Sean Bresnahan
@seantbres.bsky.social
Postdoc at MD Anderson: Omics of reproduction, development, cancer, and conflict | PhD, Penn State: functional genomics in social insects
Opinions are my own.
https://seantbresnahan.com
https://bhattacharya-lab.com
Opinions are my own.
https://seantbresnahan.com
https://bhattacharya-lab.com
Pinned
Sean Bresnahan
@seantbres.bsky.social
· Jul 2
Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function
The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale g...
doi.org
🧬🚨PREPRINT🚨- The first placental isoform reference from long-read seq & supporting data! We demonstrate how tissue-specific assembly improves transcript quantification with short-read data from multi-ancestry birth studies & reveals placenta-mediated effects of gestational diabetes on birth weight🫄
This made me cry. What are we doing allowing these ghouls to continue running our country?
Hey Megyn Kelly,
14-year-old Eloise would like a word:
“If my voice makes you uncomfortable, good…
because the minute adults start defending predators by defending the age of a child, you’re not protecting the truth, you’re protecting the predator.”
Sound up! 🔥🔊
1/2
14-year-old Eloise would like a word:
“If my voice makes you uncomfortable, good…
because the minute adults start defending predators by defending the age of a child, you’re not protecting the truth, you’re protecting the predator.”
Sound up! 🔥🔊
1/2
November 15, 2025 at 7:19 PM
This made me cry. What are we doing allowing these ghouls to continue running our country?
Reposted by Sean Bresnahan
GOOD NEWS! A groundbreaking study in MORE THAN 1,000 people reveals that cancer patients who received a COVID-19 mRNA vaccine within 100 days of starting immunotherapy lived dramatically LONGER than those who didn’t. In some cases, their survival rate was DOUBLED.
November 14, 2025 at 5:00 PM
GOOD NEWS! A groundbreaking study in MORE THAN 1,000 people reveals that cancer patients who received a COVID-19 mRNA vaccine within 100 days of starting immunotherapy lived dramatically LONGER than those who didn’t. In some cases, their survival rate was DOUBLED.
Reposted by Sean Bresnahan
“Housing shortage – Jews to blame," letter sticker, German Reich, 1938
zwangsraeume.berlin/en/context
zwangsraeume.berlin/en/context
November 14, 2025 at 2:16 AM
“Housing shortage – Jews to blame," letter sticker, German Reich, 1938
zwangsraeume.berlin/en/context
zwangsraeume.berlin/en/context
Reposted by Sean Bresnahan
Nice! Whole-genome heritability estimates in the UK Biobank. Average WGS-h2 was 26%, with 21% common and 5% rare. Broadly aligns with recent sib-reg and RDR estimates.
First time on Bsky and first big announcement!
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
I am excited to announce that our new study explaining the missing heritability of many phenotypes using WGS data from ~347,000 UK Biobank participants has just been published in @Nature.
Our manuscript is here: www.nature.com/articles/s41....
Estimation and mapping of the missing heritability of human phenotypes - Nature
WGS data were used from 347,630 individuals with European ancestry in the UK Biobank to obtain high-precision estimates of coding and non-coding rare variant heritability for 34 co...
www.nature.com
November 13, 2025 at 11:41 PM
Nice! Whole-genome heritability estimates in the UK Biobank. Average WGS-h2 was 26%, with 21% common and 5% rare. Broadly aligns with recent sib-reg and RDR estimates.
Reposted by Sean Bresnahan
Absolutely top notch preprint which has it all - a large effect mutation causing iridescence polymorphism, active TE as the basis of the mutation, AND ecological context for the phenotype. Cant wait for more on this!!!!
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 13, 2025 at 3:20 AM
Absolutely top notch preprint which has it all - a large effect mutation causing iridescence polymorphism, active TE as the basis of the mutation, AND ecological context for the phenotype. Cant wait for more on this!!!!
The PIP of remembering my keys with and without adjusting for the ADHD covariate: a memoir
Robust poisson regression for lQTLs where l is for locking oneself out of the lab
November 13, 2025 at 12:57 AM
The PIP of remembering my keys with and without adjusting for the ADHD covariate: a memoir
Reposted by Sean Bresnahan
New paper from the lab: we’re using long-read sequencing to disentangle isoform complexity at allele-specific loci 🧬💡
Here, we combine the PacBio Iso-Seq workflow with the established WhatsHap phasing approach to assign long reads to the correct allele in polymorphic F1 mouse hybrids.
Here, we combine the PacBio Iso-Seq workflow with the established WhatsHap phasing approach to assign long reads to the correct allele in polymorphic F1 mouse hybrids.
November 11, 2025 at 7:00 PM
New paper from the lab: we’re using long-read sequencing to disentangle isoform complexity at allele-specific loci 🧬💡
Here, we combine the PacBio Iso-Seq workflow with the established WhatsHap phasing approach to assign long reads to the correct allele in polymorphic F1 mouse hybrids.
Here, we combine the PacBio Iso-Seq workflow with the established WhatsHap phasing approach to assign long reads to the correct allele in polymorphic F1 mouse hybrids.
Because it feels good
I wrote this insight for eLife. A friend said, "Why would you want to step on that rake?". Well, I guess that's just who I am. Enjoy. elifesciences.org/articles/109...
Transgenerational Epigenetic Inheritance: Twists and turns in the story of learned avoidance
Evidence that learned avoidance of a pathogenic bacterium can be transmitted to future generations in C. elegans is growing.
elifesciences.org
November 11, 2025 at 11:30 PM
Because it feels good
Reposted by Sean Bresnahan
ICYMI: New online! Convergent evolution of a conserved molecular network underlies parenting and sociality
Convergent evolution of a conserved molecular network underlies parenting and sociality
Nature Reviews Genetics, Published online: 04 November 2025; doi:10.1038/s41576-025-00903-5Kay et al. review evidence that parental care, and more complex social behaviour based on parental care, evolved in multiple species through the repeated co-option of members of a pleiotropic molecular network regulating the ancestral processes of feeding, growth and reproduction.
www.nature.com
November 11, 2025 at 3:31 PM
ICYMI: New online! Convergent evolution of a conserved molecular network underlies parenting and sociality
IMO reviewing grants and papers is only a nuisance if you’re doing science wrong. I have the same sentiment about “getting scooped.”
I feel like I'm going crazy. Is reviewing grants and papers time-consuming and painful, but a vitally important part of our job and the scientific enterprise? Or is it drudge work we're supposed to outsource to AI?
November 11, 2025 at 1:02 PM
IMO reviewing grants and papers is only a nuisance if you’re doing science wrong. I have the same sentiment about “getting scooped.”
I would rather starve than capitulate to fascists and fund a government that does this:
Rafael Veraza was trying to leave a Sam’s Club parking lot when a federal agent drove alongside a line of cars, spraying chemical irritants occupants of the vehicles through open windows — including his 1-year-old daughter, Ariana.
“My daughter didn’t have to go through this."
“My daughter didn’t have to go through this."
1-year-old, pepper sprayed by federal agent in Cicero: 'My daughter didn't have to go through this'
Video shows federal agents spraying chemical irritants from a moving vehicle at a line of cars waiting to leave a Cicero Sam's Club on Saturday morning. The action appears to violate a judge's restric...
chicago.suntimes.com
November 10, 2025 at 3:58 AM
I would rather starve than capitulate to fascists and fund a government that does this:
Autumn in Oklahoma 🍂
November 9, 2025 at 5:16 PM
Autumn in Oklahoma 🍂
Reposted by Sean Bresnahan
My prediction is that LLM peer review will slow down science. It will do this for precisely the same reasons that contemporary peer review does and some extra ones. Start by reading @hansonmark.bsky.social thread below, then read on. 🧵
Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
www.qedscience.com
November 6, 2025 at 9:30 PM
My prediction is that LLM peer review will slow down science. It will do this for precisely the same reasons that contemporary peer review does and some extra ones. Start by reading @hansonmark.bsky.social thread below, then read on. 🧵
Reposted by Sean Bresnahan
Great work. Also fundamental, we find reference annotation and read mapping strategy influence these results: www.biorxiv.org/content/10.1...
Quantification method affects replicability of eQTL analysis, colocalization, and TWAS
eQTL mapping and TWAS are widely used to contextualize GWAS, yet the impact of RNA-seq processing choices remains unexplored. We find that RNA-seq quantification method and transcriptomic reference su...
www.biorxiv.org
November 7, 2025 at 10:48 AM
Great work. Also fundamental, we find reference annotation and read mapping strategy influence these results: www.biorxiv.org/content/10.1...
Reposted by Sean Bresnahan
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
How do GWAS and rare variant burden tests rank gene signals?
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!
🧬🧪🧵
www.nature.com/articles/s41...
Reposted by Sean Bresnahan
word on the street says this year the (fewer) assistant prof posts are averaging 800 applicants...
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
November 6, 2025 at 9:24 PM
word on the street says this year the (fewer) assistant prof posts are averaging 800 applicants...
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
The joys of cleaning your garage: finding an Illumina P3 flow cell from your first sequencing run in grad school.
October 31, 2025 at 6:55 PM
The joys of cleaning your garage: finding an Illumina P3 flow cell from your first sequencing run in grad school.
Reposted by Sean Bresnahan
Suharto in Indonesia, Ben Ali in Tunisia, Morales in Bolivia, Mubarak in Egypt, Yanukovich in Ukraine, Akayev Kyrgyzstan.
I'm not saying it's not hard, but the idea that autocrats don't care about protests is just wrong.
I'm not saying it's not hard, but the idea that autocrats don't care about protests is just wrong.
October 18, 2025 at 8:24 PM
Suharto in Indonesia, Ben Ali in Tunisia, Morales in Bolivia, Mubarak in Egypt, Yanukovich in Ukraine, Akayev Kyrgyzstan.
I'm not saying it's not hard, but the idea that autocrats don't care about protests is just wrong.
I'm not saying it's not hard, but the idea that autocrats don't care about protests is just wrong.
Reposted by Sean Bresnahan
A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!
October 8, 2025 at 11:31 PM
A few programming notes for #ashg25 from trainees in my group @mdanderson.bsky.social + a thread of me being a proud PI. Please drop by these sessions and talk to @taylorhead.bsky.social, @seantbres.bsky.social , @ytchang11.bsky.social, and me in Boston @geneticssociety.bsky.social next week!
This is one of the coolest things I have ever seen
See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...
October 1, 2025 at 11:34 PM
This is one of the coolest things I have ever seen
Reposted by Sean Bresnahan
My quote of the day
The sole and basic source of our strength is the solidarity of workers, peasants and the intelligentsia, the solidarity of the nation, the solidarity of people who seek to live in dignity, truth, and in harmony with their conscience.
Lech Walesa
The sole and basic source of our strength is the solidarity of workers, peasants and the intelligentsia, the solidarity of the nation, the solidarity of people who seek to live in dignity, truth, and in harmony with their conscience.
Lech Walesa
September 16, 2025 at 10:55 AM
My quote of the day
The sole and basic source of our strength is the solidarity of workers, peasants and the intelligentsia, the solidarity of the nation, the solidarity of people who seek to live in dignity, truth, and in harmony with their conscience.
Lech Walesa
The sole and basic source of our strength is the solidarity of workers, peasants and the intelligentsia, the solidarity of the nation, the solidarity of people who seek to live in dignity, truth, and in harmony with their conscience.
Lech Walesa
In this preprint, led by @nolancole.bsky.social (PhD student in Biostats at UW) and William (Undergrad! in BioSciences at Rice) we demonstrate how annotation choice and quantification method have significant downstream impacts on colocalization and TWAS results www.biorxiv.org/content/10.1...
Quantification method affects replicability of eQTL analysis, colocalization, and TWAS
eQTL mapping and TWAS are widely used to contextualize GWAS, yet the impact of RNA-seq processing choices remains unexplored. We find that RNA-seq quantification method and transcriptomic reference su...
www.biorxiv.org
September 2, 2025 at 2:36 PM
In this preprint, led by @nolancole.bsky.social (PhD student in Biostats at UW) and William (Undergrad! in BioSciences at Rice) we demonstrate how annotation choice and quantification method have significant downstream impacts on colocalization and TWAS results www.biorxiv.org/content/10.1...
Received a manuscript review I suspect was written by LLM. Critiquing analyses that weren’t even in the manuscript, no constructive criticism, conflating current claims with previous lit, same-length comments with robotic cadence, excessive em-dashes… don’t volunteer if you don’t want to review?
August 26, 2025 at 12:49 PM
Received a manuscript review I suspect was written by LLM. Critiquing analyses that weren’t even in the manuscript, no constructive criticism, conflating current claims with previous lit, same-length comments with robotic cadence, excessive em-dashes… don’t volunteer if you don’t want to review?
Reposted by Sean Bresnahan
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
August 22, 2025 at 7:50 PM
Thrilled to share the second half of my PhD work here!
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...
We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/)
doi.org/10.1101/2025...