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Gennady Gorin

@goringennady.bsky.social
350 followers 107 following 442 posts

🦠🧬📊bioinformatics, statistics, and stochastic processes.

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Reposted by Gennady Gorin
Hanbin Lee @epigenci.bsky.social · 21/09/2026
This in JASA is quite funny. How should we evaluate statistical significance when the parties involved have stakes on the results? arxiv.org/pdf/2205.06812
arxiv.org
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Reposted by Gennady Gorin
Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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Gennady Gorin @goringennady.bsky.social · 02/06/2026
early cokernut advocacy
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Pierre-Paul Axisa @ppaxisa.bsky.social · 01/06/2026
Also #singlecell RNaseq for sure 🧪🧬💻
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Reposted by Gennady Gorin
Celeste Labedz @celestelabedz.bsky.social · 27/05/2026
I'm a former Community Notes super-user interviewed for this piece. Whether the notes are written by people or language-mimicking algorithms, the central flaw of Twitter's Community Notes is the same as it's always been: it's a "fact-checking" system that doesn't involve the checking of facts.
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 08/05/2026
Efficient Stochastic Trace Generation for Transcription www.biorxiv.org/content/10.64898/20…
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Piper @the-pied-piper.bsky.social · 20/05/2026
they should invent software updates that make the software better over time instead of worse
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William DeWitt @wsdewitt.github.io · 29/04/2026
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. Preprint (w/ Gian Marco Visani and Aayush Verma): www.biorxiv.org/content/10.6... Blog: dewitt-lab.github.io/posts/2026-0...
dewitt-lab.github.io
Additivity is all you need?
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.
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Nicholas Mancuso @nmancuso.bsky.social · 06/05/2026
Super excited to see this out! Fantastic collaboration with Luke O'Connor and trainees Amber Shen and Xinran Wang. Thread with details will come soon, but linear ARG provide a HIGHLY efficient representation of genotype data that can be treated as a linear operator www.biorxiv.org/content/10.6...
biorxiv.org
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A. Murat Eren (Meren) @merenbey.bsky.social · 16/04/2026
How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...
merenlab.org
Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study
The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
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Lior Pachter @lpachter.bsky.social · 13/04/2026
If you use dim. reduction, you may be interested in two recent preprints we've posted on contrastive PCA: The Rayleigh Quotient and Contrastive Principal Component Analysis I & II w/ Maria Carilli & Kayla Jackson. They cover a lot of ground from theory to practice. 1/🧵
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Jay Shendure @jshendure.bsky.social · 10/04/2026
Latest from Shendure & Qiu labs (@cxqiu.bsky.social) )! We combined a new 4M cell mouse whole embryo scATAC-seq atlas (E10-P0), millions of 'evolutionarily coherent' orthologs from 241 mammalian genomes (Zoonomia), and the CREsted CNN framework (@steinaerts.bsky.social).
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Michael "Shapes Dude" Betancourt @betanalpha.bsky.social · 05/04/2026
Friendly reminder that ordinal values admit an ordering, but no notion of distance. Without a notion of distance even the concept of linear models is ill-defined. Please do not use ordinary least squares to analyze ordinal data. For gratuitous discussion see betanalpha.github.io/assets/chapt....
betanalpha.github.io
Ordinal Modeling
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Michael "Shapes Dude" Betancourt @betanalpha.bsky.social · 03/04/2026
You know what's better than inflating the variation of your observational model to heuristically accommodate "outliers"? Actually modeling the contaminating data generating process.
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Stephen Turner @stephenturner.us · 21/03/2026
Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes academic.oup.com/nargab/artic... 🧬💻🧪 github.com/BFL-lab/eukan
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The Public Domain Review @publicdomainrev.bsky.social · 17/03/2026
”Early Modern Memes: The Reuse and Recycling of Woodcuts in 17th-Century English Popular Print“ by @katiesisneros, on the interplay of repetition, context + meaning in woodcuts and the parallels to meme culture of today: publicdomainreview.org/essay/e...
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hoffsbeefs.bsky.social @hoffsbeefs.bsky.social · 10/03/2026
RIP ishmael you would have loved this 🐋
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Lior Pachter @lpachter.bsky.social · 09/03/2026
Ambient RNA & barcode swapping is a serious issue in single-cell genomics. Tools such as CellBender, scAR, DecontX & SoupX. We have developed CellSweep which is faster (in some cases by a lot) and much more accurate. Extensively tested and benchmarked. www.biorxiv.org/content/10.6... 1/
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Reese Richardson @reeserichardson.bsky.social · 09/03/2026
New COSIG update! 3️⃣4️⃣
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
The empty drops you threw out in your single-cell RNA sequencing analysis might be hiding mysterious things 👀 check out our bioRxiv preprint! The empty drops do not contain cells. Yet we can still use them to learn interesting things about biology and technology. 1/
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 06/03/2026
RNA-seq analysis in seconds using GPUs www.biorxiv.org/content/10.64898/20…
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Gennady Gorin @goringennady.bsky.social · 05/03/2026
How many samples should you sequence? Collect too few, and the experiment is inconclusive. Collect too many, and the costs add up very quickly. Check out our bioRxiv preprint and calculator at poweranalysis-fb.streamlit.app! 1/
poweranalysis-fb.streamlit.app
DEPower
Working repo for DEPower, accessed by the Streamlit interface.
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Gennady Gorin @goringennady.bsky.social · 03/03/2026
After years of work, the centerpiece of my PhD is published in @natmethods.nature.com! Read it to learn about the biophysical insights we can get from single-cell data! But first, I would like to talk a bit about RNA velocity and normalization. 1/
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Gennady Gorin @goringennady.bsky.social · 02/03/2026
Hi everyone, I am looking for a new industry role in computational biology! Check out my portfolio of genomics, statistics, ML, and biophysics work at gennadygorin.github.io, and reach out if you have any suggestions or open roles!
gennadygorin.github.io
Gennady Gorin, Ph.D.
Senior Scientist applying stochastic models for therapeutic discovery
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Gennady Gorin @goringennady.bsky.social · 01/03/2026
p-value of 1e-122 at a lfc of 0.67, huh
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Reese Richardson @reeserichardson.bsky.social · 28/02/2026
when your dataset is definitely real
A black and white scatterplot with Patient ID on the x axis and blood glucose level on the y axis. The caption reads:

Figure 2. Average blood glucose level plotted against the patient identifier for the stroke dataset.
The plot shows a clear shift in the distribution of glucose at half the maximum ID variable.Two black and white scatter plots with BMI on the y axis and blood glucose level or HbA1c level on the x axis. The caption reads:

Figure 3. “A” Blood Glucose level plotted against BMI. “B” HbA1c level plotted against BMI for the diabetes data. There were just 18 discrete results for blood glucose and HbA1c which is not plausible in real health data.
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Tom Gauld @tomgauld.bsky.social · 26/02/2026
I drew a cover for 'Olenka' by Budi Darma, translated by Tiffany Tsao. It's out in July but you can preorder it now. www.penguinrandomhouse.com/books/760272/olenka-by-budi-darma-translated-with-an-introduction-and-notes-by-tiffany-tsao/
A book cover for 'Olenka' by Budi Darma, translated by Tiffany Tsao.

The image is a drawing by Tom Gauld.

A moonlit scene of an american suburban landscape. We can see seven very similar women (or the same woman seven times): one in a car, one reading a book on a bench, one looking out from a dark building etc.A closeup of the book cover of 'Olenka' by Budi Darma, translated by Tiffany Tsao.

The image is a drawing by Tom Gauld.

A moonlit scene of an american suburban landscape. We can see seven very similar women (or the same woman seven times): one in a car, one reading a book on a bench, one looking out from a dark building etc.
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Gennady Gorin @goringennady.bsky.social · 23/02/2026
This is comical on account of well-known estate IP restrictions and also Salesforce's decadelong struggle to make Einstein AI a thing (paying $20M for the privilege)
theguardian.com
Who owns Einstein? The battle for the world’s most famous face
The long read: Thanks to a savvy California lawyer, Albert Einstein has earned far more posthumously than he ever did in his lifetime. But is that what the great scientist would have wanted?
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Dr. Jean Fan @jef.works · 19/02/2026
We recently updated our paper demonstrating evidence of off-target probe binding affecting the 10x Genomics Xenium spatial transcriptomics platform with key clarifications, new quantifications, and approaches for evaluating custom gene panels: biorxiv.org/content/10.1... 🧵👇1/n
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bioRxivpreprint @biorxivpreprint.bsky.social · 09/02/2026
Widespread data leakage inflates performance estimates in cancer drug response prediction www.biorxiv.org/content/10.64898/20…
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bioRxivpreprint @biorxivpreprint.bsky.social · 02/02/2026
Science should be machine-readable www.biorxiv.org/content/10.64898/20…
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Gennady Gorin @goringennady.bsky.social · 29/01/2026
This sort of take — although generally common — is especially entertaining to read two weeks after FDA guidance on Bayesian methods in clinical trials
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Gennady Gorin @goringennady.bsky.social · 25/01/2026
Version 3 is out, read it at www.biorxiv.org/content/10.1...! New additions: • Human genomics • Pig transcriptomics • Bottom-up reanalysis of long-read human data
biorxiv.org
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Gennady Gorin @goringennady.bsky.social · 19/01/2026
Heavy on potatoes and ammonia
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Nature Biotechnology @natbiotech.nature.com · 16/01/2026
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
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Waggoner Lab @labwaggoner.bsky.social · 02/01/2026
Systematic cell-type resolved transcriptomes of 8 tissues in 8 lab and wild-derived mouse strains capture global and local expression variation www.cell.com/cell-genomic... @ucirvine.bsky.social
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Martin Pacesa @martinpacesa.bsky.social · 26/12/2025
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
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Gennady Gorin @goringennady.bsky.social · 27/12/2025
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Rob Noble @robjohnnoble.bsky.social · 21/12/2025
No contest. Just read the first two sentences of the abstract. www.nature.com/articles/s41...
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New Books at Project Gutenberg @new.gutenberg.org · 15/12/2025
New #ebook at Project Gutenberg: Pan's garden by Algernon Blackwood www.gutenberg.org/ebooks/77472
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 13/12/2025
The mechanics and physics of tofu: Understanding hydrated soft solids through feature networks www.biorxiv.org/content/10.64898/20…
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Gennady Gorin @goringennady.bsky.social · 05/12/2025
lol #qveenherby
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Lior Pachter @lpachter.bsky.social · 04/12/2025
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...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 29/11/2025
A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics www.biorxiv.org/content/10.1101/202…
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Stephen Turner @stephenturner.us · 27/11/2025
Wth @nature.com? www.nature.com/articles/s41...
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Joshua G. Schraiber @jgschraiber.bsky.social · 26/11/2025
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...
biorxiv.org
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...
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Gennady Gorin @goringennady.bsky.social · 25/11/2025
"Move fast with stable infrastructure" is when both your website and your messaging app are so unreliable as to be practically unusable
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The Public Domain Review @publicdomainrev.bsky.social · 22/11/2025
With its various and playful explorations of authenticity — "found documents", metafictional games with readers, etc. — The Private Memoirs and Confessions of a Justified Sinner (1824) by James Hogg, anticipates some of postmodernism's best trickery: buff.ly/2p3UZIt
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