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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 · 28/09/2026
I have seen water-bath-based PCR machines, and distilled phenol myself.
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Gaurav Varshney @varshneylab.bsky.social · 28/09/2026
Must have book for molecular biologists, first thing I bought when I started my lab.
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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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Gaurav Varshney @varshneylab.bsky.social · 31/07/2026
Happy Birthday, Rita! Congratulations on completing a year as EIC of nBME.
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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 · 14/07/2026
Oh wow! Thank you so much, Dan!
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Gaurav Varshney @varshneylab.bsky.social · 12/07/2026
I would suggest Global Entry, which includes TSA PreCheck, and it only costs $15 more for 5 years.
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Gaurav Varshney @varshneylab.bsky.social · 12/07/2026
Even better for someone being selected "randomly" for secondary inspection.
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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 · 22/06/2026
I am so deeply sorry for your loss. Wishing you comfort and strength as you carry her memory with you. 💔
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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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Gaurav Varshney @varshneylab.bsky.social · 13/04/2026
Look delicious!
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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 · 19/03/2026
Congratulations!
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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
Conspiracy against Pis!
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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
Thanks Shawn! You trained me well.
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Gaurav Varshney @varshneylab.bsky.social · 28/01/2026
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.
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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 · 07/08/2025
Best wishes!
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Gaurav Varshney @varshneylab.bsky.social · 06/08/2025
I do it at least 2-3 times a day!
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Gaurav Varshney @varshneylab.bsky.social · 05/08/2025
Even if you do it from a phone, it will not be cleared elsewhere!
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Gaurav Varshney @varshneylab.bsky.social · 02/08/2025
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Gaurav Varshney @varshneylab.bsky.social · 01/08/2025
Congratulations!
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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
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.
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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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Gaurav Varshney @varshneylab.bsky.social · 15/06/2025
What! That's where I worked. So many fond memories. 😭
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Gaurav Varshney @varshneylab.bsky.social · 15/06/2025
Terrible! What building is it? I spent a year in this amazing campus.
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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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