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Gaurav Varshney

@varshneylab.bsky.social
1.3K followers 587 following 82 posts

Assoc. Prof. Interested in CRISPR, Zebrafish, Disease Modeling, Rare Diseases, and Neurodevelopmental Disorders. The opinions expressed here are my own.

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Gaurav Varshney @varshneylab.bsky.social · 09/09/2026
What happened to Ensembl? 😭 Why was it destroyed? I came here to browse a genome, not fight for my life against the bad UI.
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Shawn Burgess @burgesslab.bsky.social · 01/09/2026
#zebrafish An update on the M-AB genome assembly and annotations: In the process of comparing the annotations between GRCz12ab and GRCz12tu, we discovered that 2 chromosomes, chr4 and chr19, were incorrectly uploaded. The sequences are actually from GRCz12tu. We have corrected the error
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Shawn Burgess @burgesslab.bsky.social · 30/07/2026
And a final track that shows all variants identified from sequencing multiple fish from our TU/AB hybrid fish NHGRI-1 which will show common SNV in both strains:
Image showing the UCSC genome browser of the zebrafish GRCz12tu genome assembly with the common variant track on display.
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Shawn Burgess @burgesslab.bsky.social · 30/07/2026
Yet another #zebrafish genome update: We just updated our ZebrafishGenomics public datahub for the UCSC browser (available all the way at the bottom here: genome.ucsc.edu/cgi-bin/hgHu...). We added several useful tracks including:
genome.ucsc.edu
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Daniel Gorelick @danielgorelick.bsky.social · 14/07/2026
The 1996 Development issue reporting the zebrafish screen (and the special issue commemorating it 25 years later) are now free to read, thanks @biologists.bsky.social journals.biologists.com/dev/collecti...
journals.biologists.com
The zebrafish issue: 25 years on | Development | The Company of Biologists
Welcome to Development’s 2021 Subject Collection celebrating the 25th anniversary since the publication of the zebrafish issue. The issue, originally publi
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Gaurav Varshney @varshneylab.bsky.social · 12/07/2026
In 2021, the journal Development published a special issue, “The Zebrafish Issue: 25 Years On.” Unfortunately, all the articles are behind a paywall. At the very least, special issues like this should be made open access. journals.biologists.com/dev/collecti...
journals.biologists.com
The zebrafish issue: 25 years on | Development | The Company of Biologists
Welcome to Development’s 2021 Subject Collection celebrating the 25th anniversary since the publication of the zebrafish issue. The issue, originally publi
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Gaurav Varshney @varshneylab.bsky.social · 28/06/2026
What if I do not want to use my institutional email?
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Gaurav Varshney @varshneylab.bsky.social · 02/06/2026
Excited to share that Dr. Wei Qin from my lab will present his base editing work on June 25!
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Gaurav Varshney @varshneylab.bsky.social · 30/04/2026
📣 Hiring a postdoc! My lab is hiring a postdoc to model rare genetic diseases in zebrafish utilizing CRISPR, high-throughput phenotyping, and multi-omics approaches.
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Shawn Burgess @burgesslab.bsky.social · 02/04/2026
Special shoutout to Wei Qin from @varshneylab.bsky.social lab. He has done the hard work to make precise editing in zebrafish a snap! Also shout out to all the other speakers in the series!
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Gaurav Varshney @varshneylab.bsky.social · 06/03/2026
Cleaning freezers before I move to a new place. Found these plates from @burgesslab.bsky.social, these plates made my career, hard to throw them now.
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Gaurav Varshney @varshneylab.bsky.social · 19/02/2026
Is Ensembl dead? Never worked for me for the last few months.
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omrf.bsky.social @omrf.bsky.social · 03/02/2026
A 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...
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Nature Biomedical Engineering @natbiomedeng.nature.com · 31/01/2026
High-efficiency TadA cytosine base editors for precise modelling of human disease variants
nature.com
High-efficiency TadA cytosine base editors for precise modelling of human disease variants
Nature Biomedical Engineering, Published online: 28 January 2026; doi:10.1038/s41551-025-01607-1A suite of TadA-derived cytosine base editors was optimized to improve efficiency, reduce sequence bias, expand PAM compatibility and minimize artefacts, enabling precise genetic interrogation of variants of uncertain significance (VUS) in zebrafish.
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Gaurav Varshney @varshneylab.bsky.social · 28/01/2026
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...
nature.com
High-efficiency TadA cytosine base editors for precise modelling of human disease variants - Nature Biomedical Engineering
A suite of TadA-derived cytosine base editors was optimized to improve efficiency, reduce sequence bias, expand PAM compatibility and minimize artefacts, enabling precise genetic interrogation of vari...
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Shawn Burgess @burgesslab.bsky.social · 17/11/2025
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv: www.biorxiv.org/content/10.1...
biorxiv.org
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Zebrafish Rock! @zebrafishrock.bsky.social · 11/10/2025
Published 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 🧪
Structures of DNA and morpholino oligonucleotides. R and R' denote continuation of the oligomer chain in the 5' or 3' direction, respectively. Credit to Corey & Abrams (2001) Genome Biology.
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Megan Dennis @mydennis.bsky.social · 25/09/2025
While 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
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Gaurav Varshney @varshneylab.bsky.social · 06/09/2025
Does anyone have #zebrafish LC3 reporter lines and would be willing to share them with us? #askzebrafish
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Shawn Burgess @burgesslab.bsky.social · 15/08/2025
#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):
ncbi.nlm.nih.gov
JBQAYU000000000.1 Danio rerio :: NCBI
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Gaurav Varshney @varshneylab.bsky.social · 02/08/2025
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Gaurav Varshney @varshneylab.bsky.social · 31/07/2025
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...
nature.com
CRISPR-based functional genomics tools in vertebrate models - Experimental & Molecular Medicine
Recent advances in DNA sequencing have allowed scientists to gather vast amounts of genetic data, but understanding what those sequences actually do requires additional tools that allow scientists to ...
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Gaurav Varshney @varshneylab.bsky.social · 22/07/2025
Congratulations, Megan! As always inspiring work.
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Gaurav Varshney @varshneylab.bsky.social · 21/07/2025
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/...
advanced.onlinelibrary.wiley.com
Rationally Designed TadA‐Derived Cytosine Editors Enable Context‐Independent Zebrafish Genome Editing
A next-generation cytosine base editor (zTadCBE) and other variants are developed by combining the high-efficiency (TadCBEa) and low-indel (TadCBEMax) architectures, followed by the introduction of z....
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Gaurav Varshney @varshneylab.bsky.social · 18/07/2025
Congratulations!
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Kristen Kwan @blockintheback.bsky.social · 07/07/2025
🚨🚨🚨 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
tol2kitkwan.genetics.utah.edu
tol2kit for kwan lab
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Ferenc Mueller @ferencmueller.bsky.social · 11/07/2025
Dear #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.
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Kristen Kwan @blockintheback.bsky.social · 11/07/2025
The 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
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Gaurav Varshney @varshneylab.bsky.social · 18/06/2025
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?
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Xenbase @xenbase.bsky.social · 05/06/2025
Please 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
statnews.com
There is no replacement (yet) for animal models in medical research
The NIH is “reducing animal use in research.” But there is no replacement for animal models.
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Zebrafish Rock! @zebrafishrock.bsky.social · 10/05/2025
With 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 🧪
Timeline of important technological developments in zebrafish research.
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Gaurav Varshney @varshneylab.bsky.social · 02/05/2025
Get ready to pay extra for your supplies and reagents.
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Genetics Society of America @genetics-gsa.bsky.social · 30/04/2025
Welcome @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
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Ben Kleinstiver @bkleinstiver.bsky.social · 22/04/2025
In @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...
nature.com
Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning - Nature
Nature - Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning
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Shawn Burgess @burgesslab.bsky.social · 21/04/2025
New 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
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Shawn Burgess @burgesslab.bsky.social · 15/04/2025
It 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):
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Gaurav Varshney @varshneylab.bsky.social · 17/04/2025
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...
cell.com
Biallelic pathogenic variants in TRMT1 disrupt tRNA modification and induce a neurodevelopmental disorder
We identify bi-allelic variants in TRMT1, encoding a tRNA-modification enzyme, that cause intellectual disability and developmental delay. Functional studies in human cells and zebrafish provide insig...
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Zebrafish Rock! @zebrafishrock.bsky.social · 09/04/2025
@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)
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Heidi Rehm @heidirehm.bsky.social · 28/03/2025
We 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.
go.sn.pub
Call for papers - Clinical interpretation of genome variation: volume II
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Daryl Gohl @darylgohl.bsky.social · 22/03/2025
Hey 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
University of Minnesota Genomics Center Model Organism Sequencing Service Flyer. $25 for a 30x Drosophila genome.
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Gaurav Varshney @varshneylab.bsky.social · 18/03/2025
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
Graphical Abstract
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Craig Kaplan @triggerloop.bsky.social · 26/02/2025
Piece 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-...
chronicle.com
NIH Funding Is at a Standstill. This Professor Is Tracking the Delays.
More than half of the NIH grant-review meetings that were supposed to take place this year have been cancelled, she says. “Without these meetings happening, nothing can get funded.”
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Daniel Gorelick @danielgorelick.bsky.social · 26/02/2025
We 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
bit.ly
Biologists @ 100 - Programme
The Company of Biologists is committed to championing positive and progressive discovery.​ The last 100 years has been a period characterised ​​by pioneering discovery.​​ The next 100 years promises t...
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Gaurav Varshney @varshneylab.bsky.social · 26/02/2025
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. 😆
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John Wallingford @jbwallingford.bsky.social · 25/02/2025
Reminder 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-...
report.nih.gov
Success Rates | RePORT
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Annika Barber @annikabarber.bsky.social · 24/02/2025
Wondering 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...
docs.google.com
2025 Study section tracking
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Annika Barber @annikabarber.bsky.social · 23/02/2025
Kickass 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...
heraldbanner.com
Why federally funded science matters to Texas | Columns | heraldbanner.com
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Megan Zahneis @mzahneis.bsky.social · 20/02/2025
An 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...
chronicle.com
Despite a Judge’s Ruling, Large Swaths of NIH Funding Remain Effectively Frozen
The groups that review and decide on grant proposals cannot schedule their meetings because the Trump administration has barred them from posting notices in the Federal Register.
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BWJones @bwjones.bsky.social · 20/02/2025
It’s @katherinejwu.com with the receipts. The NIH memo undercutting the NIH came directly from Trump officials. www.theatlantic.com/health/archi...
theatlantic.com
The NIH Memo That Undercut Universities Came Directly From Trump Officials
NIH officials said they were given no advance warning and less than an hour to post the memo publicly.
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