early cokernut advocacy

Also #singlecell RNaseq for sure 🧪🧬💻

TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...

I'm a former Community Notes super-user interviewed for this piece. Whether the notes are written by people or language-mimicking algorithms, the central flaw of Twitter's Community Notes is the same as it's always been: it's a "fact-checking" system that doesn't involve the checking of facts.

Efficient Stochastic Trace Generation for Transcription https://www.biorxiv.org/content/10.64898/2026.05.05.722871v1

they should invent software updates that make the software better over time instead of worse

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...

Super excited to see this out! Fantastic collaboration with Luke O'Connor and trainees Amber Shen and Xinran Wang. Thread with details will come soon, but linear ARG provide a HIGHLY efficient representation of genotype data that can be treated as a linear operator www.biorxiv.org/content/10.6...

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

If you use dim. reduction, you may be interested in two recent preprints we've posted on contrastive PCA: The Rayleigh Quotient and Contrastive Principal Component Analysis I & II w/ Maria Carilli & Kayla Jackson. They cover a lot of ground from theory to practice. 1/🧵

Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).

Friendly reminder that ordinal values admit an ordering, but no notion of distance. Without a notion of distance even the concept of linear models is ill-defined. Please do not use ordinary least squares to analyze ordinal data. For gratuitous discussion see betanalpha.github.io/assets/chapt....

You know what's better than inflating the variation of your observational model to heuristically accommodate "outliers"? Actually modeling the contaminating data generating process.

Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes academic.oup.com/nargab/artic... 🧬💻🧪 github.com/BFL-lab/eukan

”Early Modern Memes: The Reuse and Recycling of Woodcuts in 17th-Century English Popular Print“ by @katiesisneros, on the interplay of repetition, context + meaning in woodcuts and the parallels to meme culture of today: publicdomainreview.org/essay/e...

RIP ishmael you would have loved this 🐋

Ambient RNA & barcode swapping is a serious issue in single-cell genomics. Tools such as CellBender, scAR, DecontX & SoupX. We have developed CellSweep which is faster (in some cases by a lot) and much more accurate. Extensively tested and benchmarked. www.biorxiv.org/content/10.6... 1/

New COSIG update! 3️⃣4️⃣

The empty drops you threw out in your single-cell RNA sequencing analysis might be hiding mysterious things 👀 check out our bioRxiv preprint! The empty drops do not contain cells. Yet we can still use them to learn interesting things about biology and technology. 1/

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result

RNA-seq analysis in seconds using GPUs https://www.biorxiv.org/content/10.64898/2026.03.04.709526v1

How many samples should you sequence? Collect too few, and the experiment is inconclusive. Collect too many, and the costs add up very quickly. Check out our bioRxiv preprint and calculator at poweranalysis-fb.streamlit.app! 1/

After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data! But first, I would like to talk a bit about RNA velocity and normalization. 1/

Hi everyone, I am looking for a new industry role in computational biology! Check out my portfolio of genomics, statistics, ML, and biophysics work at gennadygorin.github.io, and reach out if you have any suggestions or open roles!

p-value of 1e-122 at a lfc of 0.67, huh

when your dataset is definitely real

I drew a cover for 'Olenka' by Budi Darma, translated by Tiffany Tsao. It's out in July but you can preorder it now. www.penguinrandomhouse.com/books/760272/olenka-by-budi-darma-translated-with-an-introduction-and-notes-by-tiffany-tsao/

This is comical on account of well-known estate IP restrictions and also Salesforce's decadelong struggle to make Einstein AI a thing (paying $20M for the privilege)

We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1... 🧵👇1/n

Widespread data leakage inflates performance estimates in cancer drug response prediction https://www.biorxiv.org/content/10.64898/2026.02.05.704016v1

Science should be machine-readable https://www.biorxiv.org/content/10.64898/2026.01.30.702911v1

This sort of take — although generally common — is especially entertaining to read two weeks after FDA guidance on Bayesian methods in clinical trials

Version 3 is out, read it at www.biorxiv.org/content/10.1...! New additions: • Human genomics • Pig transcriptomics • Bottom-up reanalysis of long-read human data

Heavy on potatoes and ammonia

The January issue is live nature.com/nbt/volumes/44 /issues/1 On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3

Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation www.cell.com/cell-genomic... @ucirvine.bsky.social

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

No contest. Just read the first two sentences of the abstract. www.nature.com/articles/s41...

New #ebook at Project Gutenberg: Pan's garden by Algernon Blackwood https://www.gutenberg.org/ebooks/77472

The mechanics and physics of tofu: Understanding hydrated soft solids through feature networks https://www.biorxiv.org/content/10.64898/2025.12.10.693552v1

lol #qveenherby

My student Catherine Felce will be defending her thesis @caltech.edu next week. If you're in the area consider attending; it will be a treat! Cat's recent work: journals.aps.org/pre/abstract... www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics https://www.biorxiv.org/content/10.1101/2025.11.25.690568v1

Wth @nature.com? www.nature.com/articles/s41...

We've got a really cool preprint out in collaboration with @lpachter.bsky.social's awesome student Cat Felce. Using biophysical models and RNA-seq data, we explore the mechanisms of selective constraint on mRNA abundance, finding constraint on decay rate www.biorxiv.org/content/10.1...

"Move fast with stable infrastructure" is when both your website and your messaging app are so unreliable as to be practically unusable

With its various and playful explorations of authenticity — "found documents", metafictional games with readers, etc. — The Private Memoirs and Confessions of a Justified Sinner (1824) by James Hogg, anticipates some of postmodernism's best trickery: http://buff.ly/2p3UZIt

The challenges of single cell transcriptomics on difficult human tissue: the placenta #SingleCell 🧪🧬🖥️ https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1

Joint Biophysical Modeling of Paired Single-Cell RNA and Protein Measurements https://www.biorxiv.org/content/10.1101/2025.11.14.688548v1