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
Interesting article on LLM text extraction and the connection of that problem to (computational biology) sequence alignment. www.biorxiv.org/content/10.6... by @sina.bio and Aaron Streets.
www.biorxiv.org
February 11, 2026 at 5:53 PM
Interesting article on LLM text extraction and the connection of that problem to (computational biology) sequence alignment. www.biorxiv.org/content/10.6... by @sina.bio and Aaron Streets.
AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare.
www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).
www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).
February 3, 2026 at 5:19 PM
AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare.
www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).
www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).
Reposted by Lior Pachter
Peer review is often opaque and confusing. @elife.bsky.social worked to change that.
In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social
In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social
February 3, 2026 at 5:08 PM
Peer review is often opaque and confusing. @elife.bsky.social worked to change that.
In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social
In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social
Reposted by Lior Pachter
Watson. Of course.
February 1, 2026 at 5:19 PM
Watson. Of course.
Reposted by Lior Pachter
Join us tomorrow at the #SystemsVirologyJournalClub. @lauraluebbert.com will present her work with @lpachter.bsky.social on detecting viruses at single-cell resolution and uncovering associated changes in host gene expression.
Paper: pubmed.ncbi.nlm.nih.gov/40263451/
Paper: pubmed.ncbi.nlm.nih.gov/40263451/
🚨 Systems Virology Journal Club – 8th Series! 🚨
#BillSchneider and I are delighted to announce another round of cutting-edge talks in #SystemsVirology! 🦠💡
Join us and an outstanding lineup of speakers, starting Oct 30.
Free registration: shiraweingartengabbay.com/systems-viro... 🔬✨
#BillSchneider and I are delighted to announce another round of cutting-edge talks in #SystemsVirology! 🦠💡
Join us and an outstanding lineup of speakers, starting Oct 30.
Free registration: shiraweingartengabbay.com/systems-viro... 🔬✨
January 28, 2026 at 3:23 PM
Join us tomorrow at the #SystemsVirologyJournalClub. @lauraluebbert.com will present her work with @lpachter.bsky.social on detecting viruses at single-cell resolution and uncovering associated changes in host gene expression.
Paper: pubmed.ncbi.nlm.nih.gov/40263451/
Paper: pubmed.ncbi.nlm.nih.gov/40263451/
Reposted by Lior Pachter
The January issue is live nature.com/nbt/volumes/44
/issues/1
On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3
/issues/1
On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3
January 16, 2026 at 7:48 PM
The January issue is live nature.com/nbt/volumes/44
/issues/1
On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3
/issues/1
On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3
Reposted by Lior Pachter
First I'm hearing of DOPRA, love it! "Denial of peer review attack" concept by @lpachter.bsky.social
every big data paper with a bold story that is impossible to comprehend, evaluate, and independently verify reminds me of DOPRA. i've come to increasingly appreciate small, unassuming papers with humble conclusions that you can track word for word, data point by data point, assumption by assumption.
January 15, 2026 at 5:47 PM
First I'm hearing of DOPRA, love it! "Denial of peer review attack" concept by @lpachter.bsky.social
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
scottaaronson.blog?p=9030
ChatGPT and the Meaning of Life: Guest Post by Harvey Lederman
Scott Aaronson’s Brief Foreword: Harvey Lederman is a distinguished analytic philosopher who moved from Princeton to UT Austin a few years ago. Since his arrival, he’s become one of my …
scottaaronson.blog
December 26, 2025 at 11:29 AM
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
scottaaronson.blog?p=9030
Reposted by Lior Pachter
That is what a Denial of Peer-Review Attack looks like (DOPRA: credit to @lpachter.bsky.social for the term) x.com/lpachter/sta...
December 17, 2025 at 4:20 PM
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...
Cat's recent work:
journals.aps.org/pre/abstract...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 4, 2025 at 10:17 PM
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...
Cat's recent work:
journals.aps.org/pre/abstract...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Lior Pachter
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...
Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances
Evolutionary changes to gene expression are understood to be a major driver of phenotypic divergence between species. Researchers have investigated the drivers of this divergence by fitting evolutiona...
www.biorxiv.org
November 26, 2025 at 5:25 PM
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...
Reposted by Lior Pachter
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.
November 8, 2025 at 5:18 PM
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.
Reposted by Lior Pachter
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.
November 8, 2025 at 11:57 PM
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.
November 9, 2025 at 9:41 PM
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...
Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson
James Watson, who described himself as “not a racist in a conventional way”, has died at the age of 97. Below is a review of an obituary for Dr. James Watson published by Cold Spring Ha…
liorpachter.wordpress.com
November 8, 2025 at 9:58 PM
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...
liorpachter.wordpress.com/2018/05/18/j...
James Watson in his own words
“Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…
liorpachter.wordpress.com
November 8, 2025 at 4:29 AM
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...
liorpachter.wordpress.com/2018/05/18/j...
Reposted by Lior Pachter
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...
liorpachter.wordpress.com/2018/05/18/j...
November 7, 2025 at 11:44 PM
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.
Reposted by Lior Pachter
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...
liorpachter.wordpress.com/2018/05/18/j...
November 7, 2025 at 10:18 PM
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...
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...
Hunting Yellow Pigs
YouTube video by Hunting Yellow Pigs
www.youtube.com
October 3, 2025 at 3:40 PM
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...
Reposted by Lior Pachter
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...
www.nature.com/articles/s41...
September 24, 2025 at 3:12 PM
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...
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...
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
September 22, 2025 at 10:14 PM
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...
liorpachter.wordpress.com/2025/09/22/z...
Reposted by Lior Pachter
Reference-based variant detection with varseek https://www.biorxiv.org/content/10.1101/2025.09.03.674039v1
September 5, 2025 at 4:49 PM
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...
September 5, 2025 at 12:20 PM
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.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
August 3, 2025 at 10:49 PM
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.
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.
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
July 21, 2025 at 10:58 PM
This is a good article and I completely agree with its argument for comprehensible research.