Prajna Hebbar
@prajnahebbar.bsky.social
PhD Candidate, Computational Genomics Lab UC Santa Cruz.
New collaborative paper from the lab on gecko sex chromosome and genome evolution! 🧪🦎 www.science.org/doi/10.1126/...
Genomic predisposition is associated with the direction of sex chromosome evolution
Sex chromosome evolution is among the most dynamic genomic innovations in vertebrates, yet why some lineages evolve XY while others evolve ZW remains unclear. Using chromosome-level genomes from 19 ge...
science.org
NIH is planning on revoking eligibility for international students on visas for the K99/R00 pathway, a key program that supports postdocs in establishing their own labs www.statnews.com/2026/08/07/n...
NIH plans to block international researchers on visas from accessing key funding avenue
The NIH plans to close the door on one of the few pathways available to international students on visas to forge a career in biomedical research in the U.S.
statnews.com
Big news in genomics! #BaskinEngineering Ph.D. student @prajnahebbar.bsky.social led the complete sequencing of the DNA of a common marmoset. 🧬 “Now, we have this really complete, high-quality resource that people can take advantage of," she said. Via The Scientist: bit.ly/4q1O9C3
Complete Reference Genomes Set New Genomics Milestones | The Scientist
Advances in genome assembly methods helped researchers complete reference genomes for humans, marmosets, songbirds, and more, accelerating genomic research.
bit.ly
New issue alert👉https://cell.com/cell/current On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.
We’ve sequenced a marmoset! Grad student @prajnahebbar.bsky.social & @benedictpaten.bsky.social led the effort, and expect it to enable scientists to learn more about genes that contribute to memory loss and Alzheimer's. 🔗https://news.ucsc.edu/2026/08/first-complete-marmoset-genome/
For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]
Did Thoreau encounter contagious cancer? A new study finds transmissible tumors in catfish--and raises questions about whether they could arise in humans someday. Gift link: nyti.ms/4whfi6v
Deep in This Lake, a Contagious Cancer Is Spreading (Gift Article)
Transmissible tumors have been reported in a handful of animal species, but never before among fish. Is it possible in humans?
nyti.ms
Our new commentary rdcu.be/ftx6h in @natecoevo.nature.com written with folks from @inaturalist.bsky.social and @cornellbirds.bsky.social shows that use of AI to manipulate existing or create new wildlife images undermines the huge value of vast citizen science databases. 🌍🪰🪶 #Ornithology 🧵 1/10
Citizen science platforms must mitigate against the threat of generative AI
Nature Ecology & Evolution - Citizen science platforms must mitigate against the threat of generative AI
rdcu.be
How did octopuses evolve novel traits? Rishav Mitra, Richard Han, Trey Scott, et al serendipitously discover a unique ribosome adaptation that increases the accuracy of protein synthesis and evolved alongside their elaborate nervous systems vs deep sea relatives. www.biorxiv.org/content/10.6...
🚨 MANUSCRIPT ALERT 🚨 The VGP Phase I manuscript pre-print is now live on bioRxiv! 🧬 doi.org/10.64898/202... Over 8 years, the VGP generated reference genomes for more than 800 vertebrate species, spanning ~95% of vertebrate orders and delivering some of the highest-quality genomes ever produced.
There are a horrifying number of computer science professors that still just "solve problems" with no thoughts. People who publish papers like: "We made an algorithm that can detect human shapes from infrared data, and even works with children behind tent covers."
How can one be a scientist in this world and not be an activist?
I made a 2-page Take Action Flyer for anyone to download and use! We need all hands on deck! drive.google.com/file/d/1ppq4...
OMB Rule Flyer - Take Action.pdf
drive.google.com
I've been documenting a pair of black-capped chickadees nesting in our garden as they fly back & forth every few minutes, hunting meals. An avg clutch of 6 to 8 chickadees requires 3,000 to 5,000 feedings over the ~16 days from hatching to fledging. Most popular foods: caterpillars, moths, spiders.
😮 @danielgorelick.bsky.social @biologyopen.bsky.social www.nature.com/articles/d41...
Why paying peer reviewers works, according to a journal’s editor-in-chief
A biology journal that paid peer reviewers found that the approach cut the time to a first editorial decision by 85% and maintained high-quality reviews.
nature.com
The evolution of structural variation across 500 million years of vertebrate evolution https://www.biorxiv.org/content/10.64898/2026.06.26.733778v1
I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇
Being a bird nerd is now cool. Well, it always was cool, but the rest of the world is finally cottoning on. Nice write-up in the Sunday Star Times and The Post with quotes from me accessiblenews.xyz/article/www.... @birdsnewzealand.bsky.social
Why Gen Z - and me - have gone to the birds
ESSAY: Once a pastime associated with tweed jackets and thermoses, birdwatching is now soaring in popularity among young people.
accessiblenews.xyz
T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...
Happy to have played a small role in this really cool paper!
Joana L. Rocha@joanocha.bsky.social · 3mo agoWe are excited to share our pan-pangenome paper! This is a long time coming work of my postdoc with the incredible @psudmant.bsky.social, and a stellar group of people! I hope you enjoy reading it! And I am excited to talk more more about it this week at #PEQG26!! www.biorxiv.org/content/10.6...
Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n
A sibling study of variation in parental mutation rates
People are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098
biorxiv.org
Recent research explores the evolution and regulation of the human-specific NOTCH2NL gene family using near-complete long-read assemblies from humans and apes. Uncover the science behind it: www.cell.com/cell-genomic...
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications
Human-specific NOTCH2NL segmental duplications are implicated in brain cortical expansion. Analysis of 82 long-read assemblies from apes and humans shows independent duplications. Human-specific NOTCH...
cell.com
dear god PLEASE let this also lead to a wider acceptance that treatment needs to include *improving quality of life* and not just "how to make them have baby"
Maggie Astor@maggieastor.bsky.social · 4mo agoPCOS (polycystic ovary syndrome) is now PMOS (polyendocrine metabolic ovarian syndrome). The name change follows a multiyear process stemming from a recognition that ovarian cysts aren't the primary aspect of the condition, which affects multiple body systems, and many patients don't have them.
Happy to announce two-fold news! 1) The SCINKD paper is now published in @molbioevol.bsky.social - doi.org/10.1093/molb... 2) SCINKD [v2.2.4] release has reduced runtimes (about 2x) and the revitalized mode for genomes >5Gb is now live and tested on genomes up to 21Gb! 🐸 github.com/DrPintoThe2n...
Sex chromosome identification and genome curation from a single individual with SCINKD
Abstract. In most animal species, the sex-determining pathway is typically initiated by the presence/absence of a primary genetic cue at a critical point d
doi.org
We built the first complete genome for the common marmoset, fully resolving regions that were previously missing: centromeres, acrocentric short arms, and more. A new reference genome for anyone working with marmosets. This was an awesome collaborative effort & I’m grateful to all my co-authors! 🧬
bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo agoA Complete Genome for the Common Marmoset https://www.biorxiv.org/content/10.64898/2026.03.25.713844v1
A Complete Genome for the Common Marmoset https://www.biorxiv.org/content/10.64898/2026.03.25.713844v1
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
This was such a fun project. Adam's thread on it is a great summary!
Adam Phillippy@aphillippy.bsky.social · 7mo agoTime for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
