šŸ‡®šŸ‡³ | Assistant Professor @UNMC_GCBA | #NewPI | Chromatin genomics and biochemistry | Henikoff lab @fredhutch and @BlaineBartholo2 lab alumnus

Omaha, NE
Joined March 2011
Sandipan Brahma retweeted
šŸ§¬šŸ§ŖšŸ”¬Why are enhancers transcribed? How does it impact gene regulation? I’m excited to share our new paper in @ScienceMagazine showing that ncRNAs control the timing of gene activation in embryos. w/Mike Levine #ScienceResearch #RNA A few highlights šŸ§µšŸ‘‡ science.org/doi/10.1126/scie…
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Congratulations to CHRI members chosen for @unmc research distinctions this year. Special kudos to Research Leadership honoree- Jennifer Blackford, PhD, Munroe-Meyer Institute. Ted Mikuls, PhD, named UNMC’s 21st Scientist Laureate unmc.edu/newsroom/2026/08/26…
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Sandipan Brahma retweeted
"More than 18,000 questionable images found in antibody catalogues of 15 companies" - It's stuff like this that makes bio research so slow
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Sandipan Brahma retweeted
Is single nucleus RNA-seq representative of single-cell transcriptomes and proteomes ? This comparison shows that: 1⃣ Both scRNA-seq and snRNA-seq correlate weakly to single-cell proteomes. 2⃣ The correlation is much lower for snRNA-seq 1/
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Curiosity-driven basic science powers tomorrow’s cancer breakthroughs. Support postdocs @fredhutch Basic Sciences as they pursue bold ideas in the lab: secure.fredhutch.org/goto/ba…
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Our NIH/NIGMS funded T32 Training Program DECODE is designed to jumpstart graduate education with essential training to seamlessly integrate modern experimental tools with computational approaches and ethical use of AI. Congrats, Drs. Dudley, Rowley (PIs) and our entire team!!
Drs. Dudley and Rowley's new grant will lead to exciting training program. unmc.edu/newsroom/2026/08/18…
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Sandipan Brahma retweeted
Transcription Factors are central to cellular identity and function. The human genome currently contains ~1600 of them. But could there be productive human transcription factors that have not evolved? Out today in Cell, a tremendously talented graduate student Oliver Takacsi-Nagy @Oli_TN, together with the @Satpathology Lab, determined to find out. (1/10) authors.elsevier.com/sd/arti…
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Sandipan Brahma retweeted
Luo et al, 2026 (review). The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options link.springer.com/article/10… 🧐548 references!
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Congratulations to @BrahmaComplex on his recent R35! The five-year award will support a research program focused on understanding fundamental mechanisms governing gene regulation and DNA organization, and how defects in these processes can contribute to disease.
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More exciting news!! Congrats to Eglė Šidlauskaitė on receiving the competitive UNMC Graduate Student Fellowship for their work on transcription factor network rewiring in SWI/SNF-deficient cancers.
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That's three consecutive UNMC Graduate Student Fellowships for BrahmaLab students on their first attempts: Soumi Basu → Sanjana Banerjee → Eglė Å idlauskaitė. Proud of this amazing team 😃 Stay tuned for more updates - brahmalab.org/
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Some overdue good news! Earlier this month, we were thrilled to receive an NIH/NIGMS R35 MIRA award to support our research for the next 5 years. Excited to keep uncovering fundamental mechanisms of chromatin and transcription regulation, and to explore bold new directions.
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Thank you, @NIGMS and the reviewers for your confidence in our work! We're especially excited that our application received a score in the exceptional-outstanding range!
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Sandipan Brahma retweeted
Important announcement!!!šŸ«µšŸ’„šŸ’« 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 ā€œQED for Grantsā€ 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 (ā€œis this a good fit?ā€, ā€œIs this novel enough?ā€, ā€œDid I miss something?ā€). 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 threadšŸ‘‡)
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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
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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
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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.
The @ZeitlingerLab is pleased to announce @MelanieWeilert’s preprint ā€œWidespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCsā€ (biorxiv.org/content/10.1101/…). Summary below! (TLDR; low-affinity motifs are common and strong pioneers in vivo!)
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Thanks, @NEDHHS and brahmalab.org 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
🧬 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
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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!
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