Wyoming Wormboy
@wyomingwormboy.bsky.social
Science, students, and service. Serious academic meets incurable class clown.
Reposted by Wyoming Wormboy
🎉 LEE LAB PAPER ANNOUNCEMENT for this month's issue of #GENETICS! We're celebrating from both coasts, bc after defending her MS in 2024, Deepshi's now a biotech researcher in the Bay Area.
tl;dr: nucleosome remodeling is necessary to repair germline DNA damage 🧬
academic.oup.com/genetics/art...
tl;dr: nucleosome remodeling is necessary to repair germline DNA damage 🧬
academic.oup.com/genetics/art...
February 9, 2026 at 6:26 PM
🎉 LEE LAB PAPER ANNOUNCEMENT for this month's issue of #GENETICS! We're celebrating from both coasts, bc after defending her MS in 2024, Deepshi's now a biotech researcher in the Bay Area.
tl;dr: nucleosome remodeling is necessary to repair germline DNA damage 🧬
academic.oup.com/genetics/art...
tl;dr: nucleosome remodeling is necessary to repair germline DNA damage 🧬
academic.oup.com/genetics/art...
Reposted by Wyoming Wormboy
I would like to think @wyomingwormboy.bsky.social for describing the Sledgehammer Approach (to research) in WormBook. It is invaluable advice that I share with every trainee.
February 8, 2026 at 3:47 AM
I would like to think @wyomingwormboy.bsky.social for describing the Sledgehammer Approach (to research) in WormBook. It is invaluable advice that I share with every trainee.
I was feeling somewhat guilty about saying No to many recent requests but then I re-read the “children’s book”, The Giving Tree. Felt better.
Apparently some people interpret the tree’s hyper accommodating behavior as a positive example! I’m pretty sure that was not the author’s intention!
Apparently some people interpret the tree’s hyper accommodating behavior as a positive example! I’m pretty sure that was not the author’s intention!
February 5, 2026 at 11:28 PM
I was feeling somewhat guilty about saying No to many recent requests but then I re-read the “children’s book”, The Giving Tree. Felt better.
Apparently some people interpret the tree’s hyper accommodating behavior as a positive example! I’m pretty sure that was not the author’s intention!
Apparently some people interpret the tree’s hyper accommodating behavior as a positive example! I’m pretty sure that was not the author’s intention!
Reposted by Wyoming Wormboy
Please stop saying the bill allows "no more multi-year funding" - or at least be clear the 'more' is in reference to disastrous FY25 levels.
The bill allows 39% MYF, same as in FY25, which contributed substantially to a 24% drop in new research.
The bill has some wins. MYF is not one of them.
The bill allows 39% MYF, same as in FY25, which contributed substantially to a 24% drop in new research.
The bill has some wins. MYF is not one of them.
Both chambers of Congress have now passed the FY26 minibus with NIH provisions. The President will sign.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
(1) $48.7 billion for NIH
(2) Full IDC recovery
(3) No more multi-year funding
(4) No NIH reorganization, maintaining the current IC structure.
February 3, 2026 at 9:38 PM
Please stop saying the bill allows "no more multi-year funding" - or at least be clear the 'more' is in reference to disastrous FY25 levels.
The bill allows 39% MYF, same as in FY25, which contributed substantially to a 24% drop in new research.
The bill has some wins. MYF is not one of them.
The bill allows 39% MYF, same as in FY25, which contributed substantially to a 24% drop in new research.
The bill has some wins. MYF is not one of them.
Reposted by Wyoming Wormboy
For the same reason that Indiana, which is virtually the same size as Massachusetts received nearly $349 million last year in farm subsidies, while Massachusetts got only about $9 million, 1/39th of Indiana’s boon.
February 3, 2026 at 10:03 PM
For the same reason that Indiana, which is virtually the same size as Massachusetts received nearly $349 million last year in farm subsidies, while Massachusetts got only about $9 million, 1/39th of Indiana’s boon.
Reposted by Wyoming Wormboy
Excited to see this out in the world. The CGC is launching a curated strains collection, the first being protein degradation systems and this is a pilot primer to pair with it authored by myself, Dave Reiner, Ann Rougvie, and Aric Daul. We review the state of the field and provide use guidance (1)
The Caenorhabditis Genetics Center Curated Special Collections: a guide to protein degradation systems
academic.oup.com/genetics/adv...
academic.oup.com/genetics/adv...
The Caenorhabditis Genetics Center Curated Special Collections: a guide to protein degradation systems
Abstract. The Caenorhabditis Genetics Center is launching a new website feature—“Curated Special Collections”—designed to help researchers navigate the eve
academic.oup.com
January 29, 2026 at 9:16 PM
Excited to see this out in the world. The CGC is launching a curated strains collection, the first being protein degradation systems and this is a pilot primer to pair with it authored by myself, Dave Reiner, Ann Rougvie, and Aric Daul. We review the state of the field and provide use guidance (1)
I have an answer. He’s just another self promoting D-bag who traded in legit credentials for cash.
January 25, 2026 at 12:58 AM
I have an answer. He’s just another self promoting D-bag who traded in legit credentials for cash.
One reason to have kids is that they sometimes do clever things. (Note the signs on the side of the trail)
January 25, 2026 at 12:51 AM
One reason to have kids is that they sometimes do clever things. (Note the signs on the side of the trail)
Reposted by Wyoming Wormboy
Absolutely essential
NIH needs statutory protections against partisan politicized decision-making - especially around grant terminations. This bill is a solid start to achieving those aims.
degette.house.gov/media-center...
degette.house.gov/media-center...
DeGette Introduces Bill to Protect NIH From Political Interference
WASHINGTON, D.C. – Today, Congresswoman Diana DeGette (CO-01), Ranking Member of the Energy and Commerce Subcommittee on Health, introduced the Follow the Science Act to shield the National Institutes...
degette.house.gov
January 24, 2026 at 1:31 AM
Absolutely essential
Reposted by Wyoming Wormboy
January 21, 2026 at 6:42 PM
Reposted by Wyoming Wormboy
Going through boxes of old tee shirts today…
January 17, 2026 at 11:16 PM
Going through boxes of old tee shirts today…
Cool paper from Ron Ellis and colleagues.
Haldane’s law works through X:Autosome incompatibility in Caenorhabditis briggsae/C. nigoni hybrids - Nature Communications
Haldane’s rule suggests that in hybrid crosses, the heterogametic sex is often rare or sterile. This study crosses Caenorhabditis nematodes, and determines that an underlying feature of Haldane’s rule...
www.nature.com
January 17, 2026 at 2:53 AM
Cool paper from Ron Ellis and colleagues.
Reposted by Wyoming Wormboy
Job alert! Assistant professor position in the Department of Molecular Genetics (University of Toronto). Amazing department and city. jobs.utoronto.ca/job/Toronto-... Please share.
Assistant Professor - Virology
Assistant Professor - Virology
jobs.utoronto.ca
January 15, 2026 at 8:04 PM
Job alert! Assistant professor position in the Department of Molecular Genetics (University of Toronto). Amazing department and city. jobs.utoronto.ca/job/Toronto-... Please share.
Somewhat humorously, when you google "SciENcv opinions", this is the top hit. I've also been told that it will be far less informative for reviewers because you can't easily figure out what the applicant has accomplished publication-wise.
January 16, 2026 at 3:13 PM
Somewhat humorously, when you google "SciENcv opinions", this is the top hit. I've also been told that it will be far less informative for reviewers because you can't easily figure out what the applicant has accomplished publication-wise.
When I was the DGS of an umbrella-type PhD program, I worked to put in a rule that PhD students needed a minimum of one 1st-author research paper to graduate. The main intent was to protect students from advisors that were slackers about publishing. No 1st-author pubs really hurts students. 1/3
January 9, 2026 at 1:44 AM
When I was the DGS of an umbrella-type PhD program, I worked to put in a rule that PhD students needed a minimum of one 1st-author research paper to graduate. The main intent was to protect students from advisors that were slackers about publishing. No 1st-author pubs really hurts students. 1/3
Reposted by Wyoming Wormboy
Qiuyuan Yin, Chonglin Yang et al. reveal a plasma membrane-to-lysosome signaling pathway mediated by the non-receptor tyrosine kinase FGR and the serine/threonine kinase AKT2, which regulates TFEB/TFE3 activation for #lysosome biogenesis in #endocytosis. rupress.org/jcb/article/...
#Organelles
#Organelles
January 7, 2026 at 4:15 PM
Qiuyuan Yin, Chonglin Yang et al. reveal a plasma membrane-to-lysosome signaling pathway mediated by the non-receptor tyrosine kinase FGR and the serine/threonine kinase AKT2, which regulates TFEB/TFE3 activation for #lysosome biogenesis in #endocytosis. rupress.org/jcb/article/...
#Organelles
#Organelles
Reposted by Wyoming Wormboy
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
How well does TWAS estimate a gene’s direction of effect on a trait? We think of this as an important stress-test for the accuracy of TWAS.
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
In a new pre-print, we find that TWAS gets the sign wrong around 20-30% of the time!
doi.org/10.64898/202...
1/n
High false sign rates in transcriptome-wide association studies
Transcriptome-wide association studies (TWAS) are widely used to identify genes involved in complex traits and to infer the direction of gene effects on traits. However, despite their popularity, it r...
doi.org
January 6, 2026 at 2:48 AM
New preprint alert: we use sign errors as a test of how well TWAS works.
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Very worryingly we find that TWAS gets the sign wrong around 1/3 of the time (compared to 50% for pure guessing). You can read more about our analysis here, and what we think is going on 👇
Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country!
www.youtube.com/watch?v=0T9P...
www.youtube.com/watch?v=0T9P...
Core Directors' Symposium - 2025 - David Fay
YouTube video by IDeA National Resource for Quantitative Proteomics
www.youtube.com
January 4, 2026 at 3:40 PM
Another YouTube Tutorial – This one on Proximity Labeling and connected to our recent EMBO J. paper (PMID: 41381733). This is a recording of a talk at the IDeA National Resource for Quantitative Proteomics in Little Rock AR. One of the top facilities in the country!
www.youtube.com/watch?v=0T9P...
www.youtube.com/watch?v=0T9P...
This was a cool race for a bunch reasons. It was not just a test of ski prowess but also social skills. To do well you had to reach out to racers from other countries and agree to work together. That two Americans were the ones to figure this out is a point of pride and gives me some needed hope.
Diggins, Schumacher Make History in Italy
History doesn’t always arrive in a single decisive moment. Sometimes it reveals itself through patience, teamwork and the ability to give it your all and wait for the result. That was the case on Wedn...
www.usskiandsnowboard.org
January 3, 2026 at 8:22 PM
This was a cool race for a bunch reasons. It was not just a test of ski prowess but also social skills. To do well you had to reach out to racers from other countries and agree to work together. That two Americans were the ones to figure this out is a point of pride and gives me some needed hope.
Reposted by Wyoming Wormboy
Nice description of ipTM problems & how actifPTM, LIS, & ipSAE fix those for scoring protein-protein interactions.
New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
January 3, 2026 at 12:10 AM
Nice description of ipTM problems & how actifPTM, LIS, & ipSAE fix those for scoring protein-protein interactions.
New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
New script on ipSAE github: af2rechain.py takes an input AF2 model of one protein & breaks it into chains given domain boundaries for input to ipSAE to calculate intraprotein ipSAE.
Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2
www.youtube.com/watch?v=u63o...
www.youtube.com/watch?v=u63o...
David's AlphaFold WorkShop 2026
YouTube video by David Fay
www.youtube.com
January 2, 2026 at 11:03 PM
Greetings! I decided to make a YouTube video of my AlphaFold workshop that I've given a few times in the past year. Caveats aside, people seem to find this useful for thinking about how to model protein interactions and how to interpret various AF outputs 1/2
www.youtube.com/watch?v=u63o...
www.youtube.com/watch?v=u63o...
Reposted by Wyoming Wormboy
Review @cp-cancercell.bsky.social @mdanderson.bsky.social
Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications
www.cell.com/cancer-cell/...
Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications
www.cell.com/cancer-cell/...
January 2, 2026 at 1:28 AM
Review @cp-cancercell.bsky.social @mdanderson.bsky.social
Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications
www.cell.com/cancer-cell/...
Spatial omics at the forefront: emerging technologies, analytical innovations, and clinical applications
www.cell.com/cancer-cell/...
Reposted by Wyoming Wormboy
Happy new year! Sharing a 🧬🚨REVISED PREPRINT🚨 with major updates to our placental long-read transcriptome paper! Thanks to thorough reviewer feedback, we've strengthened the manuscript with new analyses & clarifications. Key figures in this thread 🧵
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 31, 2025 at 7:04 PM
Happy new year! Sharing a 🧬🚨REVISED PREPRINT🚨 with major updates to our placental long-read transcriptome paper! Thanks to thorough reviewer feedback, we've strengthened the manuscript with new analyses & clarifications. Key figures in this thread 🧵
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
My Christmas present this year was a partially detached retina!
But here was my real present. Immediate access to health care, competent caring medical professionals, health insurance, and financial security to make up the difference.
How many Americans lack this and why is that acceptable???
But here was my real present. Immediate access to health care, competent caring medical professionals, health insurance, and financial security to make up the difference.
How many Americans lack this and why is that acceptable???
December 25, 2025 at 4:50 PM
My Christmas present this year was a partially detached retina!
But here was my real present. Immediate access to health care, competent caring medical professionals, health insurance, and financial security to make up the difference.
How many Americans lack this and why is that acceptable???
But here was my real present. Immediate access to health care, competent caring medical professionals, health insurance, and financial security to make up the difference.
How many Americans lack this and why is that acceptable???