Tim Triche, Jr.🔰
@timtriche.bsky.social
Resident panhandler, http://trichelab.org/
Posts may contain trace quantities of blood🩸, chromatin 🧬, and stats 🧮
CV: https://scholar.google.com/citations?user=AOoIO74AAAAJ
Views expressed are my own (but for the right price they can be yours!)
Posts may contain trace quantities of blood🩸, chromatin 🧬, and stats 🧮
CV: https://scholar.google.com/citations?user=AOoIO74AAAAJ
Views expressed are my own (but for the right price they can be yours!)
Pinned
Tim Triche, Jr.🔰
@timtriche.bsky.social
· Jan 23
NIH funded research benefits your community even if it doesn’t (yet!) directly benefit you. Each $ invested in NIH yields significantly higher return on investment (average 254%) than the same $ invested in “defense”.
Call your reps: (202) 224-3121
www.unitedformedicalresearch.org/nih-in-your-...
Call your reps: (202) 224-3121
www.unitedformedicalresearch.org/nih-in-your-...
Reposted by Tim Triche, Jr.🔰
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression
Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases. Single cell-resolved measures of RNA levels and single-cell expre...
www.medrxiv.org
November 12, 2025 at 3:15 PM
Interesting, from @garvaninstitute.bsky.social.
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
"We identify putative common regulatory variants for 83% of all 21,404 genes tested and cumulative rare variant signals for 47% of genes...about half of the effects are observed only in one or a few cell types"
www.medrxiv.org/content/10.1...
Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested
October 22, 2025 at 3:55 PM
Guaranteed funding for five years and a 20% increase in a $39K base stipend if you haul in a fellowship. World class facilities and faculty in metabolism, structural biology, epigenetics, and beyond. Grand Rapids is half the cost of living of California or Boston. Apply by December 1st if interested
Reposted by Tim Triche, Jr.🔰
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:33 AM
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
Reposted by Tim Triche, Jr.🔰
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe https://www.biorxiv.org/content/10.1101/2025.09.29.678807v1
October 2, 2025 at 6:28 AM
🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2
Reposted by Tim Triche, Jr.🔰
We want to congratulate our President, Dr. Tony Letai, on his appointment as Director of the NCI. This announcement marks an historic moment for cancer research. Dr. Letai has been a tireless advocate and visionary leader for functional precision medicine 🧵
www.nih.gov/news-events/...
www.nih.gov/news-events/...
Secretary Kennedy Swears in Dr. Anthony Letai as Director of the National Cancer Institute
Dr. Letai will serve as NCI’s 18th director.
www.nih.gov
September 29, 2025 at 10:00 PM
We want to congratulate our President, Dr. Tony Letai, on his appointment as Director of the NCI. This announcement marks an historic moment for cancer research. Dr. Letai has been a tireless advocate and visionary leader for functional precision medicine 🧵
www.nih.gov/news-events/...
www.nih.gov/news-events/...
Good news for @alice.soragnilab.com, SFPM, and rare disease models. Bad news for mouse cancer enthusiasts (humans are unreliable models of mouse disease).
Exclusive: Anthony Letai, a cancer researcher and oncologist at the Dana-Farber Cancer Institute and Harvard University, has emerged as a leading candidate to be the next director of the National Cancer Institute. www.statnews.com/2025/09/24/n...
Anthony Letai of Dana-Farber is front-runner to lead National Cancer Institute
A popular and respected scientist is reported to be in line to lead the nation's most important cancer research office.
www.statnews.com
September 24, 2025 at 10:37 PM
Good news for @alice.soragnilab.com, SFPM, and rare disease models. Bad news for mouse cancer enthusiasts (humans are unreliable models of mouse disease).
Reposted by Tim Triche, Jr.🔰
Reposted by Tim Triche, Jr.🔰
Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
September 8, 2025 at 10:25 AM
Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Post a perfect album from the 90s that isn’t Nirvana, Pearl Jam, Soundgarden, or Alice In Chains
September 8, 2025 at 12:14 AM
Post a perfect album from the 90s that isn’t Nirvana, Pearl Jam, Soundgarden, or Alice In Chains
What gif pops up for your name?
August 15, 2025 at 1:07 AM
What gif pops up for your name?
Reposted by Tim Triche, Jr.🔰
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Tim Triche, Jr.🔰
So this happened... Useful if you want to make economic (and health) arguments about the importance of NIH.
July 25, 2025 at 12:09 PM
So this happened... Useful if you want to make economic (and health) arguments about the importance of NIH.
Reposted by Tim Triche, Jr.🔰
An intuitive visualization of the regulatory layers influencing the stoichiometry of a protein complex.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
May 20, 2025 at 11:24 AM
An intuitive visualization of the regulatory layers influencing the stoichiometry of a protein complex.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
Everyone can go home now, scholarly Bluesky has peaked
Maybe the real Ship of Theseus was the Ship of Theseus we made along the way
July 24, 2025 at 1:31 PM
Everyone can go home now, scholarly Bluesky has peaked
Reposted by Tim Triche, Jr.🔰
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
July 22, 2025 at 9:59 PM
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1...
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
Academic job search guide
While I'm at it, here are the types of success each institution wants:
SLAC: Be a rockstar at everything (teaching, research, leadership, community).
R1: Be an internationally-important scholar with a keyboard that prints grant money.
RPU: Do whatever you want, just improve the lives of students.
SLAC: Be a rockstar at everything (teaching, research, leadership, community).
R1: Be an internationally-important scholar with a keyboard that prints grant money.
RPU: Do whatever you want, just improve the lives of students.
July 21, 2025 at 9:18 PM
Academic job search guide
Me examining a new follower:
July 19, 2025 at 2:17 PM
Me examining a new follower:
“But why should I learn statistics? AI can handle it for me!” Not if you don’t know how to ask questions.
It’s the intuition about probability that we want people to walk away with: how to make decisions under uncertainty where information can be wrong.
Why does this matter? Here’s a thread.
It’s the intuition about probability that we want people to walk away with: how to make decisions under uncertainty where information can be wrong.
Why does this matter? Here’s a thread.
Kind of wonder if "American elites" have any understanding of probability.
Say you apply to 10 extremely selective schools with admissions rates of 5%. Chances of getting into none of them is 59.9%.
Do 8 selective and 2 selective state flagships (18% acceptance, Ann Arbor), chance of none is 44.6%
Say you apply to 10 extremely selective schools with admissions rates of 5%. Chances of getting into none of them is 59.9%.
Do 8 selective and 2 selective state flagships (18% acceptance, Ann Arbor), chance of none is 44.6%
July 13, 2025 at 2:20 PM
“But why should I learn statistics? AI can handle it for me!” Not if you don’t know how to ask questions.
It’s the intuition about probability that we want people to walk away with: how to make decisions under uncertainty where information can be wrong.
Why does this matter? Here’s a thread.
It’s the intuition about probability that we want people to walk away with: how to make decisions under uncertainty where information can be wrong.
Why does this matter? Here’s a thread.
Reposted by Tim Triche, Jr.🔰
I am paw-sitively thrilled to say that out latest work is out in Nature today!
#Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23
www.nature.com/articles/s41...
#Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23
www.nature.com/articles/s41...
Feline infectious peritonitis epizootic caused by a recombinant coronavirus - Nature
Nature - Feline infectious peritonitis epizootic caused by a recombinant coronavirus
www.nature.com
July 9, 2025 at 4:00 PM
I am paw-sitively thrilled to say that out latest work is out in Nature today!
#Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23
www.nature.com/articles/s41...
#Virology #Genomics #Coronavirus #AnimalHealth #InfectiousDisease #Sequencing #FIP #FCoV23
www.nature.com/articles/s41...
Reposted by Tim Triche, Jr.🔰
I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".
Learn more at: oxbow.readthedocs.io
Learn more at: oxbow.readthedocs.io
July 7, 2025 at 9:22 PM
I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".
Learn more at: oxbow.readthedocs.io
Learn more at: oxbow.readthedocs.io
Reposted by Tim Triche, Jr.🔰
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw
July 6, 2025 at 10:11 PM
Excited to share our latest by my postdoc Ben KS: we use statistical physics & Bayesian inference to model genome-wide perturbation outcomes. Remarkably, perturbation responses are encoded in gene "chatter" even before the perturbation–a fundamental insight with broad implications
shorturl.at/2LHbw
shorturl.at/2LHbw
Reposted by Tim Triche, Jr.🔰
I am incredibly honored to be named a 2025 Jane Coffin Childs Fellow! Grateful for my mentors, supporters, and the stability this award provides! Very excited to join this community of outstanding scientists.
We're thrilled to announce the 2025 class of Jane Coffin Childs Fellows!
See our latest blog post and "look book" to learn more about our newest Fellows and their exciting research!
www.jccfund.org/blog/the-jan...
www.jccfund.org/wp-content/u...
See our latest blog post and "look book" to learn more about our newest Fellows and their exciting research!
www.jccfund.org/blog/the-jan...
www.jccfund.org/wp-content/u...
www.jccfund.org
June 24, 2025 at 6:51 PM
I am incredibly honored to be named a 2025 Jane Coffin Childs Fellow! Grateful for my mentors, supporters, and the stability this award provides! Very excited to join this community of outstanding scientists.
Reposted by Tim Triche, Jr.🔰
Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....
June 17, 2025 at 2:02 PM
Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....
Reposted by Tim Triche, Jr.🔰
As grant money starts drying up, it's more important than ever not to waste it on paying publishers' open access "article processing fees" when we can host PDFs for free. Tom Morgan and I wrote a paper on this, forthcoming at Science and Public Policy. Accepted draft here: osf.io/preprints/os...
May 9, 2025 at 5:26 PM
As grant money starts drying up, it's more important than ever not to waste it on paying publishers' open access "article processing fees" when we can host PDFs for free. Tom Morgan and I wrote a paper on this, forthcoming at Science and Public Policy. Accepted draft here: osf.io/preprints/os...
Reposted by Tim Triche, Jr.🔰
June 17, 2025 at 4:21 PM