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Lior Pachter Profile picture
@lpachter
Sep 5, 2020 • 6 tweets • 2 min read • Read on X
So yesterday I received reviews back for one of my papers. The paper received 6 (yes, 6!) reviews. This has never happened before in my career. I was surprised at the number of reviews, given the pandemic and how busy everyone is. Then saw this... 🤔
The reviews were thorough and helpful, and generally positive (some comments were very positive). I was therefore disappointed with the decision (reject). I guess we'll revise the paper and submit elsewhere.
But then the paper will have been reviewed >= 9 times (!) And that is quite something... because the paper has a total of 9 paragraphs... If you do the math, that's 1 reviewer per paragraph...

This is the paper:
Peer review is COMPLETELY broken. I've participated in large consortia projects where super complex papers are getting a handful of sentences of review from just a handful of reviewers. The publication process ends up being a negotiation with editors about a "package".
In those papers, whose publication is basically a foregone conclusion because $$ citations $$, the results are not even reproducible, methods poorly described (if at all), and authorship is a joke (please fill your name in an excel spreadsheet if you'd like to be an author).
But good to know our small opinion piece is getting 1 reviewer per paragraph.

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More from @lpachter

Lior Pachter Profile picture
Apr 14
It's been great to see the positive response of @satijalab & @fabian_theis to our preprint on Seurat & Scanpy, and their commitment to work to improve transparency of their tools. One immediate benefit will be better practice of PCA in genomics. 1/🧵biorxiv.org/content/10.110…
PCA became a mainstay in genomics after the papers of @soumya_boston, Josh Stuart & @Rbaltman () and @OrlyAlter () ca. 2000 demonstrated its power for studying gene expression. 2/worldscientific.com/doi/abs/10.114…
pnas.org/doi/10.1073/pn…
Back then, having linear algebra on one's side was essential. A rich lab at that time might have something like a Sun Blade workstation clocking ~500MhZ w/ 2Gb RAM. So having fast SVD algorithms made PCA practical, when other methods based on more sophisticated models weren't. 3/ Image
Read 19 tweets
Lior Pachter Profile picture
Apr 7
The difference in @10xGenomics' Cell Ranger's default between version 6 and 7 is discussed in this thread, but it's such a big deal that it's worth its own thread.

tl;dr: in v7 Cell Ranger changed how it produces the gene count matrix leading to a huge difference in results. 1/
The change was described in release notes on May 17, 2022, which via two clicks lead to a technical note with more detail: 2/ cdn.10xgenomics.com/image/upload/v…
Image
To understand this technical note it is helpful to be familiar with the three types of reads that are produced in single-cell RNA-seq: spliced (M as a proxy for mature mRNAs), unspliced (N as a proxy for nascent RNAs), and ambiguous between both (labeled A). 3/ Image
Read 15 tweets
Lior Pachter Profile picture
Apr 5
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵 biorxiv.org/content/10.110…
Image
We looked at a standard processing / analysis summarized in the figure below. The sources of variability we explored are in red. The plots and metrics we assessed are in blue. We examined the standard benchmark 10x PBMC datasets, but results can be obtained for other data. 2/ Image
Before getting into results it's important to note that Seurat has never been published, and many of the details of Scanpy are missing in its original paper. @Josephmrich read the code & traced every function and every parameter. E.g., this is how Clustering / UMAPs are made: 3/ Image
Read 25 tweets
Lior Pachter Profile picture
Feb 21
My blog passed 3 million views today from more than 1.8 million visitors. There have been a total of 119 posts in just over 10 years.
I'm one of those visitors. The blog is an idea repository and I go back sometimes for recall. Some highlights 1/🧵 liorpachter.wordpress.com
Image
Just today I revisited the PCA post to recall some of the properties of the transform. A student, Nick Markarian, taught me the Borel-Kolmogorov paradox today (topic for a future post) and the post was helpful in thinking about some things. 2/ liorpachter.wordpress.com/2014/05/26/wha…
I've been teaching a bit of phylogenetics this year and this post on the Golden-Thompson inequality just came up. 3/liorpachter.wordpress.com/2018/10/05/rat…
Read 24 tweets
Lior Pachter Profile picture
Dec 24, 2023
This year I had the privilege of enjoying in-person conferences again, and in April I met @dvir_a & Dan Gorbonos, from whom I learned a bunch of interesting science. Here we are having burgers at Hans im Glück in Bonn.
And now, a 🧵about genocide.. 1/
The topic came up at dinner. History presents a heavy burden for Jews in Bonn.. even 78 years after WWII. The "Hans in luck" restaurant we were dining at is just a few meters from where the local synagogue was burned down during "Kirstallnacht" in 1938. 2/ Image
Although decades have passed since the holocaust, in Bonn the events felt closer in time. We were attending the Bonn Conference on Mathematical Life Sciences, which held a moment of silence for Holocaust Remembrance Day while we were there. 3/
Read 51 tweets
Lior Pachter Profile picture
Dec 12, 2023
🌌The virial theorem relates time-averaged kinetic energy of objects to their potential energy.

🧬The Price equation relates change in a trait over time in subpopulations to their fitness.

In we observe that the virial theorem is the Price equation. 1/🧵arxiv.org/abs/2312.06114
The virial theorem is a 150-year old tool in (astro)physics. First described by Rudolf Clausius in 1870 in connection with studies of heat transfer, it gained prominence after it was used by Fred Zwicky in 1933 to posit the existence of dark matter. 2/
The virial theorem is elementary calculus. For objects w/ mass m_1,..,m_n at positions z_1,..,z_n, velocities v_1,..,v_n, & acted on by forces F_1,...F_n, the virial "theorem" is the identity shown below. S = \sum_i p_iz_i (p_i is momentum), U is potential energy; T, kinetic.3/ Image
Read 15 tweets

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