We are excited to announce the ENCODE4 data collection on the UCSC Genome Browser for hg38 and mm10. This release consists of two major components: the ENCODE Registry of cCREs and the new ENCODE4 Regulation container. Learn more at: bit.ly/Encode4Release

🎉Version 500!!!🪅 Happy birthday, @ucsantacruz.bsky.social Genome Browser! 🎂 Five hundred versions later, the Browser serves thousands of genome assemblies across the tree of life, tens of thousands of annotation tracks, and a global community of researchers, clinicians, educators, and students.

UCSC Genome Browser@genomebrowser.bsky.social · 4w ago

26 years ago today, the first public assembly of the human genome went online at UC Santa Cruz. Today, we release version 500 of the UCSC Genome Browser. From Jim Kent's first assembly to thousands of genomes, the data is still free and open. genome.ucsc.edu/gold...

🧬New in Nature: leading experts (@jenniferdoudna.bsky.social, @euanashley.bsky.social, @benedictpaten.bsky.social) call for a new medical genome standard that uses diploid sequences & pangenome graphs instead of a single reference for improving clinical diagnostics 👏🏽👏🏿👏🏻 www.nature.com/articles/s41...

Harmonizing standards and resources for the medical genome - Nature

This Perspective examines the challenges and opportunities of genomic sequencing across multiple clinical applications, including genetic therapies, and calls for the establishment of new, centra...

nature.com

Growing neurons from stem cells—in high school! 🧠 A Genomics Institute platform uses cloud-connected microscopes so students design real stem cell experiments remotely. New study shows it measurably boosts STEM identity, especially for Hispanic & first-gen students. news.ucsc.edu/2026/0...

🧪🧬🖥️ New variation graph update! v1.75.0, codenamed "Spike" now does recombination-aware mapping by default, and uses a new logarithmic gap scoring scheme for its alignments, along with other added features! github.com/vgteam/vg/re...

Nature research paper: Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago go.nature.com/4oFh0eU

Lethal plague outbreaks in Lake Baikal hunter-gatherers 5,500 years ago - Nature

Analyses of ancient DNA from hunter-gatherers near Lake Baikal in southeast Siberia around 5,500 years ago indicate that highly virulent Yersinia pestis emerged earlier than previously estimated, far from the next known cases of infection in Late Neolithic Europe.

go.nature.com

In my lab's latest, we experimentally test the decades-old idea that plants switch from bee to hummingbird pollinators in tropical mountains because bee activity declines in cool cloud forest conditions nph.onlinelibrary.wiley.com/doi/10.1111/...

Pollinator efficiency, rather than bee decline, explains a shift to hummingbird pollination in tropical montane forests

Hummingbird pollination is a hallmark of American plant diversity and has long been thought to evolve in tropical mountains due to declining bee activity. Using sister species of Costus specialized o...

nph.onlinelibrary.wiley.com

Congratulations to our graduating Research Mentoring Internship (RMI) scholars - we are so proud of you!

In the 1980s, disease wiped out about 99% of black abalone. A new study from @ucsantacruz.bsky.social sequences whole genomes from shells, a feat no one had accomplished before, to reconstruct what abalone populations looked like pre-collapse: news.ucsc.edu/2026/05/anci... 📷Michael Ready

🧬🇯🇵 @ucsantacruz.bsky.social Genomics Institute researchers have collaborated to sequence near-complete Japanese genetic data, unlocking complex, medically relevant DNA regions. This work is part of the effort to dismantle reference bias for globally equitable medicine. www.nature.com/articles/s41...

Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes - Nature Communications

A Japanese human pangenome graph built from near-complete genomes brings medically important blind spots of the human genome into focus, revealing hidden diversity in complex genomic regions related t...

nature.com

New vg v1.74.0 "Petrie" update includes: 🔹Single-command way to run the haplotype sampling mapping workflow with vg giraffe 🔹 Minimap2-inspired alignment scoring approach for giraffe 🔹Ability to write v.1 GBZ files for compatibility with pangenome-aware DeepVariant github.com/vgteam/vg/re...

Like its mythical counterpart, real-life hydra are nearly immortal, and can regrow any body part. And scientists just got much better at studying them. New work from the Aide Macias-Muñoz lab is a quiet but meaningful leap for evolutionary genetics. Learn more: integrativeandcompar...

What if you could measure the health of a waterway from the genetic information contained in a single sample of water? It sounds like science fiction, but it’s exactly what we’re scaling across the state, thanks to a $2.2M grant from the CA Department of Fish and Wildlife! news.ucsc.edu/2026/0...

Get excited- DNA DAY is HERE!!! Join us TODAY in the Rob Baskin Engineering Courtyard from 11-1pm to celebrate the wonders of DNA. There will be a science fair and fun activities for all ages, plus free DNA swag and shirts!

eDNA is possibly the coolest application! Below: read-level placement across a pan-vertebrate mitochondrial pangenome (left) where a clear cluster of read assignments supports the presence of many mammoth reads (right). Processing ~9 billion reads took just 8 minutes!

Pangenomes, but scalable. Panmap: phylogeny-guided framework for read alignment, genotyping, sample placement on pangenomes. 600x smaller indexes, faster builds, and placement from 20K to 8M genomes. @amkram.bsky.social @alanbyzhang.bsky.social @russcd.bsky.social www.biorxiv.org/content/10.6...

In the past 25 years, scientists have sequenced the DNA of thousands of species. But what can genomics actually do for ecological conservation? 🧬 Join us on campus May 1st for a special symposium on conservation genomics, with a keynote from Beth Shapiro! Register: events.ucsc.edu/event/sequen...

🧪🧬🖥️ New vg v1.73.0 release, codenamed "Ducky," features off-linear-reference VCF generation in vg call and vg deconstruct, and GBZ-to-GBZ chunking in vg chunk. Distance indexes have also been improved: github.com/vgteam/vg/re...

Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes. www.biorxiv.org/content/10.6...

🧠🧬 Exciting new project: @ucsantacruz.bsky.social is partnering with UCLA on a $13.9M @cirmnews.bsky.social grant to identify drug targets for autism & schizophrenia. Our Institute will lead work on how genetic mutations impact brain "circuits" & cell communication 🔗 news.ucsc.edu/2026/03/cirm...

"AI will soon be in a position to replace us." 🧬💻 UCSC Genomics Institute Scientific Director David Haussler & Professor J. Xavier Prochaska share why they've moved from denial to concern regarding the future of AI in science in a @mercurynews.com op ed: www.mercurynews.com/2026/03/18/o...

Opinion: We’re scientists. We use AI. And we fear it.

‘Both of us have recently moved from denial to contemplation that AI will soon be in a position to replace us.’

mercurynews.com

New study finds the mating antics of animals can alter an ecosystem. Constant sexual harassment of female mosquitofish by males results in depletion of prey lower in the food web due to both sexes needing to maintain the energy for all the chasing and evading 🐠 💨 🐠 news.ucsc.edu/2026/03/sexu...

Does sexual harassment behavior matter for ecosystems?

Intense harassment of females by male mosquitofish increases the ecosystem consequences of this highly invasive fish

news.ucsc.edu

Happy time-change Monday! We've got a proposal that might help cheer you up as you struggle to overcome that lost hour of sleep ☕😴: Genomics Institute affiliate @russcd.bsky.social takes on the absurdity of academic metrics with a new proposal in @molbioevol.bsky.social 😆🙃

Molecular Biology and Evolution@molbioevol.bsky.social · 5mo ago

@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever. 🔗 doi.org/10.1093/molbev/msag026 #evobio #molbio

@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.

First study using sedaDNA to assess genetic impact of a natural disaster found Ice Age megafauna 🦣🐴🦬 showed no genetic diversity loss or population turnover after a volcano covered the landscape in 2.5ft of ash.🌋 news.ucsc.edu/2026/0...

Associate Professor Olena Vaske, leader of the Colligan Clinical Diagnostics Lab (CCDL) at the UC Santa Cruz Genomics Institute, will be speaking at Science on Tap! ⏱️ March 2 at 6:00 PM. 📍 The Garden at The Crepe Place: 1134 Soquel Ave, Santa Cruz 🎟️ Free and open to the public

We grew some brain tissue in the lab and taught it to balance a virtual pole 🕹️🤯 This isn't just a cool party trick — it's giving us a window into how neural circuits learn and adapt. news.ucsc.edu/2026/02/brai... @mrbadash.bsky.social

Open Culture Science is a new startup that could transform how labs grow cells and tissues worldwide. Founded by two UCSC Genomics Institute grads, it aims to automate processes that are currently painstakingly manual. 🔬🧠 news.ucsc.edu/Open-C...

Our pangenome team has released a new vg update, v1.72.0, codenamed "Littlefoot" 🧪🧬🖥️ github.com/vgteam/vg/re... New features: 📈 Support for supplementary alignments in vg giraffe 📈 Sequence compression GBZ graph file format

New research from @ucsantacruz.bsky.social Genomics Institute affiliate Shaheen Sikandar shows that pregnancy may “reset” how breast tissue ages, reducing cell changes that are linked to higher breast cancer risk later in life. news.ucsc.edu/2026/01/preg...