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Lior Pachter @lpachter.bsky.social · 5d

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...

Hunting Yellow Pigs

YouTube video by Hunting Yellow Pigs

www.youtube.com

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Reposted by Lior Pachter

Arnau Sebé-Pedrós @arnausebe.bsky.social · 14d

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...

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Lior Pachter @lpachter.bsky.social · 15d

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...

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…

liorpachter.wordpress.com

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Reposted by Lior Pachter

bioRxivpreprint @biorxivpreprint.bsky.social · Sep 5

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

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Lior Pachter @lpachter.bsky.social · Sep 5

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!

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Lior Pachter @lpachter.bsky.social · Sep 5

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.

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Lior Pachter @lpachter.bsky.social · Sep 5

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

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Lior Pachter @lpachter.bsky.social · Sep 5

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.

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Lior Pachter @lpachter.bsky.social · Sep 5

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

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...

arxiv.org

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Lior Pachter @lpachter.bsky.social · Sep 5

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...

Dr. Ali Barry @aliibarry.bsky.social · Apr 5

Required reading by @lpachter.bsky.social. Seurat vs Scanpy processing, and how package versions affect your analysis 👀 www.biorxiv.org/content/10.1...

The impact of package selection and versioning on single-cell RNA-seq analysis

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

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Lior Pachter @lpachter.bsky.social · Sep 5

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.

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Lior Pachter @lpachter.bsky.social · Sep 5

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...

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Lior Pachter @lpachter.bsky.social · Aug 3

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.

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Lior Pachter @lpachter.bsky.social · Jul 21

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

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jul 9

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

Which Kind of Science Reform

What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

elevanth.org

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Lior Pachter @lpachter.bsky.social · Jul 6

Is there such a device?

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Lior Pachter @lpachter.bsky.social · Jul 6

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.

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Lior Pachter @lpachter.bsky.social · Jul 6

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.

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Lior Pachter @lpachter.bsky.social · Jul 6

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, ..

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Reposted by Lior Pachter

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jun 23

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)

Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · Jun 23

ah here's where I saw it! x.com/lpachter/sta...

Tweet by Lior Pachter from 26 July 2024: "I think this paper is a Denial Of Peer Review Attack (DOPRA). It's kind of like a DoS (denial of service) attack. There is so much data, so many methods, so much code, so many figures, so many panels, so much supplement, so much text, that it is overwhelming. 18/"

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Lior Pachter @lpachter.bsky.social · Jun 16

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

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…

liorpachter.wordpress.com

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Lior Pachter @lpachter.bsky.social · Jun 12

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". 👀

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Lior Pachter @lpachter.bsky.social · Jun 7

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

Call for Nominations: Trevisan Prize 2025

cs.unibocconi.eu

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Reposted by Lior Pachter

Babak Alipanahi @babak-a.bsky.social · Jun 4

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...

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…

liorpachter.wordpress.com

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Lior Pachter @lpachter.bsky.social · Jun 4

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

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

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

www.nature.com

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Lior Pachter @lpachter.bsky.social · Jun 3

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...

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.

www.berkeleyside.org

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