Lior Pachter

YouTube video by Hunting Yellow Pigs Hunting Yellow Pigs

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...

Zbąszyń The mathematician Carl Friedrich Gauss invented the heliotrope for long-distance surveying in 1821. Just a year later, he proved that least squares regression provided the BLUE estimator for data w…

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

Brilliant work by Joseph Rich and Conrad Oakes working out the math and implementing wompwomp. It has been submitted to @bioconductor.bsky.social and in the future we may also implement it in Python to facilitate usage with single-cell genomics packages. Any feedback will be appreciated. Thx!

he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.

The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros

The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.

Optimizing alluvial plots Alluvial plots can be effective for visualization of multivariate data, but rely on ordering of alluvia that can be non-trivial to arrange. We formulate two optimization problems that formalize the ch...

The underlying optimization questions turned out to be really interesting. The methods underlying wompwomp are described in the accompanying preprint on @cscg-bot.bsky.social. arxiv.org/abs/2509.03761

Work on wompwomp was motivated by plots made for this paper, where we first implemented a naïve approach to optimizing an alluvial plot (Fig. 1 panel D)
bsky.app/profile/alii...

wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.

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.

Is there such a device?

It’s true that there is a lot of room for improvement of warnings and there are many false positives right now. Then again, even a single life saved is as if the world was saved.

Yes there is. At schools during the day teachers may be out of the classroom- even if brief it can happen, and kids may not be with teachers when they are, e.g. in bathrooms. At night kids at camps sleep without adults in their room.

For many natural or man-made disasters even seconds can matter.

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)

Reply to: Reply to: False positives in the study of memory-related gene expression In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

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...

The amoral nonsense of Orchid’s embryo selection If you haven’t heard about Clubhouse yet… well, it’s the latest Silicon Valley unicorn, and the popular new chat hole for thought leaders. I heard about it for the first time a fe…

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...

False positives in study of memory-related gene expression - Nature Nature - False positives in study of memory-related gene expression

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

Remembering George Leitmann, Nazi fighter, Nuremberg interrogator, Cal engineering professor He was a decorated WWII veteran who helped liberate a concentration camp, a rocket scientist, a leading authority in game theory and the University of California's first ombudsman, in the 1960s.

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...

Epistemic failure of epistemic failure Earlier this year I came across this interesting post by mathematician Daniel Litt, where he pondered how many intrinsically true results in mathematics have been published with erroneous proofs: D…

liorpachter.wordpress.com/2025/06/03/e...

A win for Arakelov theory.

Unfortunately, right now this is the rubbish super talented and exceptional students such as Delaney are dealing with: bsky.app/profile/dela...

In addition to his research, Delaney @delaneyksull.bsky.social is a great computational biology citizen, donating hours of his time every week to help thousands of biologists via Biostars: www.biostars.org/u/30020/

Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq Abstract. In single-cell and single-nucleus RNA sequencing (RNA-seq), the coexistence of nascent (unprocessed) and mature (processed) messenger RNA (mRNA)

See
academic.oup.com/nar/article/...
www.nature.com/articles/s41...
academic.oup.com/bioinformati...
... more to come...