Gaurav Varshney
Assoc. Prof. Interested in CRISPR, Zebrafish, Disease Modeling, Rare Diseases, and Neurodevelopmental Disorders. The opinions expressed here are my own.
- Reposted by Gaurav VarshneyA powerful new technology developed at OMRF could dramatically speed up the process of diagnosing rare genetic diseases. Read more: omrf.org/2026/02/03/o...
- Reposted by Gaurav VarshneyHigh-efficiency TadA cytosine base editors for precise modelling of human disease variants
- Our paper on TCBE-Umax is out in @natbiomedeng.nature.com! We developed these high-efficiency cytosine base editors for zebrafish, enabling rapid functional testing of disease variants. This work is led by a talented scientist, Wei Qin. www.nature.com/articles/s41...
- TCBE-Umax delivers: ✓ 2x higher efficiency ✓ Works across diverse sequence contexts ✓ Minimal indels ✓ Expanded PAM options for hard-to-target sites Grateful to ORIP/NIH and the Presbyterian Health Foundation for supporting this work.
- Reposted by Gaurav VarshneyFolks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv: www.biorxiv.org/content/10.1...
- Reposted by Gaurav VarshneyPublished October 25 years ago, “Effective targeted gene ‘knockdown’ in zebrafish” by Nasevicius & Ekker detail use of antisense morpholino-modified oligonucelotides or #morpholinos that inhibit translation. This landmark spurred a revolution in targeted gene knockdown in vivo. #ZebrafishFunFacts 🧪
- Reposted by Gaurav VarshneyWhile I'm sad our cover submission wasn't selected for our recent human duplication paper, check out the super cool illustration created with @lazaroillustration.bsky.social ! Certainly, you will be seeing Dennis lab members running around with "fishman" t-shirts at future meetings, inspired by Ohno
- "Fishman", proposal for a journal cover. Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social #art #digitalart #sciart #fish
- Does anyone have #zebrafish LC3 reporter lines and would be willing to share them with us? #askzebrafish
- Reposted by Gaurav Varshney#zebrafish genome update, our T2T assembly of the inbred strain of AB (M-AB) generated by my buddy Nori Sakai has now been released at NCBI and will be a second reference genome for zebrafish (GRCz12ab):
- CRISPR technologies have transformed genetic research since their adaptation for genome editing in 2012. @burgesslab.bsky.social and I summarize key functional genomics tools being used in vertebrate models. www.nature.com/articles/s12...
- Congratulations, Megan! As always inspiring work.
- Check out our latest work co-led by @dcsoto.bsky.social and @jmuribescr.bsky.social identifying hundreds of human duplicated gene families using the new T2T-CHM13 assembly, with a focus on those potentially contributing to brain evolution 🧪: authors.elsevier.com/a/1lTQtL7PXu...
- Our paper on TadA-based cytosine base editors is now online in Advanced Science. We introduce zTadCBEs—a next-generation CRISPR base editor optimized for zebrafish. advanced.onlinelibrary.wiley.com/doi/10.1002/...
- By engineering TadA-based cytosine base editors with enhanced PAM flexibility and reduced off-targets, we overcome key limitations of existing CBEs, including poor editing at CC and GC motifs.
- Congratulations!
- Grateful to receive an R24 NOA from NIH/ORIP to advance phiC31-based transgenesis tools in #zebrafish. 🐟 Collab with @aburger2009.bsky.social & Breuss labs @cuanschutz.bsky.social. 🧬 ...and: big THX to everyone who already helped w/ sharing #pIGLET reagents! 🐽 #ShareYourTools #MakeMoreTransgenics
- Reposted by Gaurav Varshney🚨🚨🚨 Tol2kit announcement! We have rebuilt the wiki that was corrupted a few months ago! We’re in the process of also linking it to the original address. Please visit us here: tol2kitkwan.genetics.utah.edu Thank you for your patience!! #zebrafish #transgenesis #plasmids #sharing
- Reposted by Gaurav VarshneyDear #izfc2025 participants, if anyone of you are interested in how transcription control defines mRNA fate and translation in zebrafish development, there are/will be several PhD and postdoctoral positions (funded by the Wellcome Trust) for this research. Please find me if interested.
- Reposted by Gaurav VarshneyThe winners of the 2025 George Streisinger Award are the Course Directors of the Zebrafish Development and Genetics course at MBL, for their tremendous contributions to our amazing community for >25 years! #izfc2025
- The new impact factors are out: Development – 3.6, Developmental Cell – 8.7. Why the steady decline in two of Dev Bio's flagship journals?
- Reposted by Gaurav VarshneyPlease read and share this opinion piece written by Carole LaBonne (our fellow Xenopus researcher) published in STAT in support for animal models in biomedical research. www.statnews.com/2025/05/19/a... #science #devbio #xenopus #frogs
- Reposted by Gaurav Varshney[This post could not be retrieved]
- Reposted by Gaurav VarshneyWith a published genome & advancements in gene editing, the field of #zebrafish genetics has exploded in recent decades. We take a look back at major achievements in this infographic. For more, read this book chapter by @varshneylab.social et al (2015)($) doi.org/10.1016/bs.a... #ZebrafishFunFacts 🧪
- Get ready to pay extra for your supplies and reagents.
- Reposted by Gaurav VarshneyWelcome @burgesslab.bsky.social as an Associate Editor for #GENETICS 👋 Burgess, who will be joining the Experimental Technologies and Resources section, studies tissue regeneration in zebrafish and genome function. We’re delighted to have him on the team! Read more: buff.ly/k0yDk5c
- Reposted by Gaurav VarshneyIn @nature.com we describe the use of scalable #proteinengineering & #machinelearning to predict millions of bespoke CRISPR enzymes, offering safer & more efficient genome editing tools 🧬🖥️ @rachelsilverstein9.bsky.social @mgbresearch.bsky.social @harvardmed.bsky.social www.nature.com/articles/s41...
- Reposted by Gaurav VarshneyNew preprint just dropped! I really love this paper for many reasons, but the biggest is that this is a really old school genetics/devbio paper, traditional genetics approaches still have the JUCHE. Several years ago now visiting professor Chunxin Fan participated in an ongoing screen for
- Reposted by Gaurav VarshneyIt has been a while since I advertised some of the tools we have released to help researchers analyze the zebrafish genome. So a brief Bluetorial on our zebrafish genomics UCSC public data hub and the bigger effort led by @ferencmueller.bsky.social to create a zebrafish ENCODE project (Danio-CODE):
- Our Collaborative work on TRMT1, a tRNA-modifying enzyme, is out in @ajhgnews.bsky.social. A team of human geneticists led by Drs. Houlden' @qs-neurogenetics.bsky.social and Dragony Fu' labs identified 43 individuals from 31 families with biallelic TRMT1 variants. www.cell.com/ajhg/fulltex...
- My lab contributed to functional data showing zebrafish trmt1 knockouts recapitulated patient phenotypes: abnormal brain morphology, altered behavior, and dysregulated gene expression linked to neurodegeneration.@sheng-jia.bsky.social
- Reposted by Gaurav Varshney@varshneylab.social @sheng-jia.bsky.social (gRNA selection/ Phenotypic penetrance/ Neurodevelopmental disorders) doi.org/10.1093/nar/gkaf180 @jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking) github.com/HenHus/Husmorph (32/34)
- Reposted by Gaurav VarshneyWe are excited to announce a call for papers for a special issue of Genome Medicine genomemedicine.biomedcentral.com on "Clinical interpretation of genome variation". The submission deadline is Dec 18, 2025. More info here: go.sn.pub/gskvsk.
- Reposted by Gaurav VarshneyHey fellow Drosophila researchers - if you haven't heard, the UMGC is offering ultra low-cost genome sequencing! See here to learn more: z.umn.edu/UMGC-MOSS #Dros25
- Our paper "Optimizing gRNA selection for high-penetrance F0 CRISPR screening for interrogating disease gene function" is now published in @narjournal.bsky.social doi.org/10.1093/nar/.... This work was led by our super postdoc @sheng-jia.bsky.social
- Several papers on F0 mutagenesis have been published, including those by Jao et al., Burger et al., Wu et al., Kroll et al., and others—all methods work well. We set out to test and compare strategies to achieve the highest phenotype penetrance using minimal resources.
- We utilized indel prediction models such as Lindel (or inDelphi/ForeCast and others) to design gRNAs with high predicted success. Targeting the N-terminal half of functional domains worked best. We tested 324 gRNAs across 125 genes, targeting key protein domains with just 1-2 gRNAs.
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View full threadWe validated 37 candidate disease genes across 8 tissues and screened 63 hearing-related genes, identifying 52 with hearing defects. Also, we identified 10 new neurodevelopmental disorder (NDD) genes in zebrafish.
- Reposted by Gaurav VarshneyPiece by @stephaniemlee.bsky.social on one way we are trying to band together to get information about what the hell is going on. Kudos to @annikabarber.bsky.social interviewed here www.chronicle.com/article/nih-...
- Reposted by Gaurav VarshneyWe pay our academic editors (we don't do special issues with guest editors). Beginning in April, we also pay peer reviewers @biologyopen.bsky.social details to be announced at #biologists100 bit.ly/4h1cmCC @biologists.bsky.social
- A journal contacted me to serve as guest editor; I sent them my hourly rates. They came back saying, please suggest someone else who is willing to volunteer. 😆
- Reposted by Gaurav VarshneyReminder that NIH grants are NOT reckless spending. They are extremely competitive. The mean success rate of all grants is <24%. Far lower for R01's that are the lifeblood of most academic labs. All the data can be found here: report.nih.gov/funding/nih-...
- One of the remarkable things about #NIH is how rigorously its grants, research, and employees are reviewed. NIH science and scientists are held to a high standard by external reviewers — via study sections and councils, or BSC/site visit reviewers. And the reviews have teeth. 🧪
- Reposted by Gaurav VarshneyWondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...
- Reposted by Gaurav VarshneyKickass worm-friend @rnareylab.bsky.social wrote a piece for @sciencehomecoming.bsky.social and you should read it and send it to your red-state friends and fam. Hurting research hurts all of us. #invertsolidarity 🧪 www.heraldbanner.com/opinion/colu...
- Reposted by Gaurav VarshneyAn update on NIH funding and the loophole that's keeping it out of scientists' reach. H/T to @avaskham.bsky.social, who had it first. #HigherEd #AcademicSky www.chronicle.com/article/desp...
- Reposted by Gaurav VarshneyIt’s @katherinejwu.com with the receipts. The NIH memo undercutting the NIH came directly from Trump officials. www.theatlantic.com/health/archi...
- Reposted by Gaurav VarshneyMNG study section scheduled in person for 2/20-2/21. Put together in Dec, assignments out 1/14, travel arrangements made mid-Jan. Was NOT posted to Fed Reg. Critiques due 2/14. All normal to that point. Moved to zoom 2/18 in am, discussion order posted 2/18 pm. CANCELLED just now.
- I just found out that the study section for my grant has been canceled one day before its scheduled meeting.
- AJHG @ajhgnews.bsky.social has a weird policy of allowing only two authors to be listed as senior authors; HGG Advances goes even further, allowing only one person to be listed as a corresponding author. It only hurts the junior investigator.
- Reposted by Gaurav Varshney🆘 Email from my colleague on the Hopkins Research Council🆘 Can anyone confirm? 🧪
- Reposted by Gaurav VarshneyDisruptions to the NIH impact more than just science; they will hit all Americans in our wallets. I spoke yesterday with Becky Fogel from @kutnews.bsky.social about the important role NIH-funded research plays in the economy. 🧵 1/n www.kut.org/education/20...
- Reposted by Gaurav Varshney“zTadCBE variants thus offer a robust set of [cytosine base editors] for precise and efficient C-to-T editing in zebrafish, promising to advance the rapid functional assessment of genetic variants in vivo.” New work from @varshneylab.social et al. 🧬🐟
- Can we fast forward to 2026? I am done with 2025.
- Reposted by Gaurav VarshneyA request for the incoming @NIHDirector Director: Please increase the modular R01 DC budget cap that some ICs such as @NLM_NIH use. Budgeting two faculty at 20% effort each leaves .75 FTE of computational staff support to do all the work. Not enough for AI research! #nih #nlm
- Reposted by Gaurav VarshneyOur first manuscript on maternal nutrition and development, which was driven entirely by postdoc Katie Ranard, is now out. @cudevbio.bsky.social #devbio doi.org/10.1016/j.jl...
- Last week, I completed eight years at OMRF. It feels like I just left the @burgesslab.bsky.social lab.
- Reposted by Gaurav VarshneyAs far as I can tell, people complaining that Bluesky is an echo chamber are the ones who don't understand the nature of internet communities. I don't post here so I can debate (especially ideas that have been proven demonstrably false over and over again), I don't come here to challenge my world 1/
- Reposted by Gaurav VarshneyZebrafish model with defective actin N-terminal acetylation uncovers hearing defects. From the cover of Life Science Alliance @embopress.bsky.social - image from @varshneylab.social @sheng-jia.bsky.social #zebrafish #PTMs #acetylation #cytoskeleton www.life-science-alliance.org/content/7/12...
- Reposted by Gaurav VarshneyHeard that NINDS payline is now at 8%. I’ve sent most of my grants to NINDS (a few to NIDDK and NEI). But the emphasis at NINDS to fund basic neuroscience research (emphasized by POs) was encouraging even at the toughest of times. However, a 8% payline is a new low and unsustainable
- Reposted by Gaurav VarshneyLet's build a rare disease starter pack! go.bsky.app/LExn7SZat://did:plc:rdqdpqpzohi6hohetbggg44s/app.bsky.graph.starterpack/3lba37vq5de2d
- Reposted by Gaurav Varshneyat://did:plc:bcnm6q4p4ai25lryrv4ni7vr/app.bsky.graph.starterpack/3lblzm2bonf2e
- Reposted by Gaurav VarshneyI couldn't spot a starter pack for rare disease / clinical genomics, so I started one: go.bsky.app/SUWZ9Hw Very much a work in progress, and biased by who I have already found here, so please suggest people to add! Self-nominations encouraged. #ClinicalInformatics #genomics #bioinformatics 🖥️🧬at://did:plc:q6g2iowtzf3zln6luofy7e7z/app.bsky.graph.starterpack/3lay46eeejp23
- Lab lunch to celebrate recent papers and grants!
- Out of state Tuition should also go!
- Carnegie Mellon will be free to students in families making under 75K. www.wesa.fm/education/20...
