Lior Pachter
@lpachter.bsky.social
Bren Professor of Computational Biology @Caltech.edu. Blog at http://liorpachter.wordpress.com. Posts represent my views, not my employer's. #methodsmatter
Proof of the 40-year old Bandelt-Dress conjecture on the maximum quartet distance between phylogenetic trees (and an interesting connection to independence testing). arxiv.org/abs/2608.03542
The maximum quartet distance between phylogenetic trees
The quartet distance counts the four-leaf subsets on which two binary phylogenetic trees display different topologies. We prove that its maximum over trees on $n$ leaves is $(2/3+o(1))\binom{n}{4}$, r...
arxiv.org
One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to Joe Rich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/p... It's super easy to use! 1/🧵
GitHub - pachterlab/paperpush
Contribute to pachterlab/paperpush development by creating an account on GitHub.
github.com
Efficient sampling of reads (with replacement). www.biorxiv.org/content/10.6...
fastQpick: scalable bootstrap and subsampling of FASTQ reads
fastQpick is a command-line tool and Python library for sampling FASTQ reads with replacement. Sampling with replacement turns a single FASTQ file into an arbitrary number of bootstrap replicates, whi...
biorxiv.org
I wonder what @elife.bsky.social board and behrenstimb.bsky.social thinks about the 1% list and their coll/ with @qedscience.bsky.social now? They’re facilitating the innovation of a system that will be bought by #Elsevier & #Springer w/funds from a charity.
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...
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
reeserichardson.blog
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...
Additivity is all you need?
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.
dewitt-lab.github.io
Vito Volterra (of the Lotka-Volterra model) was born on this day (May 3rd) in 1860. Volterra was in the 1%. That is, he was one of only 12 out of ~1,200 Italian professors who refused to sign the compulsory oath of allegiance to Mussolini's Fascist government in 1931.
Behind every extrernally lauded ‘disruptor’, there seems to be a half dozen (minimum) actual subject matter experts shaking their heads “no” and grimacing dramatically. Good to keep in mind, for those of us prone to a bit of epistemic…moseying.
Lior Pachter@lpachter.bsky.social · 4mo agoOn Martin Nowak, the evolution of cooperation, Jeffrey Epstein, and the corruption of mathematicians. liorpachter.wordpress.com/2026/04/10/n...
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/🧵
Some people seem quite fond of finding third fundamental principles. They get fixated on their new third law of thermodynamics or of evolution. Perhaps there is a third law of misunderstanding.
On Martin Nowak, the evolution of cooperation, Jeffrey Epstein, and the corruption of mathematicians. liorpachter.wordpress.com/2026/04/10/n...
I don't understand rewrites.bio at all. Most bioinformatics software is distributed with a license. The license specifies exactly what is and is not permitted to do with the software. Yet now one is supposed to ignore the license and adhere to requirements specified by someone on a website??
rewrites.bio - A manifesto for bioinformatics
Principles for responsible AI-assisted rewriting of bioinformatics tools.
rewrites.bio
Phil Ewels@ewels.bsky.social · 4mo agorewrites.bio is all pretty common sense stuff: credit original authors, emulate output exactly, maintain what you ship, don't spam open-source maintainers with AI-generated bug reports. I wrote a second blog post covering this part of the story here: seqera.io/blog/rewrite...
Spectral requirements for cooperation https://www.biorxiv.org/content/10.64898/2026.04.07.716994v1
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
The fitness costs of reproductive specialization scale inversely with organismal size
pnas.org
Happy to see multiple optimizations to the edgePython codebase, with more on the way: github.com/pachterlab/e... I have already experimented with porting to Rust, and have it mostly done (with some extra speedup); useful to complete an end-to-end single-cell Rust ecosystem.
GitHub - pachterlab/edgePython: Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.
Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data. - pachterlab/edgePython
github.com
Interesting to see people who have spent their careers talking about how important open source is, now upset that someone has taken their MIT or BSD licensed code and ported or modified it with an LLM.
A new long-read preprint: run PIP-seq then PCR & put the library on ONT. Sadly, no data available so comparisons to other tech not possible (also scripts missing). Requires Fluent Biosciences kits (they tried to reverse engineer the PIP-seq whitelist which seems to breach the Fluent EULA).
bioRxiv Genomics@biorxiv-genomic.bsky.social · 5mo agoBenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing https://www.biorxiv.org/content/10.64898/2026.03.12.706999v1
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/
"In the end, I started wondering if all of BioConductor could be ported to Python - or perhaps Julia or Rust for pure language implementations that also cover the optimized parts written in C, C++, or Fortran."
New blog post on #ai and #bioinformatics code - and {edgePython} - a port of {edgeR} from #rstats to #python https://brianrepko.github.io/blog/posts/2026-02-26-edgepython-and-ai/
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
kallisto sped up RNA-seq quantification by 50x. Now another 50x speedup... quantify hundreds of millions of reads in a few seconds. This seems too good to be true. But it's true! Incredible accomplishment by @pmelsted.bsky.social.
Páll Melsted@pmelsted.bsky.social · 5mo agoExcited 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
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/
Nature Methods@natmethods.nature.com · 9mo agoMonod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social www.nature.com/articles/s41...
Introducing a Clytia planula cell atlas, and demonstrating broad-level relations with medusa cells via another updated atlas. By @annaferraioli.bsky.social with @juliarmateu.bsky.social and collaborators in a project led by @rcply.bsky.social @biodev-vlfr.bsky.social www.biorxiv.org/content/10.6...
years ago my student and I translated LD score regression form Python to R, it took months, and LDscore at the time was like 3/4 reasonably functions! Translating EdgeR to Python in a week is absolutely crazy…
Lior Pachter@lpachter.bsky.social · 6mo agoI 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...
got curious, codex translated the core features of LD score regression from python to R in under an hour... Obv not a whole package but enough to see you'd soon be able to flick things between Python and R as it suits you...
GitHub - MichelNivard/ldsc-r-codex-translation
Contribute to MichelNivard/ldsc-r-codex-translation development by creating an account on GitHub.
github.com
On April 24, 2026 a new rule kicks in whereby state and local governments will require WCAG 2.1 Level AA for web content. The PDF for the preprint describing this project is UA-2 which is a "gold standard" for PDF accessibility. I built it using luatex in combination with verapdf and LLM assistance.
Lior Pachter@lpachter.bsky.social · 6mo agoI 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...
