Souvik Sinha
@sou_svk
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Postdoc @palermo_lab @UCRBioengineeri . Doing simulations of biomolecules is one part of getting sense of things around me. Otherwise, I'm just curious.
Joined May 2018
Excited to share our back-to-back publications @NAR_Open ! A great collaboration between @palermo_lab and @mitchellrayoco1 lab. Cheers to @Amunie1 @pablitoarantes @ammolinavargas and all other authors! #RNA #CRISPR #Cas13a #chemcomp
Now @NAR_Open our two back-to-back papers with @mitchellrayoco1 lab! Our #chemcomp paper unravels the #RNA-mediated allosteric regulation in #CRISPR-Cas13a and discloses functional mutations. https://t.co/gKxJX6wbke
@sou_svk @pablitoarantes @ammolinavargas & Amun Patel
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The plan at FutureHouse has been to build scientific agents and use them to make novel discoveries. We’ve spent the last year researching the best way to make agents. We’ve made a ton of progress and now we’ve engineered them to be used at scale, by anyone. Today, we’re launching
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Check out our latest work on DNA base editors and the key evolutionary selection rules that drive their efficiency.
Do you want to know why hashtag#ABE8e is the most efficient adenine base editor? Read our paper with the amazing @Sarkele1 @NAR_Open! The dimerization of TadA8e and its exclusive interactions with #CRISPR Cas9 boost #BaseEditing efficiency! https://t.co/aMwTPjiebS
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Thanks for the highlighting our latest review from @palermo_lab
Graph theory approaches for molecular dynamics simulations 1. This review highlights the integration of graph theory with molecular dynamics (MD) simulations, providing a powerful framework to analyze biomolecular systems, including allosteric regulation, conformational
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Paper alert from @palermo_lab and Lisi lab @ScienceAdvances showing how mutations at Recognition domain (REC) of high fidelity Cas9 variants rewire communication with distally located nuclease domain to improve specificity.
New paper from our lab @ScienceAdvances! Molecular simulations and #NMR by the Geoge Lisi lab @BrownMolBio show that the HF1, Hypa, and Evo variants of #CRISPR-Cas9 rewire the atomic-level communication in the Cas9 enzyme to improve its specificity. https://t.co/0w8vnM59Ie
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New paper from our lab @NatureComms! @aakashsahha and colleagues reveal the dynamics and mechanism of target DNA traversal in #CRISPR-Cas12a, a conundrum in the field! https://t.co/vdNfnLHtjd
#compchem We thank the amazing #HPC resources @psc_live (#Anton2) and @SDSC_UCSD
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The first FDA approval for CRISPR! A historic milestone! Thanks @URochester_SMD for getting a chance on riff on about this special occasion (unrehearsed and unscripted as you might be able to tell!). #URochesterResearch
.@mitchellrayoco1, asst prof of Biochem and Biophysics, who trained w/ Nobel Prize winner Jennifer Doudna, one of the inventors of the revolutionary gene-editing technology CRISPR, weighs in on today's approval for using CRISPR to treat sickle cell patients. #URochesterResearch
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Now @NAR_Open our two back-to-back papers with @palermo_lab lab! 1) We show that MD-directed point mutations select against #offtargets in #Cas13a, paving the way for new SNP-detecting #RNA-diagnostics. https://t.co/fup7isOmNc
@ammolinavargas @sou_svk @pablitoarantes Amun Patel
academic.oup.com
Abstract. An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are s
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In the companion paper, the @mitchellrayoco1 lab demonstrates that these functional mutations display heightened sensitivity to single-nucleotide mismatches, offering potential for improved Cas13a-based RNA detection tools. Check it out! https://t.co/orbrqru0sL
academic.oup.com
Abstract. An increasingly pressing need for clinical diagnostics has required the development of novel nucleic acid-based detection technologies that are s
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First, we reveal how we detected the origins of noise-free signals in the Cas13a complex. And then we traced it back to get to the functional hotspots. Check it out! https://t.co/k5D0twM5U9
academic.oup.com
Abstract. Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilize
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For a quick summary https://t.co/w8WvpSczA8
1/n Super excited to share our latest pre-print from the lab, where we reveal important considerations when designing Cas13a-based SNP-detection assays to ensure specificity and anticipate designs caveats. 🧵
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Grateful to everyone involved in this project, and a special shoutout to @palermo_lab , including @pablitoarantes and @Amunie1, for this exciting exploration we had. Thank you all!
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These findings have enabled us to design variants with enhanced specificity, important for Cas13a-based SNP-detection assays. https://t.co/iTQmoRBtCo
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Excited to share a couple of preprints, in collaboration with @mitchellrayoco1 lab and @ammolinavargas , where we've identified regions sensitive to #RNA-mediated allosteric activation of the #CRISPR-Cas13a system. https://t.co/Qzr5837O5E
biorxiv.org
Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. The protein uses a CRISPR RNA (crRNA) to target RNA sequences,...
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Our News&Views @NatureNV @NatureChemistry article https://t.co/wb5pvyTCEB discussing the work on establishing the game rules for genetic code expansion by Watson et al. https://t.co/3Ltzkn2T4M Thanks to @palermo_lab for the opportunity.
nature.com
Nature Chemistry - Genetic code expansion to incorporate non-α-amino acid monomers is limited by predictability of monomer reactivities in the context of the ribosome. Now the use of...
In our @NatureNV, we discuss the discoveries by Zoe Watson et al. published in @NatureChemistry. The authors masterfully use metadynamics to establish the basis for genetic code expansion. Original paper: https://t.co/m7uxTQEfxJ Our News&Views: https://t.co/LWKQ6a2I2E
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Passion can hinder your career if it’s not supported by a strategy. Why? Because passion alone is not enough. Knowing how and why people are hired and promoted is essential to thrive in your professional journey. We often hear that passion is key for our career. And it is
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New cover on machines on genes visualized through #compchem The paper @JCIM_JCTC reports innovative computational methods and applications to study dynamics and mechanisms of #DNA, #transcription, #RNA, #splicing, #GeneEditing, #CRISPR, #chromatin & more https://t.co/aL1L1diikU
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Finally out in @JCIM_JCTC our review on ‘computational microscope’ in understanding the ‘jiggling and wiggling’ of fundamental molecules of life!
Inspired by #MachinesOnGenes, this @JCTC_JCIM review flexes the muscles of computational power to understand the fundamental processes of life. #DNArepair #chromatin #RNA #splicing #GeneEditing #CRISPR
https://t.co/aL1L1diikU
@sou_svk @pablitoarantes @Ahsan09966804 Chinmai Pindi
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