I highly recommend reading @harveylederman.bsky.social's essay on the meaning of life, the universe, and everything as you ponder the end of 2025, and other things that may soon end as well... scottaaronson.blog?p=9030

That is what a Denial of Peer-Review Attack looks like (DOPRA: credit to @lpachter.bsky.social for the term) x.com/lpachter/sta...

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...

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...

When I was 17, I attended a seminar Watson gave about the RNA tie club and their 1954 summer in Woods Hole. During the seminar, the 76 year old shared headshots of young women he took on beach dates. He also showed lab group photos and took the time to point out the women he had harangued for dates.

In 1982, I was in the Jackson Laboratory Research Training Program. As part of the program, we got to attend the Short Course lectures. At the end of one lecture by a young researcher, this old guy very viciously and aggressively lit into him. Turned out that the nasty old guy was Jim Watson.

One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.

I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted. liorpachter.wordpress.com/2018/05/18/j...

No, James Watson was not a "complicated" person. He was a bad person, and also a bad scientist. These racist, sexist statements, his sincere beliefs, are both morally indefensible and scientifically absurd. With every year that passes, let his name fade and Rosalind Franklin's shine the brighter.

In case anyone is wondering if Watson was really THAT bad, @lpachter.bsky.social compiled a list of quotes that are absolutely not for the faint of heart. liorpachter.wordpress.com/2018/05/18/j...

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?