Rahul K
@theresearch.bsky.social
1.9K followers 640 following 240 posts
I run, ski, and engineer cells and materials; asking how nutrient sensing & signaling work: bit.ly/RK-GoogleScholar 🇪🇪: TalTech| Ex: Tartu Ülikool; 🇸🇪: Karolinska Institutet, Chalmers; 🇯🇵: Kyutech; 🇮🇳: IITD
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theresearch.bsky.social

I’d like to invite everyone working on engineering living materials to share this starter pack. Please drop me a message or leave a comment if you like to join the #ELMs community. go.bsky.app/RinsDZh
Reposted by Rahul K
tetsuharimoto.bsky.social
My postdoc work is now on bioRxiv!

We combined engineered bacteria and hydrogels to create implantable living materials that safely confine bacteria while letting them sense disease and release drugs from within.

🔗 www.biorxiv.org/content/10.1...
theresearch.bsky.social
Pooled #CRISPR screens with joint single-nucleus #chromatin accessibility and #transcriptome profiling

h/t @albacorp7.bsky.social congratulations 🎉🍾
Reposted by Rahul K
Reposted by Rahul K
Reposted by Rahul K
tuuliel.bsky.social
Reminder of our postdoc position! Happy to meet at #ASHG25 this week to discuss.
tuuliel.bsky.social
We're hiring! My team at @nygenome.org is looking for a statistical genetics postdoc to decipher functional architecture of complex diseases from cutting-edge CRISPR+scRNA-seq data, with @nevillesanjana.bsky.social lab. Happy to meet at #ASHG25, apply here
jobs.silkroad.com/NYGenome/Car...
Postdoctoral Research Associate, Lappalainen & Sanjana Labs - 101 Avenue of the Americas, 7th Floor, New York, New York - New York Genome Center
Find a career with New York Genome Center
jobs.silkroad.com
Reposted by Rahul K
Reposted by Rahul K
engbioirc.bsky.social
Join us at our EngBio Forum on 10 Nov to hear from Andreas Walther @waltherlab.bsky.social
on creating programmable materials and DNA-based synthetic cells that can process information, adapt,and communicate.
Don't miss it! Sign up 🫱 buytickets.at/engineeringb...

#SyntheticCells #LifeLikeSystems
Reposted by Rahul K
raduzabet.bsky.social
DNA methylation is one of the most studied epigenetic modification associated with regulation of gene expression. Bisulfite-converted genomic DNA sequencing has been the current gold standard in the field for building genome-wide DNAm maps at base pair resolution.
Reposted by Rahul K
lucasbsullivan.bsky.social
Our work detailing the metabolic roles of serum for cancer cell proliferation is now out at JBC, @asbmbjournals.bsky.social!

Congrats to Oliver and Eric and many thanks to the editor and reviewers for a thoughtful and efficient review process.

See here:
www.sciencedirect.com/science/arti...
Reposted by Rahul K
biorxivpreprint.bsky.social
μGrowthDB: querying, visualizing, and sharing microbial growth curve data https://www.biorxiv.org/content/10.1101/2025.10.13.682118v1
Reposted by Rahul K
nucleosomepolice.bsky.social
Our paper on the strange ATP-dependent chromatin remodeler Smarcad1 paper is out and freely accessible. Differential regulation of its many activities by phosphorylation. Congrats to Briana and @nhoitsma.bsky.social 🧪https://www.sciencedirect.com/science/article/pii/S0021925824023950?via%3Dihub
Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange
Maintaining the dynamic structure of chromatin is critical for regulating the cellular processes that require access to the DNA template, such as DNA …
www.sciencedirect.com
Reposted by Rahul K
adrianwoolfson.bsky.social
Reprogrammed Serine Integrases Enable Precise Integration of Synthetic DNA
Despite recent progress in the ability to manipulate the genomes of eukaryotic cells[1][1]–[3][2], there is still no effective and practical method to precisely integrate large synthetic DNA constructs into desired chromosomal sites using a programmable integrase. Serine integrases can perform the necessary molecular steps[4][3], but only if their natural target site is first installed into the recipient genome by other methods. A more elegant approach would be to directly reprogram the serine integrase itself to target a desired genomic site that is different from the natural recognition site of the integrase[5][4]. Here, we describe the development of a Modular Integrase (MINT) platform, a versatile protein-guided genome editing tool that can facilitate site-directed targeted integration (TI) of synthetic DNA into chromosomal sites. Through a combination of structural modeling, directed evolution, and screening in human cells we have reprogrammed the specificity of the serine integrase Bxb1. We demonstrate the therapeutic potential of the MINT platform by retargeting Bxb1 to the human AAVS1 and TRAC loci where wild-type Bxb1 has no detectable activity. By combining the MINT platform with known activity-increasing Bxb1 mutants, we achieved 14% TI at the AAVS1 locus, and by additionally fusing zinc finger DNA binding domains to engineered Bxb1 variants, we achieved 35% TI at the TRAC locus in human K562 cells. To further demonstrate clinical potential, we achieved stable 15% TI of a functional donor construct in human T cells. ### Competing Interest Statement All authors contributed to this work as full-time employees of Sangamo Therapeutics. Sangamo Therapeutics has filed patent applications regarding Integrase systems described in this study, listing F.F., S.A.-F., N.A.S., and J.C.M. as inventors. [1]: #ref-1 [2]: #ref-3 [3]: #ref-4 [4]: #ref-5
www.biorxiv.org
Reposted by Rahul K
biorxivpreprint.bsky.social
A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1
Reposted by Rahul K
obenaufa.bsky.social
Acidosis is not just a byproduct of an altere Metabolism - it drives cancer cells‘ stress resilience mechanisms. Big congratulations to our friends from the @johanneszuber.bsky.social lab as well as the team around @wilhelmpalm.bsky.social on this wonderful story now out in Science.
johanneszuber.bsky.social
Just out in @science.org: Together with the lab of @wilhelmpalm.bsky.social, we used sequential in-vitro/in-vivo CRISPR screens to decipher metabolic adaptations in tumors. We find that acidosis is a dominant factor that shapes energy metabolism and stress resilience. www.science.org/doi/10.1126/...
Reposted by Rahul K
needhibhalla.bsky.social
“The scientific Nobels announced this week underscore that point. All three awards — granted each year in physiology or medicine, physics and chemistry — honored achievements rooted in fundamental research…Decades of inquiry paved the way for the technology, treatments and toys of tomorrow.” 🎁
Nobel Prizes This Year Offer Three Cheers for Slow Science
www.nytimes.com
Reposted by Rahul K
joachim123.bsky.social
My OpEd piece in US News & World Report, about not wanting my life to be book-ended by two fascist regimes and about the state of higher education in this country,

www.usnews.com/opinion/arti...

has now been republished in German translation by JOSHA:

josha-journal.org/en/categorie...
www.usnews.com
Reposted by Rahul K
coledeforest.bsky.social
Our new paper entitled “Boolean Logic-gated Protein Presentation through Autonomously Compiled Molecular Topology” is now live at Nature Chemical Biology (@natchembio.nature.com)! Check it out!

📜: www.nature.com/articles/s41...

@uwnews.uw.edu feature write-up: www.washington.edu/news/2025/10...
Stimulus-responsive materials have enabled advanced applications in biosensing, tissue engineering and therapeutic delivery. Although controlled molecular topology has been demonstrated as an effective route toward creating materials that respond to prespecified input combinations, prior efforts suffer from a reliance on complicated and low-yielding multistep organic syntheses that dramatically limit their utility. Harnessing the power of recombinant expression, we integrate emerging chemical biology tools to create topologically specified protein cargos that can be site-specifically tethered to and conditionally released from biomaterials following user-programmable Boolean logic. Critically, construct topology is autonomously compiled during expression through spontaneous intramolecular ligations, enabling direct and scalable synthesis of advanced operators. Using this framework, we specify protein release from biomaterials following all 17 possible YES/OR/AND logic outputs from input combinations of three orthogonal protease actuators, multiplexed delivery of three distinct biomacromolecules from hydrogels, five-input-based conditional cargo liberation and logically defined protein localization on or within living mammalian cells.