UC Santa Cruz Genomics Institute
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ucscgenomics.bsky.social
UC Santa Cruz Genomics Institute
@ucscgenomics.bsky.social
Focusing the power of genomics to create a healthier world. Leader in pangenomics, conservation genomics, cancer genomics, pathogen genomics, and nanopore sequencing. Home of the UCSC Genome Browser, @ucscxena, UShER, Dockstore, and other high-power tools.
🪲 Meet an unassuming climate warrior: the tunneling dung beetle.

New research using environmental DNA (eDNA) metabarcoding uncovered that dung beetles are quietly reshaping the invisible microbial world in ways that could help pasturelands store carbon: doi.org/10.1002/edn3...
December 22, 2025 at 9:43 PM
New paper shares lessons learned from building 10+ data portals (ENCODE, HCA, 4DN). Key insight—FAIR data needs defined rules and human wranglers. Practical guide for how to build and run effective & sustainable portals: doi.org/10.1038/s415... @benedictpaten.bsky.social @genomebrowser.bsky.social
December 17, 2025 at 5:40 PM
Announcing bamdam: a new open source tool for studying ancient DNA 🧬 It shrinks massive metagenomic files by 10x and helps distinguish ancient sequences from contamination. Tested on the oldest DNA yet uncovered (2M years) link.springer.com/article/10.1... @bdesan.bsky.social @russcd.bsky.social
Bamdam: a post-mapping authentication toolkit for ancient metagenomics - Genome Biology
Ancient metagenomic studies using capture or shotgun sequencing often perform pairwise alignment of individual reads against large reference databases followed by lowest common ancestor assignment for...
link.springer.com
December 16, 2025 at 9:04 PM
New research maps seizure activity at the single-neuron level in human brain tissue from epilepsy patients.
Scientists used high-density electrode arrays with 26,400 (😲) recording sites to discover patterns that could help us understand the onset of seizures.
doi.org/10.1152/jn.0...
Microscale maps of bursting dynamics across human hippocampal slices from epilepsy patients | Journal of Neurophysiology | American Physiological Society
Neuronal firing patterning in the dentate gyrus of epilepsy patients remains unknown at the microcircuit level. Advancements in high-density CMOS-based microelectrode arrays can be harnessed to study network activity with unprecedented spatial and temporal resolution. We use novel computational methods with high-density electrophysiology recordings to spatially map network activity of human hippocampal brain slices from six patients with mesial temporal lobe epilepsy. Two slices from the dentate gyrus exhibited synchronous bursting activity in the presence of low magnesium media with kainic acid, representative of seizure-like behavior. We bridged microscale circuit dynamics with alterations in theta oscillations at the network scale. Future studies may apply this approach to spatially elucidate functional networks and their possible role in seizures.
doi.org
December 15, 2025 at 8:11 PM
🎉 Congratulations to our Scientific Director David Haussler and our emeritus affiliate Dave Deamer on being named fellows of the National Academy of Inventors! ⚙️ 👏🏿👏🏻👏🏽 news.ucsc.edu/2025/12/nai-...
David Deamer and David Haussler elected Fellows of the National Academy of Inventors
The recognition is the highest professional distinction awarded to academic inventors.
news.ucsc.edu
December 12, 2025 at 7:31 PM
Reposted by UC Santa Cruz Genomics Institute
NEW #ELSIFridayForum: Dextinction and Deliberate Extinction🦕

Scientists are turning the tools of genetics to the elimination–and recreation–of entire nonhuman species. How should such existential decisions be made ethically and responsibly?

Sign up: www.addevent.com/event/bfqx9d...
December 1, 2025 at 6:12 PM
🐝 How did aggressive Africanized honey bees in Puerto Rico become gentle in just decades? New research from @russcd.bsky.social shows how genetic diversity from admixed populations enabled this change through selection on genes affecting serotonin signaling & behavior! 🧬
doi.org/10.1093/gbe/...
December 8, 2025 at 6:49 PM
📢 We're hiring a Genomics Senior Systems Architect!
The incumbent will be responsible for the Genomics Institute's complex computing infrastructure, including central and departmental systems, high-throughput storage, web systems, & cloud environments.
Apply at jobs.ucsc.edu using job code 82880.
December 4, 2025 at 8:17 PM
Our first thoughts begin before we are born 🧠👶🏻

This exciting finding from UCSC Genomics Institute researchers challenges the popular “blank slate” theory & opens new possibilities for studying developmental disorders.

👉 Read in @discovermag.bsky.social : www.discovermagazine.com/our-brains-m...
Our Brains May Have Pre-Configured Instructions to Understand the World When We're Born
Discover how brain organoids are helping us uncover whether early thought patterns emerge from experience or are hardwired into our DNA.
www.discovermagazine.com
December 4, 2025 at 4:28 PM
POSTDOCS: We're hosting our fourth-annual Next Wave of Faculty in Genomics symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖
APPLY BY JAN 15: genomics.wordpress.ucsc.edu/calendar_eve...
December 3, 2025 at 5:01 PM
Reposted by UC Santa Cruz Genomics Institute
Meet our plenary speakers 💁‍♂️

BETH SHAPIRO (@ucscgenomics.bsky.social)

Beth is a leader in the study of ancient DNA from extinct species and is now trying to develop tools to de-extinct prehistoric life.

Conference info 👉 icp2026.palaeogenomics.org

⚠️ Abstract submission closing soon, 30th Nov! ⚠️
November 24, 2025 at 10:39 AM
Now available: vg 1.70.0 release, code name "Zebedassi,"
with a new "vg describe" tool for inspecting files. 🧪🧬🖥️
github.com/vgteam/vg/re...
November 20, 2025 at 2:27 PM
📢 Our project has received a generous $3K matching gift! Generous donors like you have already matched $2220 - give now to help us match the remaining $780 and DOUBLE YOUR IMPACT!
It's Giving Day!!! You can help support 🎗pediatric cancer research AND a "degree-defining experience" for undergraduates by:

💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!

🔗 🎁 bit.ly/give2treehouse
November 6, 2025 at 1:38 AM
It's Giving Day!!! You can help support 🎗pediatric cancer research AND a "degree-defining experience" for undergraduates by:

💸 Donating to Treehouse Childhood Cancer Initiative
🗣 Sharing this post to spread the word!

🔗 🎁 bit.ly/give2treehouse
November 5, 2025 at 12:32 PM
Support diversity and excellence in STEM by giving to our Research Mentoring Internship (RMI) this Giving Day 🎁 Federal cuts to DEI grants have made your gifts VITAL to keeping this program alive. Please support student mentorship today: www.givecampus.com/schools/Univ...
November 5, 2025 at 12:30 PM
Reposted by UC Santa Cruz Genomics Institute
Can lab-grown brain tissue learn like #AI? 🧠🤖 @ucscgenomics.bsky.social researchers led by #BaskinEngineering prof Tal Sharf will explore whether brain organoids can learn from experience, respond to feedback, and solve tasks in real time. bit.ly/4howct5
Effort aims to uncover the learning and reasoning potential of brain organoids
The Braingeneers team will to test the ability of brain organoids to solve tasks in real time
bit.ly
October 22, 2025 at 7:37 PM
Reposted by UC Santa Cruz Genomics Institute
😷 Ever had a stomach bug? New #BaskinEngineering research brings us one step closer to stopping one of its viral causes! Prof Rebecca DuBois's lab revealed how human astroviruses—a cause of the stomach bug—bind to human cells, paving the way for future therapies and vaccines. bit.ly/3JfDrqY
Researchers pinpoint target for treating virus that causes the stomach bug
New study reveals how human astroviruses bind to humans cells and paves the way for new therapies and vaccines
bit.ly
November 4, 2025 at 5:00 PM
Reposted by UC Santa Cruz Genomics Institute
Creating brains in a lab doesn't have to be like Frankenstein this Halloween. 🧠👻

The Braingeneers team at the UC Santa Cruz Genomics Institute recently received a $1.9 million grant to grow miniature 3D brains from stem cells.
The challenge of creating brains in a lab
Lab-grown brains don’t have to inspire horror.
voxdotcom.visitlink.me
October 31, 2025 at 6:57 PM
🦟 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
October 30, 2025 at 4:45 PM
Reposted by UC Santa Cruz Genomics Institute
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...
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.
www.santacruzworks.org
October 25, 2025 at 12:01 AM
Reposted by UC Santa Cruz Genomics Institute
@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"
Scaling back DEI programmes and the loss of scientific talent
Nature Cell Biology - Programmes that support diversity, equity and inclusion (DEI) in science are under attack in the USA. Data indicate that diversity in the scientific workforce increases...
www.nature.com
October 23, 2025 at 4:36 PM
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
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...
github.com
October 24, 2025 at 6:20 PM
Reposted by UC Santa Cruz Genomics Institute
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - @ucscgenomics.bsky.social go.nature.com/4qa6m0d
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.
go.nature.com
October 16, 2025 at 4:13 PM
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...
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
news.ucsc.edu
October 7, 2025 at 8:52 PM