This is one of the coolest things I have ever seen

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

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?

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...

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...

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...

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 :)

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...

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

🧬🚨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🫄

Much more important things going on in the world, but wanted to share this new work on parent-of-origin effects & “non-canonical” genomic imprinting in developmental plasticity of honey bees, out now in Genome Biology 🧪🧬🔄 link.springer.com/article/10.1...

If randomly kidnapping people (including first grade kids) from places of work, education, worship, and immigration appointments and disappearing them without due process to foreign prisons does not meet your definition of fascism, then your definition of fascism is wrong.

With Rob's team, we are working to help users track data provenance during long read RNA-seq workflows, for both annotated (e.g. GENCODE) and novel transcripts (assembled during sequencing). Part of this involves formally designating the two sets, so they can be properly handled downstream.

THREAD 🧵 Internal State Department records show that months of warnings have become a reality: The Trump administration’s sudden withdrawal of foreign humanitarian aid has brought about death, violence and unrest. 1/

In NY for Biology of Genomes @cshlnews.bsky.social this week. During a layover on the way here, I tried to write a bit to communicate some of the work our group is doing, and why federal research funding for basic science matters substack.com/home/post/p-...

Love is All. Yesterday, one year of marriage with my dearest friend @veronicarichards.bsky.social 🖤

Now hiring! The Health Promotion Research Center is hiring 6 faculty (Assistant Prof start @ $125,000). Details attached. Please repost! Submit application here: apply.interfolio.com/159819 @policysrnt.bsky.social @cpddorg.bsky.social @theaacr.bsky.social @sbm.org @abctnow.bsky.social

The Genetics research community has a problem. Most recent articles do not consider #splicing/isoforms. Here, we analyze how important this opportunity gap is - and spoiler warning - we find it is essential for both analysis of common and rare variants More info👇 www.medrxiv.org/content/10.1...

“To meet this moment, to survive as a field, and to serve our patients and society, the only way forward is to stand together and speak out continuously and forcefully. We must speak for those who cannot: muzzled colleagues…, vulnerable patient populations, and future generations.”

I am begging, pleading in fact, for my fellow academics to find some courage and start speaking up. Because you can't just keep your head down and ride out this storm. And even if you could, is that really what you want being a scholar and educator to be?

Le Monde reporting that a French scientist traveling to Houston to attend a conference was denied entry to US after a search of his phone & computer revealed messages critical of Trump's science cuts, "which [says CPB] conveyed hatred of Trump & could be qualified as terrorism". Computer confiscated

everything is so shitty, read this story about a genuinely good man who saw he had an opportunity to save millions of lives and threw himself into doing so. the world is full of heroes like him.

Human genetics folks - we need to pay attention to this and have salient points ready to go. IQ is a poorly defined trait, is not predictive of either the rate of cognitive growth or the rate of decline in old age, etc. A good time to read gusevlab.org/projects/hsq/ by @sashagusevposts.bsky.social

If your state isn’t represented among the plaintiffs, call your state’s AG office *right now*. Here’s an example script, filled in with info for OK: Hi there, my name is ___, I live at ___. I work as a ___ at ___. 🧵

Get in Dorks, we are going protesting. STAND UP FOR SCIENCE. MARCH 7th 12-4pm. DC AND YOUR STATE CAPITALS. More information to come.

We really lost something allowing science to be cleaved off from the liberal arts into the economically instrumentalized "STEM" bin in public discourse. Science is one of the purest expressions of humanism.

What's happening is precisely outlined in Project 2025. Read it to understand what's coming next. None of this is a surprise. Also, I know this is extremely unnerving if u weren't expecting this. But let's not panic. Let's organize & give this the best fking fight of our lives.

Earnest post, but: a thing I like here is it’s okay to have moments of happiness in public without being broadly scolded, and I believe that sustaining this kind of humanity will be very important as we resist fascism. We have to sustain each other. Making joy isn’t denial, it’s how we will survive

Couldn’t focus this afternoon *for some reason* so we burnt off some energy getting the biggest possible stick. A common persimmon - Diospyros virginiana - we unfortunately had to remove to prevent Lola from an obstructed bowel (would not stop eating the fruit, which are ~1% flesh and ~99% seeds!)

🎄spending the day with @veronicarichards.bsky.social, making espresso martinis for my family and slipping Lola strips of ham

TE-exonization is really in the spotlight today! Right after reading through @yarribas.bsky.social et al exciting paper on human proteome expansion by TEs bsky.app/profile/yarr..., this marvelous meticulously dissected example from @edchuong.bsky.social

Pathetic! (I love them)

As I start writing up my first paper in the world of human genomics, I thought I’d share my last preprint on parent-of-origin intragenomic conflict in reproductive caste determination in honey bees 🧪🧬🖥️🔄🐝 www.biorxiv.org/content/10.1... #Genomics #Epigenomics #Entomology #Evolution

It’s been a year since I last opened bsky and MAN it’s great to see how it evolved! Deleting X for good, so reintroducing myself here. I’m a postdoc with @arjunbhattac.bsky.social at MDACC, using functional + statistical genomics tools for studying cancer & development. 🧪🧬🖥️🔄

Career milestone reddit.com/r/science/s/... 🧬 #evosky

Hey 🟦 place! I'm a 5th-year PhD candidate at Penn State, my projects examine the transcriptional and gene regulatory basis of phenotypic variation (in 🐝 bees), focusing on intragenomic conflicts. I'm ISO academic & industry positions in bioinformatics. See seantbresnahan.com for more info. #HiSciSky