UC Santa Cruz Genomics Institute

🦟 The mosquito is the most deadly animal in the world. The Mosquito Cell Atlas is an incredible new resource to help us understand more about their ability to transmit pathogens to humans.

Data is available on the UC Santa Cruz @genomebrowser.bsky.social at mosquito.cells.ucsc.edu

Genomics Rooftop Mixer: Mapping Gene Isoforms to Improve Treatment — Santa Cruz Works Angela Brooks and her team are rewriting cancer research with FLAIR, a tool that reveals hidden RNA isoforms driving tumor growth and drug resistance—insights that could revolutionize precision medicine.

UCSC's Brooks Lab tool FLAIR is helping to rewrite the story of cancer research—pushing precision medicine closer to truly individualized care. Learn how: santacruzworks.org/n...

@joann-trejo.bsky.social, @marymunson4.bsky.social and I have a commentary in @natcellbio.nature.com on recent attacks on DEI in biomedical research: "If scientific research, especially biomedical research, is meant to serve everyone, then it requires that everyone has an opportunity to participate"

The people to ask why this release is codenamed "bologna" are: @benedictpaten.bsky.social @adamnovak.graphs.vg @thinks.lol @jltsiren.bsky.social @xian-chang.bsky.social @jmonlong.bsky.social

Release vg 1.69.0 - Bologna · vgteam/vg Don't forget to mark the static binary executable: chmod +x vg Docker Image: quay.io/vgteam/vg:v1.69.0 Buildable Source Tarball: vg-v1.69.0.tar.gz Includes source for vg and all submodules. Use th...

Researchers using vg - a new release is now available at github.com/vgteam/vg/re... 🎉
vg giraffe now has
🧬 Improved support for cyclic snarls
🧬 An experimental recombination-aware mode

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - Nature Biotechnology Somatic small variants in cancer genomes are identified in both short-read and long-read data.

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - @ucscgenomics.bsky.social go.nature.com/4qa6m0d

Carol Greider receives American Cancer Society Professor Award The award includes a grant that will support Greider's research that advances her Nobel-winning discovery of the DNA caps at the ends of chromosomes called telomeres

Nobel laureate Carol Greider has been named an @americancancersoc.bsky.social Professor 🎉 Her work at @ucsantacruz.bsky.social aims to overcome longstanding barriers to new cancer treatments—understanding how telomere length is regulated and accurately measuring it.
🔗 news.ucsc.edu/2025/10/grei...

Genomics Rooftop Mixer: Kelp and the Future of Our Oceans — Santa Cruz Works Join us October 28 for the Genomics Rooftop Mixer, featuring Malin Pinsky’s kelp genomics research. Discover how resilient kelp can safeguard California’s coasts, fisheries, and biodiversity against warming oceans. Science, community, and conservation meet.

Although kelp can be frustrating to get tangled in when you're going for a swim in the ocean, resilient kelp can actually safeguard California’s coasts, fisheries, and biodiversity against warming oceans. Learn how: santacruzworks.org/n...

A man in a lab coat and glasses examines a snip of hair in a plastic bag.

A court ruling in favor of @ucsantacruz.bsky.social Genomics Institute associate Ed Geen's startup Astrea Forensics paves the way for whole-genome sequencing, a cutting-edge technique used on degraded DNA in fossilized remains, to be admitted as evidence in trials 🦴🔍 www.nature.com/articles/d41...

UCSC Genome Browser User Satisfaction Survey | SurveyMars I have posted a survey titled 'UCSC Genome Browser User Satisfaction Survey' on SurveyMars. Please help me by filling it out. Thank you very much!

Please take a moment to tell us how you use the Genome Browser: surveymars.com/q/mnb...

Your feedback supports future improvements and our continued funding.

We are pleased to announce the release of the Developmental Disorders Genotype-to-Phenotype (DDG2P) track for hg19 and hg38. The DDG2P track displays genes associated with severe developmental disorders.

Learn more at:
genome.ucsc.edu/gold...

Karen Miga and Krizia Chambers standing on the steps of Capitol Hill

Krizia Chambers, Karen Miga, and two other women sit at a coffee table. Krizia is speaking to Representative Jimmy Panetta, who is standing listening to her with his hands clasped in front of him.

Breakthrough disease treatments are being developed, but they need #NIH funding! @khmiga.bsky.social and Krizia Chambers joined #RallyForMedicalResearch on Capitol Hill to tell lawmakers how important federal funding is to their research.

🧪🔬 Message your lawmakers: news.ucsc.edu/2025/09/advo...

A decorative illustration of a petri dish underneath what looks like a high-powered microscope. It is attached via a tube to another dish.

Scientists at @ucsc have built an automated platform to grow and monitor brain organoids (brain tissue in a dish) 24/7 🧠🤖. It captures neural activity missed by manual methods—boosting reproducibility & paving the way for breakthroughs in brain research.
www.sciencedirect.com/science/arti...

AnVIL Data Explorer logo

📢 Announcing the AnVIL Data Explorer!
This tool makes it easier to access and reuse high-value datasets, including those that focus on specific diseases like Alzheimer’s, cancer, and rare genetic disorders. Over 280 datasets are already available, with more to come.
news.ucsc.edu/2025/08/new-...

Do humans and chimps really share nearly 99% of their DNA? The frequently cited 99% similarity between human and chimp DNA overlooks key differences in the genomes.

🧑🧬🐒 Are humans and chimps *really* 99% similar? New telomere-to-telomere (T2T) genomes and other sequencing advancements are helping scientists reveal more differences, primarily in the "non-coding" regions of DNA that turn genes on and off.

www.livescience.com/archaeology/...

🌎 The Earth BioGenome Project is proposing to sequence 150,000 species over 4 years--which means releasing 3,000 new genomes a month ‼️

We're proud to be participating in this effort to create a rich resource to inform conservation, ensure food security, and even advance medicine.

Woman standing in front of a poster at a conference

Woman smiling holding a certificate

Congratulations to lab member Maria! Maria joined us this summer as an NHGRI GREAT scholar @ucscgenomics.bsky.social Within 8 weeks she learned new wet lab techniques, bioinformatics, and carried out independent research. Proud to share that she received an award for outstanding research poster.

ASHG 2025 Workshop: The Human Pangenome: Data, Tools, and Workflows Introducing participants to the new Human Pangenome Reference, how samples were chosen to maximize variation, & technologies used to build the pangenome

Headed to #ASHG25?

Don’t miss HPRC’s workshop on the Human Pangenome: Data, Tools & Workflows.

📅 Oct 14 | 10AM–12PM

Learn how to access data & use pangenome tools!

www.ashg.org/product/ashg...

We are excited to announce the release of the MaveDB Experiment Heatmaps and Alignment track for hg38. Each heatmap shows the results of many small substitutions that were tested within a gene to examine their functional consequences.

Learn more at:
http://bit.ly/4lCIlLq

Google AI Releases DeepPolisher: A New Deep Learning Tool that Improves the Accuracy of Genome Assemblies by Precisely Correcting Base-Level Errors

Google AI, in collaboration with the UC Santa Cruz Genomics Institute, has introduced DeepPolisher, a cutting-edge deep learning tool designed to…

It's exciting to see the continuing legacy of T2T sequencing methods being discussed on @scifri.bsky.social ! 🧬
Complete genomes are helping us understand more and more about genetic function and diversity in areas of our DNA that were unreadable just a few years ago.

We’re excited to announce support for bedMethyl and bigMethyl, new track formats for visualizing base-resolution DNA methylation from bisulfite sequencing or similar methods at single-base resolution across the genome in the UCSC Genome Browser. More info: genome.ucsc.edu/gold...

YouTube video by D4I TDR D4I Tribal Data Repository - Protecting Tribal Data & Why It Matters

The @nativebio.bsky.social is working to create the D4I Tribal Data Repository to uphold Indigenous data sovereignty 🧬🤝

In this video, a few of our collaborators on this project explain what it means to protect tribal data, and why it matters: www.youtube.com/watch?v=twp6...

A scared-looking rat with a hunched back stands in a corner looking wearily in the direction of the viewer.

Can a father’s stress influence the health of his future children?

Science says yes. Affiliate @upasnasharma.bsky.social studies this effect in mice, and she has received a new McKnight Foundation award to uncover the molecular signals in sperm that are behind it: news.ucsc.edu/2025/07/upas...

Two male elephant seals face each other in a display of dominance, with chests puffed and their large noses in the air. Female seals and their pups lie around the bull on the left.

🦭🧬 After nearly going extinct, northern elephant seals bounced back, but lost almost all genetic variation.

Now, thanks to a new tool out of @ucsantacruz.bsky.social, we can trace family lines for species with low genetic diversity and improve conservation strategies.

📄: doi.org/10.1111/acv....

YouTube video by Biochemistry Channel Letter from NAS Members to the Honorable Senators and Representatives of the United States

Over 1,100 members of the National Academies of the Sciences, representing both political parties, have signed a letter urging Congress to reject the FY26 science budget cuts that threaten U.S. leadership in science, health, and national security. #StandUpForScience www.youtube.com/watch?v=Vkv0...

@benedictpaten.bsky.social @adamnovak.graphs.vg @thinks.lol @jltsiren.bsky.social @xian-chang.bsky.social @jmonlong.bsky.social

vg graphs logo

🧪🧬🖥️ We have a new variation graphs (vg) update: github.com/vgteam/vg/re...

Changes include:
🤝Improved compatibility with other GFA graph files and transcript annotation files
🪲Various bug fixes, especially for mis-named or broken command-line options

📣 JOB ALERT: We are looking for a Senior Software Engineer to join our pathogen genomics team! Be a part of creating and maintaining tools that public health officials are using to track the spread of dangerous pathogens 🦠

Apply here:
careerspub.universityofcalifornia.edu/psc/ucsc/EMP...

A new species of Anemonefish from French Polynesia, Amphiprion maohiensis, (Pomacentridae, Amphiprioninae), the Polynesian anemonefish Anemonefishes (Teleostei, Pomacentridae) comprise approximately 28 species of damselfishes that exclusively live symbiotically with sea anemones. Distribution ranges vary, with some species only found...

New anemonefish species alert! After many years working with this species, we finally also described it as a the Polynesian Anemonefish. zookeys.pensoft.net/article/1414...