Sign in

siddhartha jena

@epijenatics.bsky.social
247 followers 667 following 24 posts

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

PostsRepliesMedia
Reposted by siddhartha jena
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
022
Reposted by siddhartha jena
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...
3231104
Reposted by siddhartha jena
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, ...
1175
Reposted by siddhartha jena
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...
215277
Reposted by siddhartha jena
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!
426789
Reposted by siddhartha jena
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/
26430
Reposted by siddhartha jena
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.
1143
Reposted by siddhartha jena
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.
69036
Reposted by siddhartha jena
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...
01313
siddhartha jena @epijenatics.bsky.social · 02/02/2026
😍
000
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!
030
Reposted by siddhartha jena
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...
615467
Reposted by siddhartha jena
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 ...
0136
siddhartha jena @epijenatics.bsky.social · 25/11/2025
Phenomenal work!
110
Reposted by siddhartha jena
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.
093
Reposted by siddhartha jena
bioRxivpreprint @biorxivpreprint.bsky.social · 30/10/2025
Ancient amino acid sets enable stable protein folds www.biorxiv.org/content/10.1101/202…
022
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)
020
Reposted by siddhartha jena
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...
03414
Reposted by siddhartha jena
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!
1830490
Reposted by siddhartha jena
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.
59619
Reposted by siddhartha jena
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/...
16327
Reposted by siddhartha jena
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.
517652
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!
010
siddhartha jena @epijenatics.bsky.social · 23/09/2025
very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!
020
Reposted by siddhartha jena
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...
57634
Reposted by siddhartha jena
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...
17727
Reposted by siddhartha jena
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 11/09/2025
Engineered histones reshape chromatin in human cells www.biorxiv.org/content/10.1101/202…
045
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
18832
Reposted by siddhartha jena
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!
0299
Reposted by siddhartha jena
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
671319277
Reposted by siddhartha jena
Letterboxd @letterboxd.social · 13/07/2025
spending the day watching movies isn’t procrastination, it’s leveling up your cinephile game😎
1980693
Reposted by siddhartha jena
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...
1214530
Reposted by siddhartha jena
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...
04216
Reposted by siddhartha jena
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.
03313
Reposted by siddhartha jena
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
1657583
Reposted by siddhartha jena
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/
311439
Reposted by siddhartha jena
Will Ratcliff @wcratcliff.bsky.social · 05/03/2025
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...
nature.com
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...
16373166
siddhartha jena @epijenatics.bsky.social · 18/02/2025
Check out some awesome new work from my labmate @snaga13.bsky.social on inflammation-induced epigenetic memory!
000
siddhartha jena @epijenatics.bsky.social · 31/12/2024
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.
000
Reposted by siddhartha jena
Philip Ball @philipcball.bsky.social · 10/12/2024
I occasionally did little threads over at The Other Place on papers in biology that seem only to make biology sound even more complicated and arbitrary but in fact illustrate some important generic principles. So here's one. This is the paper I’m looking at. 1/n www.science.org/doi/10.1126/...
science.org
A microRNA is the effector gene of a classic evolutionary hotspot locus
In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a “hotspot” locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 mi...
37920
siddhartha jena @epijenatics.bsky.social · 05/12/2024
Congrats @toettch.bsky.social and Ileana!
041
Reposted by siddhartha jena
Sebastian S. Cocioba @atinygreencell.bsky.social · 18/11/2024
I am ***absurdly*** excited to announce the launch of a new funding opportunity through Experiment dot com!!! You have one month to pitch something wonderful in the realm of plant biology/biotech research and education. $10,000 max grant. PLEASE RE-POST + SHARE!!! 1/3 experiment.com/programs/pla...
experiment.com
Plant Biology Exploratory Research Microgrant | Experiment
For Science!
10247155
siddhartha jena @epijenatics.bsky.social · 17/11/2024
Can't wait to try this out - congratulations to the Boltz-1 team!
020
Reposted by siddhartha jena
Jason Buenrostro @jbuenrostro.bsky.social · 16/11/2024
Excited to see our T-cell exhaustion preprint published! This work is led by Tristan Tay and collaborators at AstraZeneca. See the sub-thread (reformatted for bluesky) originally composed and posted by the newly minted Dr. Tay www.cell.com/cell-reports...
cell.com
Degradation of IKZF1 prevents epigenetic progression of T cell exhaustion in an antigen-specific assay
Tay et al. demonstrate an antigen-specific assay producing exhausted T cells that reflect those found in human tumors. They identify IKZF1 (IKAROS) as a driver of exhaustion progression and validate t...
24411
siddhartha jena @epijenatics.bsky.social · 15/11/2024
excited to be here and for cool chromatin data to finally outnumber bots on my newsfeed!
010
Reposted by siddhartha jena
Vijay Ramani @vram142.bsky.social · 15/11/2024
The latest from our group, led by Megan Ostrowski and @martyyang.bsky.social, is now published in final form (www.cell.com/cell/fulltex...! Many thanks to our excellent peer reviewers for suggesting several experiments (including CAF-1 perturbation) to really improve the study =) #epigenetics
cell.com
The single-molecule accessibility landscape of newly replicated mammalian chromatin
By developing a long-read sequencing method to simultaneously map replication status and protein-DNA contacts in cells, Ostrowski, Yang, et al. show that newly replicated chromatin is enriched for unw...
1420775
Reposted by siddhartha jena
zack chiang @zchiang.bsky.social · 11/11/2024
7 years ago, I met a junior fellow named Jason Buenrostro who blew me away with a vision of futuristic genomic technologies Today, we (Ajay Labade, Caroline Comenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/
714357