Loyal Goff

I used Claude Opus 4.5/4.6 (and a bit of Codex GPT-5.3) to port edgeR to Python. See edgePython github.com/pachterlab/e...
This allowed me to develop a single-cell DE method that extends NEBULA with edgeR Empirical Bayes. All in one week. Details in doi.org/10.64898/202...

Neuroscience has a species problem If neuroscience is serious about building general principles of brain function, cross-species dialogue must become a core organizing principle.

If neuroscience is serious about building general principles of brain function, cross-species dialogue must become a core organizing principle rather than an afterthought, writes @suthanalab.bsky.social.

#neuroskyence

www.thetransmitter.org/animal-model...

I feel this so much…you are not alone.

Peer review is often opaque and confusing. @elife.bsky.social worked to change that.

In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social

Common variation in meiosis genes shapes human recombination and aneuploidy - Nature Analysis of data from pre-implantation genetic testing sheds light on the genetic basis of meiotic-origin aneuploidy, the leading cause of human pregnancy loss, identifying common genetic variants ass...

Pregnancy loss is common in humans, and chromosomal abnormalities are the leading cause. Using genetic data from ~140,000 IVF embryos, we show that maternal variation in meiosis genes influences recombination and aneuploidy risk.

First authors: @saracarioscia.bsky.social & @aabiddanda.github.io

Less than two weeks left to apply for the Cephalopod Neuroscience Gordon Conference! An exciting lineup of speakers and posters, and financial aid is available upon request. 🐙🦑
www.grc.org/cephalopod-n...

A preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from
Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...

Excellent analysis and insights here Igor. Nice to see this result and continued efforts to refine/critique methods widely used in the field. Thanks for this perspective.

Yeah, I no longer have ESI status due to collaborative work, but because I didn't get an ESI MIRA first, I'm probably locked out of a MIRA forever, because only unicorns get NIGMS R01s these days. The "must have an NIGMS R01" requirement might have worked at the start, but definitely doesn't now.

On the nature of a NSF (or NIH) graduate training fellowship I had a thought about graduate school fellowships and added it to the prior past about the NSF GRFP limitations to first year graduate students. [ETA 09/29/2025: I forgot to mention something impor…

On the nature of a NSF (or NIH) graduate training fellowship drugmonkey.wordpress.com/2025/09/29/o...

Alfonso-Gonzalez, C., Shi, M., Gorey, S., Holec, S., Carrasco, J., Rauer, M., Tsagkris, S., Mateos, F., Hilgers, V. (2025). ELAV mediates circular RNA biogenesis in neurons. Genes Dev, genesdev.cshlp.org/content/earl...

A new brightly colored mural of Henrietta Lacks just outside of Johns Hopkins Hospital in Baltimore.

A few weeks ago, this beautiful and inspired mural was painted on the building behind my lab space at Johns Hopkins. I walk past it each day and honestly feel humbled by how it makes me feel. Feeling compelled to share it with others today.

If you are someone actively involved in cephalopod research whether you are a Masters student, PhD student, Postdoc, Professor, Emeritus, reach out to me via the Bsky chat so we can get you invited to the Cephalopod Research Network Discord server! It's essentially a year-round CIAC!

Congrats!

America's retreat from research risks exodus of world's 'brightest minds' Johns Hopkins neuroscientist Uli Mueller came to the U.S. from Germany decades ago because of the unrivaled opportunities for research and discovery. He worries that cuts to research funding will upen...

hub.jhu.edu/2025/05/21/u...

Congratulations Debby! Such a cool finding and a great story.

Science Magazine cover 28 Feb 2025; "An oval squid (Sepioteuthis lessoniana)"

With more mollusk genomes available, a new genome-based phylogeny is featured on the cover of Science. Paper from @sigwartae.bsky.social at www.science.org/doi/10.1126/... Cover photo by Magnus Lundgren.

Mosquito Cell Atlas: A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito The female mosquito's remarkable ability to hunt humans and transmit pathogens relies on her unique biology. Here, we present the Mosquito Cell Atlas (MCA), a comprehensive single-nucleus RNA sequenci...

A mosquito cell atlas www.biorxiv.org/content/10.1... ht @leslievosshall.bsky.social

RNA xkcd.com/3056

'Trans-differentiation of neutrophils from plasmablast' is an artefact caused by over-reliance on machine algorithms in single cell RNA sequencing analysis: Lesson learnt and steps ahead https://www.biorxiv.org/content/10.1101/2025.02.07.636761v1

Just saw this. NIH is capping indirects at 15%. This will crush so many institutions. grants.nih.gov/grants/guide...

70% of scientists say they experience the imposter syndrome. I still experience it too sometimes, and what helps is talking with a science buddy with whom it’s ok to say stupid things, which may actually turn out to be good ideas.

New method for identifying spatially variable genes in spatial transcriptomics.

We use spectral graph theory to extract 1D curves related to tissue morphology, creating a more relevant coordinate system. Improves sensitivity.

with @PhillipNicol et al.

www.biorxiv.org/content/10.1...

Decoding disease: Novel tool helps identify mutations in mitochondrial DNA Geneticists looking inside the nuclear genome for mutations that contribute to disease have long relied on a principal known as constraint modeling, which allows researchers to assess the degree of se...

Nice work from Nicole Lake and Monkol Lek (with a small contribution from our group):
medicalxpress.com/news/2024-11...

Thanks for compiling. Please count me in as well!

You already want to block me? :)