Sandipan Brahma

🇮🇳 | Assistant Professor @UNMC_GCBA | #NewPI | Chromatin genomics and biochemistry | Henikoff lab @fredhutch and @BlaineBartholo2 lab alumnus

[Sandipan Brahma @BrahmaComplex]

Our paper on RNAPII-BAF-TF synergy is now out in @NatureGenet! Since publishing the preprint (🧵➡️ https://t.co/itxuBmMjmX), we added expt to show that enhanced nucleosome eviction upon stabilization of BAF by RNAPII, assayed by CUT&RUN.ChIP, is ATP-dep. ➡️https://t.co/RYfRBxlOSz

[Oded Rechavi @OdedRechavi]

Important announcement!!!🫵💥💫

Would you have a tooth pulled if it helped your chances to get an important grant funded?

Absurd question (obviously), but the situation right now is so bad funding-wise, that I bet some of you actually considered it for a second…

Well, don’t get desperate - we created a new tool that might help! (keep your teeth!)

I’m excited to announce that as of today we are officially releasing “QED for Grants” for everyone. What started off as an extension of our existing paper review platform, grew in the last few months to an entirely new design. We’ve been working like crazy on this, and although we have more things we want to add in the (very near) future, we decided to release our AI for grants NOW, earlier than planned. It’s not perfect, no AI is, but for the first time, when I run my own grants through @qedscience, I feel it gets the research, finds real problems, and gives me very useful feedback that I can implement before submission. It’s like sending it to 20 scientists from my domain, knowing they’ll agree to dedicate their entire week to carefully read and comment on every line.

It’s very important to write your own grants yourself, it makes you think hard and you learn a lot from doing it, and q.e.d’s system is designed to preserve these positive aspects and augment them - you get feedback on your own writing, we don’t write for you!!

But at the same time, a typical PI spends many months every year writing proposals and sadly only a tiny fraction gets funded, even if the ideas are good. When you are forced to submit an unreasonable amount of grants the quality of the writing drops, and rejection rates increase. Not because the essence is bad. It’s simply too competitive right now (the cuts made it so much worse) and if your proposal is not super clear and tight, and if it’s not a perfect fit for the grant you’re submitting, you’re doomed.

Our grant solution is not an authoring, text-generating tool. It gives you constructive feedback on your writing (it comments on the deep things, not grammar and typos). It’s meant to help you with the questions that torment you late at night (“is this a good fit?”, “Is this novel enough?”, “Did I miss something?”). Tens of thousands of you already use q.e.d to improve your manuscripts and critically read papers, we built the grant tool by the same principles (you’ll identify many of the features that you told us you like).

We’ve processed thousands of proposals, learned where things fail, where reviewers get stuck, why good ideas come out weak. We interviewed hundreds of scientists, and also experts who work in funding agencies and university research authorities, and implemented their feedback (we’re constantly looking for more feedback). Our AI is always happy to give you constructive (and polite!) critique, and it will go through your grant line-by-line, forcing you to improve clarity, flag weak points, and push the whole thing to a higher standard. We study, in scale, what gets funded and what doesn’t, and what is the perfect fit for each type of grant.

So please, use it, pressure-test it, tell us where it fails, and together we’ll improve it every day to put you in the best position for actually testing your ideas in the real world. As always with q.e.d, the system is completely secured and private, and we are NOT training on your data (see the FAQ on our website).

Please like, retweet, and share with your favorite colleagues! (link to the platform below in the thread👇)

[UNMC Dept of Genetics, Cell Biology & Anatomy @UNMC_GCBA]

GCBA Seminar Series announces Dimple Notani, PhD, EMBO Global Investigator, National Centre for Biological Sciences - TIFR presenting "RNA as a Key Regulator of Enhancer Hierarchies and Promoter Priming." @DimpleNotani @UNMC_GCBA @UNMC_BISB

[UNMC Dept of Genetics, Cell Biology & Anatomy @UNMC_GCBA]

GCBA Seminar Series announces Jean-Paul Armache, PhD, PennState University, Department of Biochemistry presenting " Translating Motion and Heterogeneity into Insights Using Cryo-EM" @UNMC_GCBA @UNMC_BISB @valendraica

[Michael 英泉 Eisen @mbeisen]

Nice paper. It's kind of cool/funny to watch over the last few decades the idea that low-affinity motifs play an important role in gene regulation going from basically the lunatic fringe to mainstream.

[Fred & Pamela Buffett Cancer Center @BuffettCancer]

Proud to be part of the Upper Midwest Emerging Scholars Exchange Program! Read about how we're building collaborative networks across institutions to advance #CancerResearch

@GrinuMathew @BrahmaComplex
@UWCarbone @MCWCancerCenter @UMNCancer
https://t.co/1ItereRpkP

[Sandipan Brahma @BrahmaComplex]

Thanks,
@NEDHHS and https://t.co/shYrTtSHbB members! We are excited to take our tools and fundamental mechanistic insights on chromatin regulation to the next level and apply them directly to address critical knowledge gaps in cancer biology. @UNMC_GCBA @CHRI_ResearchNE

[Fred & Pamela Buffett Cancer Center @BuffettCancer]

🧬 Congrats to @BrahmaComplex on receiving the @NEDHHS Stem Cell Research Award ($105K)! His team's novel genomics method could unlock critical insights into how aggressive pediatric brain tumors develop during embryonic neural formation.
#PediatricCancer #GenomicsResearch

[Fred & Pamela Buffett Cancer Center @BuffettCancer]

The 2025 Henry M. Lemon Short Course in Cancer Biology was outstanding! Thanks to incredible speakers @BlaineBartholo2 (@MDAndersonNews) @HargreavesLab (@salkinstitute) @TheRobertsLab1 (@StJudeResearch) Anthony Imbalzano (@UMassChan) & faculty hosts Angie Rizzino @BrahmaComplex!

[Shilatifard Lab @ShilatifardLab]

My lab has been working for the past 15 years to develop a method to isolate specific genomic loci to identify its chromatin composition & protein interactome. Finally,… our superb physician/scientist Dr. Bercin Cenik @bkcenik did it and here it is https://t.co/f0vKe8pCFS Not only was she able to develop this method, which she calls TurboCAS, she was able to identify known & novel regulators of heat shock & Myc expression. Cannot wait to see what Bercin and TurboCAS will discover about the molecular basis of transcriptional regulation with great impact on clinic in the next few years! @NU_BMG_SQE @NUFeinbergMed @MolecularCell

[Itai Yanai @ItaiYanai]

My guidelines for exploratory data analysis

[UNMC Dept of Genetics, Cell Biology & Anatomy @UNMC_GCBA]

GCBA Seminar Series announces Aparna Bhaduri, PhD, Assistant Professor, University of California, Los Angeles (UCLA), Dept of Biological Chemistry presenting "Characterizing Cell Fate Specification in the Developing Human Brain and Glioblastoma" @BhaduriLab @UNMC_GCBA @UNMC_BISB

[Kazuhiro Maeshima @kazu_maeshima]

Thrilled to share our new work @biorxivpreprint:
https://t.co/6unXV2pn2C
Our Repli-Histo labeling marks nucleosomes in euchromatin and heterochromatin in live cells. We reveal genome chromatin is essentially replicated from regions with greater nucleosome motions. 1/2

[Jitendra Thakur @Thakur_G2]

Kudos to my outstanding team for developing genomic and epigenomic maps of mouse satellite regions (centromeres and pericentromeres), which account for ~11% of the mouse genome. Very excited to share the preprint. https://t.co/wjjVcjWftz

[Paul T Kim @paultkim_ipd]

With David and the Baker Lab in the spotlight today, I wanted to share some insights into the @UWproteindesign and how it operates, a glimpse behind the curtain. I had planned to write this post-graduation, but now seems as good a time as any. (Got twitter blue free trial so this could all fit in less tweets!)

First, the lab is enormous. ~60 grad students, ~60 postdocs, a handful of visitors, undergrads, and a surrounding institution of another 150 or so. Collaboration is strongly encouraged (even mandated) by David, who sets up pro-collaboration incentives. Notably, he's fine with grad students graduating without a sole first-author paper—it's acceptable to "only" have worked as a co-first author. This is a key ingredient in the secret sauce: the tight collaboration between wet lab and dry lab. It ensures that all our work is ultimately grounded in strong wet-lab validation—our "oracle" is the real world, not another computational model.

While we have regular meetings for different subgroups and the entire group, much information travels through the lab via informal one-on-one interactions. In some ways, it reminds me of a classic "tribe of humans in the state of nature"—100-200 people with no clear hierarchy, passing information via "gossip". It’s maybe not the most complete way of ensuring everyone is on the same page, but saves time as we aren’t drowning in endless meetings.

Does David stay in touch with all these grad students and post-docs? Remarkably, yes. Unlike some very large labs known for being run entirely by post-docs, he knows exactly what everyone is working on and the stage of their projects. Each member has monthly one-on-ones with him, and monthly subgroup meetings that David attends. If he suggests you try something at your previous one-on-one, you'd better have it done by the next.

Does he actually contribute research ideas, or is he more of a detached big-picture project manager? Definitely the former. He understands the intricacies of a shocking range of topics. I'll be discussing some arcane deep learning concept with him, and then he'll turn around and talk to someone about the details of a catalytic mechanism. He's actually the most hands-on PI I've ever had—if anything, he verges on over-managing rather than being too detached.

How does he keep track of everything? Partly, he's just a brilliant person with exceptional recall. But he has also built infrastructure above and below him in the lab to handle many of the details, bureaucracy, big picture, and management tasks. This allows him to spend most of his day doing what he's most passionate about and skilled at: walking around talking to people about science. He also lives very much in the moment and in his own words, “never thinks very far ahead". To keep up with tools, methods, and wet lab techniques, he does the occasional project and design campaign himself on the side when time allows.

It's still a tremendous cognitive load to keep all this in his head, but as much as possible, he has offloaded non-scientific cognitive burdens. It helps that he’s in the lab in person most days of the year, rarely traveling for conferences or talks, instead doing them over Zoom or not attending. (1/2).

[Teif Lab @TeifLab]

Happy to contribute to this new preprint by @ElenaPugachev12, @boris_ctcf & Co. What determines differential CTCF binding, beyond DNA methylation and TF/nucleosome competition? Answer: a specific nucleosome downstream of CTCF motif. Directionality matters! https://t.co/MAPYsftzDj

[Kasit Chatsirisupachai @KasitC10]

Excited to share the latest story from the @arnaud_kr lab @embl ! Together with @ChristineMoene we used Single Molecule Footprinting to reveal that RNA Pol II occupancy occurs at surprisingly low-frequency at mammalian promoters! Thread below (⬇️) 1/11

[Sandipan Brahma @BrahmaComplex]

This looks pretty cool!

[Samuel John Taylor @SamuelJohnTayl1]

Super thrilled to share our article on pharmacological PU.1 repositioning published in Nature Genetics today! Massive thanks to everyone involved!
Article -> https://t.co/h0rPMMq8qH
A digestible PUree of the main findings (aka Research Brief) -> https://t.co/1IoXUygs5p

[FragileNucleosome @FNucleosome]

🎊🎉 #FragileNucleosome is back! You can now register for our 25th of September seminar session! We are excited to have @RemiXCoux and @VondriskaLab talk about their research and kick-off #FragileNucleosome seminar series!
🗓️https://t.co/BShfnpXxp0

[Sandipan Brahma @BrahmaComplex]

@poly_microbial Congratulations, that's awesome!

[Kirkland_Lab @kirkland_lab]

The first paper from our lab is now out in peer-reviewed form @LSAjournal. Huge congratulations to the first author Mary Bergwell, @STEMinistSkater, now in grad school at UPenn, and second author @JY_Park102! I am very proud of their hard work. They even let me do a few expts!

[Sandipan Brahma @BrahmaComplex]

Transcriptional control from stochastic action at the single-molecule scale

[Peter H Whitney @phw_phd]

I just wrote a review on transcriptional regulation and I want to talk about something that has been bothering me for 5 years, which ended up changing how I think about science in general. A brief thread:
https://t.co/dWsE7VGJDN