Ian Holmes
@ianholmes.org
Berkeley professor (Bioeng, Compbio). Visiting Scientist at Calico. JBrowse genome browser / Apollo annotation editor, ML for gene regulation / molecular evolution / synbio. Occasional music, games, jokes
Pinned
Ian Holmes
@ianholmes.org
· Jan 25
Sophie Wilson - Wikipedia
en.m.wikipedia.org
I feel moved to write about one of my technological heroes, possibly the most influential on my youth as an 8-bit hacker: a trans woman named Sophie Wilson. en.m.wikipedia.org/wiki/Sophie_...
Reposted by Ian Holmes
Molecular effects of transposable element sequences in mammalian cells #TESky
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
Molecular effects of transposable element sequences in mammalian cells - Genome Biology
Transposable elements (TEs) are often epigenetically repressed in eukaryotic cells, but still affect the molecular state of the cell in certain contexts. A flurry of recent studies have elucidated new...
doi.org
November 28, 2025 at 8:05 AM
Molecular effects of transposable element sequences in mammalian cells #TESky
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
(Wen, MC.C., Welch, J.D. Genome Biol 26, 403 (2025)).
Interesting review of new-found functions of TEs in mammalian genomes, especially over the last three years.
doi.org/10.1186/s130... #TEWorldwide
Reposted by Ian Holmes
I will host a student researcher at Google DeepMind and am looking for PhD students interested in the intersection of creative writing and human-computer interaction.
Your work will contribute to moving beyond generative AI towards formative AI.
Your work will contribute to moving beyond generative AI towards formative AI.
November 28, 2025 at 2:00 PM
I will host a student researcher at Google DeepMind and am looking for PhD students interested in the intersection of creative writing and human-computer interaction.
Your work will contribute to moving beyond generative AI towards formative AI.
Your work will contribute to moving beyond generative AI towards formative AI.
Reposted by Ian Holmes
Mapping spatial gradients in spatial transcriptomics data with score matching https://www.biorxiv.org/content/10.1101/2025.11.24.690257v1
November 27, 2025 at 4:46 PM
Mapping spatial gradients in spatial transcriptomics data with score matching https://www.biorxiv.org/content/10.1101/2025.11.24.690257v1
Reposted by Ian Holmes
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
November 27, 2025 at 5:46 PM
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
Reposted by Ian Holmes
Mozilla, Microsoft, Google, Intel, Apple all came together to celebrate this great milestone:
WebGPU is now supported in major browsers!
Check out our post.
WebGPU is now supported in major browsers!
Check out our post.
WebGPU is now supported in major browsers | Blog | web.dev
Read about the biggest web graphics launch since WebGL. WebGPU is supported across major browsers, bringing unparalleled performance to the web.
web.dev
November 25, 2025 at 5:07 PM
Mozilla, Microsoft, Google, Intel, Apple all came together to celebrate this great milestone:
WebGPU is now supported in major browsers!
Check out our post.
WebGPU is now supported in major browsers!
Check out our post.
Amazing www.google.com/search?q=%22...
November 25, 2025 at 6:10 PM
Amazing www.google.com/search?q=%22...
Reposted by Ian Holmes
Next week at the British Society of Soil Science annual conference Dr Christopher Quince - Group Leader at Earlham Institute and @quadraminstitute.bsky.social - will be sharing his latest work with @ukceh.bsky.social on @ukceh.bsky.social on #soilhealth and the #soil #microbiome.
November 25, 2025 at 8:08 AM
Next week at the British Society of Soil Science annual conference Dr Christopher Quince - Group Leader at Earlham Institute and @quadraminstitute.bsky.social - will be sharing his latest work with @ukceh.bsky.social on @ukceh.bsky.social on #soilhealth and the #soil #microbiome.
Reposted by Ian Holmes
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Sally is arbitraging kleptoconchia (desire to steal shells) and thalassoacouphilia (desire to hear the sea) against psammophobia (fear of sand). There. We have replaced a tongue twister with a neologistic marketing-jargon abomination
something that has always irked me is that the seashore is the actual worst fucking place for her to sell seashells.
November 23, 2025 at 5:55 PM
Sally is arbitraging kleptoconchia (desire to steal shells) and thalassoacouphilia (desire to hear the sea) against psammophobia (fear of sand). There. We have replaced a tongue twister with a neologistic marketing-jargon abomination
Reposted by Ian Holmes
"While other universities report that the humanities are shrinking, at Berkeley, the opposite is true. The music major is the fastest-growing major on campus. We are finding bigger classrooms because film is exploding. English is back to the numbers we saw 15 years ago. We are hiring" bit.ly/4ohKuOe
"The humanities really are a resource — a confidence for living in our times.” Dean Sara Guyer on the modern utility of humanities degrees
This interview originally appeared on the Division of Arts
bit.ly
November 23, 2025 at 3:38 PM
"While other universities report that the humanities are shrinking, at Berkeley, the opposite is true. The music major is the fastest-growing major on campus. We are finding bigger classrooms because film is exploding. English is back to the numbers we saw 15 years ago. We are hiring" bit.ly/4ohKuOe
Reposted by Ian Holmes
Trevor Graham (Institute for Cancer Research, London) will be speaking in 24 hours on "Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data" www.youtube.com/watch?v=8shM...
Phyloseminar #153: Trevor Graham (Institute for Cancer Research, London)
Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data
Cancers evolve. Current methods to measure evolutionary dynamics rely on genome sequencing of…
www.youtube.com
November 23, 2025 at 5:01 PM
Trevor Graham (Institute for Cancer Research, London) will be speaking in 24 hours on "Quantitative measurement of cancer evolutionary history from single-sample bulk DNA methylation data" www.youtube.com/watch?v=8shM...
Kleptosquamy! Finally, a word for the behavior of the protagonist of Jack Vance’s “Cugel’s Saga”, who steals the Pectoral Skybreak Spatterlight, the most valuable scale in Sadlark’s armor, while being pursued by various other kleptosquamists
en.wikipedia.org/wiki/Cugel%2...
en.wikipedia.org/wiki/Cugel%2...
November 23, 2025 at 5:00 PM
Kleptosquamy! Finally, a word for the behavior of the protagonist of Jack Vance’s “Cugel’s Saga”, who steals the Pectoral Skybreak Spatterlight, the most valuable scale in Sadlark’s armor, while being pursued by various other kleptosquamists
en.wikipedia.org/wiki/Cugel%2...
en.wikipedia.org/wiki/Cugel%2...
Excellent conclusion to this thread, a solid counterpoint to “There are four lights” and “They got me a long time ago, Winston”
In Tesco’s this afternoon: an elderly Polish man at the self-checkout, trying to buy a pint of milk and a white radish. There is no picture for the radish on the machine. The assistant doesn’t know what it is. She asks a colleague: “It’s a white radish.” There is no entry for it on the machine.
November 22, 2025 at 7:21 PM
Excellent conclusion to this thread, a solid counterpoint to “There are four lights” and “They got me a long time ago, Winston”
Reposted by Ian Holmes
middlebury college student lia smith killed herself one month ago after facing harassment for being a trans athlete
you will not hear her name once on cable tv
don’t let them erase her
#TDOR #TransDayOfRemembrance
you will not hear her name once on cable tv
don’t let them erase her
#TDOR #TransDayOfRemembrance
November 20, 2025 at 1:50 PM
middlebury college student lia smith killed herself one month ago after facing harassment for being a trans athlete
you will not hear her name once on cable tv
don’t let them erase her
#TDOR #TransDayOfRemembrance
you will not hear her name once on cable tv
don’t let them erase her
#TDOR #TransDayOfRemembrance
RIP Mani. Breaking Into Heaven www.theguardian.com/music/2025/n...
Gary ‘Mani’ Mounfield, the Stone Roses and Primal Scream bassist, dies aged 63
Ian Brown and Tim Burgess were among those to pay tribute to Mani, whose death was announced by his brother and nephew
www.theguardian.com
November 20, 2025 at 5:24 PM
RIP Mani. Breaking Into Heaven www.theguardian.com/music/2025/n...
Agree. If we must load up the season with feasts, then front load it, and keep the run-up to the solstice clear
Y'all should just do like we do in Canada and move Thanksgiving to early October!
November 20, 2025 at 5:09 PM
Agree. If we must load up the season with feasts, then front load it, and keep the run-up to the solstice clear
My least popular opinion is that Thanksgiving ruins the rhythm of the season, is a nationalist tax on the winter solstice holiday, and should be quietly dropped
November 20, 2025 at 5:05 PM
My least popular opinion is that Thanksgiving ruins the rhythm of the season, is a nationalist tax on the winter solstice holiday, and should be quietly dropped
Reposted by Ian Holmes
For the first time in my career, I can’t tell people to trust what the CDC website says. And that is an incredibly sad and devastating place for this country to be.
CDC has overhauled its website to assert that “the claim ‘vaccines do not cause autism’ is not an evidence-based claim”
November 20, 2025 at 4:22 AM
For the first time in my career, I can’t tell people to trust what the CDC website says. And that is an incredibly sad and devastating place for this country to be.
Reposted by Ian Holmes
A deep learning framework for building INDEL mutation rate maps https://www.biorxiv.org/content/10.1101/2025.11.18.689146v1
November 19, 2025 at 3:34 PM
A deep learning framework for building INDEL mutation rate maps https://www.biorxiv.org/content/10.1101/2025.11.18.689146v1
Reposted by Ian Holmes
Excited to share a new preprint! Wireless devices use FM modulation to transmit multiplexed noise-resistant data. Led by @born2raisecell.bsky.social, we create a biochemical analogue of this paradigm using genetically encoded oscillators (GEOs) for single-cell FM streaming tinyurl.com/nbs8rw42 🧵
March 4, 2025 at 4:28 PM
Excited to share a new preprint! Wireless devices use FM modulation to transmit multiplexed noise-resistant data. Led by @born2raisecell.bsky.social, we create a biochemical analogue of this paradigm using genetically encoded oscillators (GEOs) for single-cell FM streaming tinyurl.com/nbs8rw42 🧵
1) this video
2) the word “suctorian”
2) the word “suctorian”
Cellular structure self-organizes through an interplay between internal mechanisms and external cues. The single-celled suctorian P. collini builds a trap structure to capture large prey using microtubule feeding tentacles, creating feedback between cell morphology and prey availability.
November 19, 2025 at 12:38 AM
1) this video
2) the word “suctorian”
2) the word “suctorian”
Reposted by Ian Holmes
Microscopic programmable ‘flowers’ made from DNA. Autonomous behavior at microscale.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reversible metamorphosis of hierarchical DNA–inorganic crystals - Nature Nanotechnology
Actuators based on DNA–inorganic hybrid crystals reversibly change shape, which can be programmed by the length and composition of the DNA polymer, and induce cascaded reactions of compartmentalized e...
www.nature.com
November 18, 2025 at 2:42 AM
Microscopic programmable ‘flowers’ made from DNA. Autonomous behavior at microscale.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
November 17, 2025 at 6:05 PM
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
Reposted by Ian Holmes
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
@gbretman.bsky.social Excellent: A period of abstinence from Microsoft Office
November 16, 2025 at 10:48 PM
@gbretman.bsky.social Excellent: A period of abstinence from Microsoft Office