The @HCSSiM program has been an educational gem for decades, leading "to a world where people value the truth and the project of finding the truth". www.youtube.com/watch?v=lnL2...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life. www.nature.com/articles/s41...

I recently visited the town of Zbąszyń in Poland. I took some time there to reflect on the plight of refugees and to bear witness for the dead and the living. This led me to write something up about its history. liorpachter.wordpress.com/2025/09/22/z...

Reference-based variant detection with varseek https://www.biorxiv.org/content/10.1101/2025.09.03.674039v1

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

Glacial area reduced by 41.6% from 1896 to 1921. Between 2015 and 2021, the rate at which Mount Rainier glaciers were losing area was more than two times faster than the rate estimated for the period of 2009 to 2015. irma.nps.gov/DataStore/Do... I took this photo on July 26, 2025.

This is a good article and I completely agree with its argument for comprehensible research.

The confiscation of cell phones from children at schools & summer camps is largely the result of a national campaign by @jonathanhaidt.bsky.social But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..

Many such cases - be on guard against DoPRA (science is complex, but let's not fool ourselves that pre-pub peer review functions in these situations; need a year of post-pub to read these things)

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Fly connectome, Willow, TOI-715 b, Alphafold3, R21/Matrix‑M, geometric Langlands, O4 run, lenacapavir... just to name a tiny sliver of science last year.. and some people think "science was not vibrant in 2024". 👀

Call for nominations for the Trevisan prize: cs.unibocconi.eu/call-nominat...

I developed accurate polygenic risk scores at 23andMe using its huge database and can attest to their limitations, I see this craze stemming from a deep ignorance about this topic. @lpachter.bsky.social wrote an amazing piece on this back in 2021: liorpachter.wordpress.com/2021/04/12/t...

As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...

George Leitmann, Berkeley professor who authored an iconic textbook on optimal control in the 1960s passed away 2 weeks ago www.berkeleyside.org/2025/06/03/g...

A win for Arakelov theory.

Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social). His thesis is on software, tools, and methods development for single-cell transcriptomics.

Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...

Come with me as I try to build a modular open-source 24-well Plate Reader from scratch. I'll post updates regularly on this thread and then compile it to my open lab notebook later. Let's make some tools! 🛠️🧵 1/n

Great illustrative use cases of the Ledidi sequence design framework by @jmschreiber91.bsky.social. Also nicely highlights how sequence design + attribution methods can be very useful to explore diverse facets of sequence syntax simultaneously beyond the space of training/test/genomic sequences.

Kári Stefánsson, founder and CEO of deCODE Genetics, the Icelandic company wholly owned by Amgen but operated largely independently, has been fired. www.mbl.is/frettir/innl...

Very excited to finally see this out! 🦠🧬 Huge thanks to all of my amazing co-authors! @lpachter.bsky.social @delaneyksull.bsky.social Original paper thread: x.com/neuroluebber... Free access link to the paper: rdcu.be/eiIWC

Where does great science come from? Who produces it? To answer these questions it is helpful to listen to Ludwig van Beethoven's Ode to Joy, which premiered on May 7th, 1824. www.youtube.com/watch?v=AUGU...

New preprint out! This is probably my most important paper. To my deep chagrin, it has no math. XIST is a non-coding RNA exclusive to XX females. It silences one of the X chromosomes. So what is it doing in male heart Schwann cells?

Awesome new paper by @lucalivraghi.bsky.social et al. doi.org/10.1016/j.cu... in @currentbiology.bsky.social on the evo-devo of a butterfly color variation enjoy the show!

I made a complete and comprehensive starter pack for computational biology: Follow @lh3lh3.bsky.social.

Well one of the things I learned this week is that apparently 0/0 = 0.1.

The news yesterday was a horrible gut punch. Devastated to learn of Sayan Mukherjee's passing. Every conversation with him was a delight; he was brilliant and deep and kind. A huge loss. Heartbreaking. www.mis.mpg.de/news/loss-sa...

Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment https://www.biorxiv.org/content/10.1101/2025.02.24.640007v1

The National Cancer Institute Early Detection Research Network Scientific Workshop planned for March 4 - 6, 2025 has just been postponed "to ensure that all aspects of this event align with current priorities." edrn.nci.nih.gov/about-edrn/g...

The first LIGO detection was announced on this day 9 years ago.

Also missing some references -- looking at data at different scales is not new -- we published a similar idea ten years ago! Simply binning fragments by size gets you 95% there.

Statisticians don't have to answer for the crimes of scientists who don't bother learning the tools they think they are using.

of a single problem: doing an experiment and writing a formulaic paper that mixes and matches plausible methods in a way proven to be publishable, without an obvious goal. (At least in seq). If enough people do that, it becomes standard practices.

Great and important review! Differences between Seurat and Scanpy have always been sort of a black box to me... www.biorxiv.org/content/10.1...

Apropos of nothing: less than 10% of pilots are women (5% for airline). And yet it's male pilots (specifically older & w/ experience) who are more likely to be involved in a fatal accident. www.sciencedirect.com/science/arti... There's a pilot shortage. Shouldn't one try hard to recruit women?

Even a pawn can checkmate a king.

If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...

I found this small charred fragment from Gray’s Anatomy in our backyard. 😢

LOL

Oh, the good stuff.

UMAP by Ralph Lauren. For @lpachter.bsky.social . #singlecell #sequencing

TIL that Jimmy Carter was the only president to have taken graduate-level coursework in science / engineering.

I wrote a similar sentence more than three years ago and was skewered for it. Good to see others coming around to the same conclusion (albeit @rafalab.bsky.social fails to critique many of the issues, e.g. the use of UMAPs for RNA velocity etc.) x.com/lpachter/sta...

Interviewer: Can you explain this gap in your UMAP? No.

I hear you can't make 10 without first making 1. Thanks @lpachter.bsky.social for open-sourcing a great design.

Looks like Gerver's sofa is optimal. arxiv.org/pdf/2411.19826