Gaurav Varshney
@varshneylab.bsky.social
Assoc. Prof. Interested in CRISPR, Zebrafish, Disease Modeling, Rare Diseases, and Neurodevelopmental Disorders. The opinions expressed here are my own.
Reposted by Gaurav Varshney
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 17, 2025 at 11:22 PM
Folks, it is finally out! Our paper on T2T assemblies of the zebrafish genome is on BioRxiv:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Gaurav Varshney
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 🧪
October 11, 2025 at 11:44 AM
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 🧪
Reposted by Gaurav Varshney
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
"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
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
September 25, 2025 at 8:19 PM
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
Does anyone have #zebrafish LC3 reporter lines and would be willing to share them with us? #askzebrafish
September 6, 2025 at 4:08 PM
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):
JBQAYU000000000.1 Danio rerio :: NCBI
www.ncbi.nlm.nih.gov
August 15, 2025 at 4:17 PM
#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...
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 ...
www.nature.com
July 31, 2025 at 11:05 AM
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...
authors.elsevier.com
July 22, 2025 at 2:25 AM
Congratulations, Megan! As always inspiring work.
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/doi/10.1002/...
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....
advanced.onlinelibrary.wiley.com
July 21, 2025 at 2:58 PM
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/doi/10.1002/...
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
Collab with @aburger2009.bsky.social & Breuss labs @cuanschutz.bsky.social. 🧬
...and: big THX to everyone who already helped w/ sharing #pIGLET reagents! 🐽
#ShareYourTools #MakeMoreTransgenics
piglet from winnie the pooh says thank you
ALT: piglet from winnie the pooh says thank you
media.tenor.com
July 18, 2025 at 3:01 AM
Congratulations!
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
tol2kitkwan.genetics.utah.edu
Thank you for your patience!!
#zebrafish #transgenesis #plasmids #sharing
tol2kit for kwan lab
tol2kitkwan.genetics.utah.edu
July 7, 2025 at 6:01 PM
🚨🚨🚨 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
Thank you for your patience!!
#zebrafish #transgenesis #plasmids #sharing
Reposted by Gaurav Varshney
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.
July 11, 2025 at 9:28 PM
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.
Reposted by Gaurav Varshney
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
July 11, 2025 at 10:40 PM
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
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?
June 18, 2025 at 8:43 PM
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 Varshney
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
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.
www.statnews.com
June 5, 2025 at 5:13 PM
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
Reposted by Gaurav Varshney
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)($) doi.org/10.1016/bs.a... #ZebrafishFunFacts 🧪
May 10, 2025 at 9:23 AM
With a published genome & advancements in gene editing, the field of #zebrafish genetics has exploded in recent decades. We take a look back at major achievements in this infographic. For more, read this book chapter by @varshneylab.social et al (2015)($) doi.org/10.1016/bs.a... #ZebrafishFunFacts 🧪
Get ready to pay extra for your supplies and reagents.
May 2, 2025 at 3:29 PM
Get ready to pay extra for your supplies and reagents.
Reposted by Gaurav Varshney
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
April 30, 2025 at 4:03 PM
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
Reposted by Gaurav Varshney
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...
www.nature.com/articles/s41...
Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning - Nature
Nature - Custom CRISPR—Cas9 PAM variants via scalable engineering and machine learning
www.nature.com
April 22, 2025 at 8:57 PM
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...
www.nature.com/articles/s41...
Reposted by Gaurav Varshney
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
Tnfrsf10 Signaling is Required to Maintain the Stem Cell Niche in the Zebrafish Lateral Line https://www.biorxiv.org/content/10.1101/2025.04.18.649014v1
April 21, 2025 at 3:19 PM
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
Reposted by Gaurav Varshney
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):
April 15, 2025 at 4:54 PM
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):
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...
www.cell.com/ajhg/fulltex...
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...
www.cell.com
April 17, 2025 at 3:13 AM
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...
www.cell.com/ajhg/fulltex...
Reposted by Gaurav Varshney
@varshneylab.social @sheng-jia.bsky.social (gRNA selection/ Phenotypic penetrance/ Neurodevelopmental disorders)
https://doi.org/10.1093/nar/gkaf180
@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking)
https://github.com/HenHus/Husmorph (32/34)
https://doi.org/10.1093/nar/gkaf180
@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking)
https://github.com/HenHus/Husmorph (32/34)
April 9, 2025 at 7:30 PM
@varshneylab.social @sheng-jia.bsky.social (gRNA selection/ Phenotypic penetrance/ Neurodevelopmental disorders)
https://doi.org/10.1093/nar/gkaf180
@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking)
https://github.com/HenHus/Husmorph (32/34)
https://doi.org/10.1093/nar/gkaf180
@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking)
https://github.com/HenHus/Husmorph (32/34)
Reposted by Gaurav Varshney
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.
Call for papers - Clinical interpretation of genome variation: volume II
go.sn.pub
March 28, 2025 at 10:21 PM
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.