Yangwode Jing @yangwode
Ph. D. candidate @PrincetonChem in @bsadamson lab B. Sc. in Chemical Biology, @Tsinghua_Uni Genomics, CRISPR, DNA repair A reductionistic genomicist Princeton, NJ Joined July 2021-
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This week we publish in @NatureBiotech "High-precision cytosine base editors by evolving nucleic-acid-recognition hotspots in deaminase". In this work, we show that both nucleotide and context specificity of deaminases can be reprogrammed by hotspot-focused directed evolution 1/n
Plasmid-based reporter assays are the bedrock of regulatory genomics. But a basic question has gone unanswered for decades: Do chromatin architectures form on plasmids transfected into mammalian cells—and does it matter? We finally have answers. biorxiv.org/content/10.110…
🔬 New from the Farnung Lab: We have established a fully in vitro reconstituted chromatin replication system and we report the first cryo-EM snapshots of the human replisome engaging nucleosomes. 🧬✨tinyurl.com/replisome
Happy to share our new paper published today @CellCellPress. Thanks to all our coauthors from @dgsomucla, @UCLASemel, and CHDI. Distinct mismatch-repair complex genes set neuronal CAG-repeat expansion rate to drive selective pathogenesis in HD mice: Cell cell.com/cell/fulltext/…
Exciting results! Using AID-Degron system, Dr. Yimeng Zhu found that Ku suppresses RNA-mediated innate immunity to accommodate Alu-expansion in primates - solving the misery of Ku essentiality in human cells! Thank@chaolinzhang biorxiv.org/content/10.110…
1/Delighted to announce the newest paper from our lab, “Homologous recombination promotes non-immunogenic mitotic cell death upon DNA damage”, is out today in @NatureCellBio, nature.com/articles/s4155….
A dream come true- published in @Nature Using CRISPR–Cas9, we analyzed the functional effect of >6500 missense Variants of Uncertain Signficance (VUS) lBRCA2, and reclassified >90% of variants as pathogenic, likely pathogenic, benign, or likely benign. This work changes the…
Happy to share our newly published article in Nature Communications! In this work, we uncover the novel role of KLF5 in sensitizing cells to ATR inhibition, identifying it as a synthetic lethal partner with the tumor suppressor ARID1A. @SPJacksonGroup nature.com/articles/s4146…
Exciting work by fantastic postdoc @kaitlynakiernan @ut_mbs @TexasScience visualizing 25 states of SpCas9! Pulled out a product release state and provides insight extremely low turnover of SpCas9 with a canonical guide RNA. Thanks to @jpkbravo for image that I could grab quick!
From @bsadamson and colleagues, a prime editing platform for high-throughput functional interrogation of up to tens of thousands of small genetic variants. nature.com/articles/s4159…
Thrilled to see our work out in @naturemethods today! We applied prime editing to multiplexed dropout screens and benchmarked the tool’s ability to induce phenotypes when installing premature stop codons in essential genes.
Thrilled to see our work out in @naturemethods today! We applied prime editing to multiplexed dropout screens and benchmarked the tool’s ability to induce phenotypes when installing premature stop codons in essential genes.
Finally my PhD work is published now in Molecular Cell! Many thanks to my supervisor Prof. Matthew Whitby and all the other co-authors!
Finally my PhD work is published now in Molecular Cell! Many thanks to my supervisor Prof. Matthew Whitby and all the other co-authors!
Excited that our work on transcription-coupled DNA repair is now published @CellCellPress! We recapitulated TC-NER in Xenopus egg extract and identified STK19 as a core repair factor that couples stalled Pol II to TFIIH. 🧬🐸 ➡️ cell.com/cell/fulltext/…
Genome engineering excelled at small nucleotide changes, but large edits remained challenging. Recent innovations are changing this. We reviewed the field of structural variant engineering @NatureGenet 🧬 @JulianeWeller @TVanderstichele @LeopoldParts nature.com/articles/s4158…
Happy Birthday PDB, announced #OTD in 1971 In Nature New Biology. Today we celebrate the 53rd anniversary of the Protein Data Bank and the PDB depositor community, and congratulate the 2024 Nobel Prize in Chemistry Awardees rcsb.org/news/feature/6…
Excited to share our preprint of my PhD work in the Jasin lab @MSKCancerCenter! We find that CRISPR Cas9-induced DNA double strand breaks, even at a single locus, cause large-scale loss of heterozygosity. biorxiv.org/content/10.110…
CAST enables physical alignment of spatial omics data across replicates, techs, modalities at single-cell resolution. Such accurate alignment enables spatial atlas searching, unbiased DEG identification, and reconstruction of spatial multi-omics. DM for questions and collabs!
CAST enables physical alignment of spatial omics data across replicates, techs, modalities at single-cell resolution. Such accurate alignment enables spatial atlas searching, unbiased DEG identification, and reconstruction of spatial multi-omics. DM for questions and collabs! https://t.co/IfCwaciAV6
Congrats to @RebecaOLE_ and Andrew Waters for delivering this one. Thanks also to the patients and our team collaborators including @clare__turnbull and Maria Jasin/MSKCC. High-resolution functional mapping of RAD51C by saturation genome editing: Cell cell.com/cell/fulltext/…
We’re presenting AlphaProteo: an AI system for designing novel proteins that bind more successfully to target molecules. 🧬 It could help scientists better understand how biological systems function, save time in research, advance drug design and more. 🧵 dpmd.ai/3XuMqbX
A central challenge of AI-driven biotech is that in drug discovery a fully validated medicine is worth a million times more than a million early-stage ideas that only have little validation. This is unfortunately at odds with the AI domain where we almost always attempt to…
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Omenn-Darling Bioengi... @omenndarlingbio
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