demonstrate optimized heterochromatin-repressing activity. 6/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
This process was able to alter cellular plasticity to transcription factor inputs: T cells expressing the tail mutant G4D displayed increased accessibility of heterochromatin-associated transcription factors and were able to respond to overexpression of those factors with proliferation! 5/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
We were surprised to see that some mutations in the N-terminal tail of H4 caused outsized effects on chromatin structure- digging in deeper, we found that these mutations alter nucleosomes in cis, ablating the heterochromatin mark H3K9me3 and shaping spatial compartmentalization in the nucleus. 4/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
The first step was defining sequence-to-function relationships. To do this, we turned to high-throughput screening of 1000s of variants for effects on chromatin accessibility and histone marks. We found that some single-residue changes have global effects on chromatin structure! 3/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
Organisms across the tree of life, including humans, have evolved histone sequences that remodel chromatin in diverse ways. As I learned about these examples, I grew mildly obsessed with the idea of designing histones to do what *I* wanted them to do. 2/9
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siddhartha jena @epijenatics.bsky.social · 11/09/2025
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
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Mo Khalil @mokhalil.bsky.social · 21/07/2025
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!
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City of Boston Streets Cabinet @streets.boston.gov · 14/07/2025
What'd you do over the weekend? Public Works began resurfacing the street in front of the Chipotle where Thomas Paine wrote Common Sense
Boston Public Works Department crews raising castings on School Street
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Letterboxd @letterboxd.social · 13/07/2025
spending the day watching movies isn’t procrastination, it’s leveling up your cinephile game😎
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Ruth Franklin @ruthfranklinlab.bsky.social · 11/07/2025
🎉 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/...
science.org
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...
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Dame lab at Leiden University @damelab.bsky.social · 30/06/2025
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
cell.com
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...
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 19/03/2025
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.
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Kaia Mattioli @kaiamattioli.bsky.social · 10/03/2025
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
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Kazuhiro Maeshima @kazu-maeshima.bsky.social · 07/03/2025
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/
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