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Sean Bresnahan

@seantbres.bsky.social

510 followers 410 following 110 posts

Postdoc at MD Anderson: molecular epi + statistical genomics of human development & cancer | PhD, Penn State: functional genomics in social insects. Opinions are my own. https://seantbresnahan.com https://bhattacharya-lab.com

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Sean Bresnahan @seantbres.bsky.social · Jul 2

🧬🚨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🫄

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

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Sean Bresnahan @seantbres.bsky.social · 8d

This is one of the coolest things I have ever seen

Kate Cavanaugh @katecavanaugh.bsky.social · 8d

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 🧵...

Reposted by Sean Bresnahan

Jeremy Berg @jeremymberg.bsky.social · 24d

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

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Sean Bresnahan @seantbres.bsky.social · Sep 2

Always important to remember our maps and methods are approximations that we aim to continually improve. These sources of uncertainty must be accounted for and highlighting the need for standardized practices to ensure reproducible genetic association studies.

Sean Bresnahan @seantbres.bsky.social · Sep 2

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

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Sean Bresnahan @seantbres.bsky.social · Aug 26

@cellpress.bsky.social please do better

Sean Bresnahan @seantbres.bsky.social · Aug 26

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?

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Reposted by Sean Bresnahan

Matthew Aguirre @aguirre404.bsky.social · Aug 22

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...

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Sean Bresnahan @seantbres.bsky.social · Aug 16

Missing a whale carcass

Sean Bresnahan @seantbres.bsky.social · Aug 14

Minor release v0.1.1: Reframes ODint and components as exploratory; defaults to bootstrap-based OD per Baldoni et al. Fixes v0.1.0 bug in extract_feature_vector() causing user-defined OD vectors to be missed.

Plot comparing the biological coefficient of variation between 4 single-cell sequencing libraries between the raw and OD-corrected counts.

Plots comparing the biological coefficient of variation between 4 single-cell sequencing libraries between the raw and OD-corrected counts.

Sean Bresnahan @seantbres.bsky.social · Aug 12

Hi friends - thanks for checking this out. The project is now available as an R package: github.com/sbresnahan/s...

GitHub - sbresnahan/scAmbi: Mapping Ambiguity Overdispersion Correction for scRNA-seq

Mapping Ambiguity Overdispersion Correction for scRNA-seq - sbresnahan/scAmbi

github.com

Sean Bresnahan @seantbres.bsky.social · Aug 12

Hi friends - thanks for checking this out. The project is now available as an R package. Many improvements & better documentation. Thanks again to Srivastava, Dongze He, @robp.bsky.social, @mikelove.bsky.social, and @plbaldoni.bsky.social for all the methods & glue! github.com/sbresnahan/s...

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Reposted by Sean Bresnahan

Fairlie Reese @fairlie.bsky.social · Jul 18

Happy to see the ENCODE4 long-read RNA tracks now up on UCSC! Thank you to Jeltje, Mark, and any others at UCSC for working to make this happen 🤩

👉 Read the preprint: www.biorxiv.org/content/10.1...

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Reposted by Sean Bresnahan

Michael Love @mikelove.bsky.social · Aug 9

I just helped here and there with the R "glue" to import the bootstraps into Bioc data structures. True credit to Avi Srivastava, Dongze He and @robp.bsky.social :)

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Sean Bresnahan @seantbres.bsky.social · Aug 9

For the placenta transcriptome assembly, see: www.biorxiv.org/content/10.1...

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

www.biorxiv.org

Sean Bresnahan @seantbres.bsky.social · Aug 9

Applied this pipeline to public placenta scRNA-seq & quantified against our (@arjunbhattac.bsky.social @jonhuang.bsky.social et al) long-read derived placenta transcriptome (in-review). R functions for per-cell overdispersion correction and BCV plotting included in the vignette.

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Sean Bresnahan @seantbres.bsky.social · Aug 9

In bulk RNA-seq, @plbaldoni.bsky.social et al showed that correcting overdispersion (OD) from read-to-transcript mapping ambiguity improves downstream analyses. Here I extend this to scRNA-seq using @mikelove.bsky.social et al Alevin’s bootstraps to correct per-cell OD github.com/sbresnahan/O...

GitHub - sbresnahan/Overdispersion-Correction-for-Alevin: Processing Salmon Alevin bootstrap replicates to account for technical uncertainty before integrating single-cell RNA-seq datasets in Seurat

Processing Salmon Alevin bootstrap replicates to account for technical uncertainty before integrating single-cell RNA-seq datasets in Seurat - sbresnahan/Overdispersion-Correction-for-Alevin

github.com

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Sean Bresnahan @seantbres.bsky.social · Aug 5

Greenbeard genes give me goosebumps - what even is a “individual”. Fascinating study

Tera Levin @teralevin.bsky.social · Aug 5

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium

Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

www.biorxiv.org

Sean Bresnahan @seantbres.bsky.social · Jul 30

I think most people need this spelled out. Most average flyover state voters I talk to still think this is about efficiency or “waste, fraud, & abuse”.

Sean Bresnahan @seantbres.bsky.social · Jul 29

This slaps.

Sean Bresnahan @seantbres.bsky.social · Jul 25

How about “grifter”

Sean Bresnahan @seantbres.bsky.social · Jul 2

These were bulk tissue samples, so cell heterogeneity definitely contributes. Next step is scRNA-seq + cross-referencing with trophoblast etc cultures to tease that apart.

Sean Bresnahan @seantbres.bsky.social · Jul 2

Dog-land sounds like the best place ever

Sean Bresnahan @seantbres.bsky.social · Jul 2

Thanks, Mike! Looking forward to future collabs with your group :)

Sean Bresnahan @seantbres.bsky.social · Jul 2

Thanks, Rob! And for helping with Qs about Oarfish, Salmon etc!

Sean Bresnahan @seantbres.bsky.social · Jul 2

For me, transitioning from bee 🐝 to human 👤 genomics has been challenging & rewarding. Collab-ing w/ scientists & clinicians worldwide is thrilling - the best parts of science. Excited to keep contributing to omics & epi, & supporting colleagues facing incredible challenges in the current landscape.

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