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Gennady Gorin

@goringennady.bsky.social
350 followers 108 following 447 posts

🦠🧬📊bioinformatics, statistics, and stochastic processes.

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Gennady Gorin @goringennady.bsky.social · 11/10/2026
bsky.app/profile/gori... A great deal has changed since 1959.
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Gennady Gorin @goringennady.bsky.social · 11/10/2026
pretty much. Older drugs got in without much MOA, but the current generation of obesity drugs, for instance, has a truly staggering amount of mechanistic work. My impression is there is more leeway for vague-MOA analgesics and antidepressants just because the state of those fields is more dire.
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Gennady Gorin @goringennady.bsky.social · 10/10/2026
There are many drugs with unknown mechanisms of action. But I am not so sure today's pharma culture has much appetite for that.
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Gennady Gorin @goringennady.bsky.social · 09/10/2026
My wife @rileyisyelling.bsky.social wrote another book! Join us for the release party!
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Hanbin Lee @epigenci.bsky.social · 06/10/2026
We studied the evolution of genome-wide linkage disequilibrium and its influence on genetic architecture with genetic drift. We found that the Bulmer effect is population size and demography dependent. For nerds: genetic architecture follows from solving PDEs.
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Gennady Gorin @goringennady.bsky.social · 04/10/2026
finally, Audrey III
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Riley E. Smith @rileyisyelling.bsky.social · 04/10/2026
The Last Meeting of the Henchmen's Union, Citadel Branch. Are you Team Henchmen or Team Cardinal? Watch to find out: youtu.be/R5JtUoSgu7k #bookrelease
youtu.be
The Last Meeting of the Henchmen's Union, Citadel Branch
YouTube video by Riley E. Smith - Writer // Comedian
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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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Gennady Gorin @goringennady.bsky.social · 15/09/2026
could be. the risk profile of one or another model seems like a wide open hypothetical. the risk profile of centralization, however, sure seems worse
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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 · 28/07/2026
Check out one of mine, which will be direly counterproductive to learning how cryptics work!
puzzleme.amuselabs.com
Play this Crossword - A Comedy of Errors
A Comedy of Errors
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Gennady Gorin @goringennady.bsky.social · 20/06/2026
coincidentally, also the name of 2027's most popular Lin-Manuel Miranda musical
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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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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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Gennady Gorin @goringennady.bsky.social · 03/05/2026
Vivek Murthy just finished off his second term
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Gennady Gorin @goringennady.bsky.social · 30/04/2026
AI: the premier solution for automating making up vacuous numbers
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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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Gennady Gorin @goringennady.bsky.social · 13/04/2026
I am holding out for measure theory in Vol. VII
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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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Gennady Gorin @goringennady.bsky.social · 05/04/2026
Oh, fantastic. You might also be interested in www.nature.com/articles/s41..., where we go into a great deal of detail on the multimodal and technical modeling.
nature.com
Monod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data - Nature Methods
Monod fits biophysically motivated models to single-cell transcriptomics data, empowering multifaceted and integrative insights of gene expression dynamics, stochasticity and regulation.
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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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Gennady Gorin @goringennady.bsky.social · 17/03/2026
As for ethics, that's for the ethicists. Which is to say there's a lot of ground aside from ethics and bare usefulness. In the petroleum industry just as much as the tech industry. I should hope that ground would also come into it.
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Gennady Gorin @goringennady.bsky.social · 17/03/2026
Sure. Plenty of people post to massive audiences about bioplastics imminently taking over, or about photovoltaics being a dead end. Both are misinformation-adjacent, and maybe these people would be better off starting from the stronger point that the oil industry has been very useful.
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Gennady Gorin @goringennady.bsky.social · 16/03/2026
Sure. So what? Or to put it another way: I am a chemical engineer from Texas. I can go on about how useful the oil industry is and has been for 150 years or so. And I would be correct. But so what? Is that a convincing middle ground to stop at? Maybe it is. But I am not sure everyone would agree.
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Gennady Gorin @goringennady.bsky.social · 16/03/2026
I do not believe there is. Because beginning and ending the discussion there (so treating every other aspect as beneath consideration or immaterial) is itself extreme.
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Gennady Gorin @goringennady.bsky.social · 14/03/2026
"clever" satire in the genre of formatmypaper.com gets tedious if there is no trace of human execution beyond half an idea behind it. It's because layers of contempt for the idea and the reader are the opposite of compelling
formatmypaper.com
FormatMyPaper - The End of Manuscript Formatting
Paste your paper, choose your journal, and let our AI handle the tedious rest. Get back to the science.
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Gennady Gorin @goringennady.bsky.social · 12/03/2026
Every paper invents its own idiosyncratic and unique analysis. In seeming contradiction, they also crib or inherit analyses, whether sensible or not, from previous papers. Perhaps someday these best practices will coalesce to be summarized in such a paper (they would have to be created first)
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Gennady Gorin @goringennady.bsky.social · 11/03/2026
The Devil and Daniel Webster AI
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Gennady Gorin @goringennady.bsky.social · 11/03/2026
Einstein AI C&D charging bsky.app/profile/gori...
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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
I am currently looking for work, so do not hesitate to reach out if this experience sounds interesting! You can find the rest of my portfolio at gennadygorin.github.io. 13/13
gennadygorin.github.io
Gennady Gorin, Ph.D.
Senior Scientist applying stochastic models for therapeutic discovery
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
This is a complex and exciting topic, and we have a lot to learn about modeling, artifact detection, and the sheer range of unexpected biology we can learn from existing experiments! Big thanks to @lindabgoodman.bsky.social, and to the Gracheva/Bagriantsev labs that published the data! 12/
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
But this is a squirrel hypothalamus dataset, and here we also see the RNA coding for hypothalamic neuropeptides, distributed as in the real cells: Pomc, Sst, Npy, Agrp, and Cartpt! Perhaps a trace of RNA secretion or trafficking to the dendrites? 11/
pubmed.ncbi.nlm.nih.gov
RNA trafficking and local protein synthesis in dendrites: an overview - PubMed
It is now widely accepted that mRNAs localize to dendrites and that translation of these mRNAs is regulated in response to neuronal activity. Recent studies have begun to reveal the underpinnings of these processes and to underscore the importance of local protein synthesis to synaptic remodeling an …
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
Yet even if we do our filtering, some genes still come up non-Poisson, and many of them end up mutually correlated! We have seen this before with hemoglobins and mitochondrial genes, because their packaging is incorporated into empty drops and the RNA are captured together. 10/
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
Adjust your read filtering accordingly: some TSO content is fine, but feature barcoding primers are bad news. Not all the artifacts are so easy to spot, and I go into a great deal of detail about different classes of issues. These are only a starting point. 9/
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
Feature barcoding primers! Somehow 👀 the primers are missing their UMIs and antibody capture sequences. The result: vast numbers of reads with TSO/primer/FB cell barcode/poly(A). If the barcode/poly(A) is close enough to a real transcript, it gets counted, giving outliers. 8/
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
Some of them are TSO artifacts that happen to be similar to poly(A) regions in the transcriptome. Some are real reads that happened to get filtered out in the second pipeline. But it turns out that the vast majority come from... 7/
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Gennady Gorin @goringennady.bsky.social · 09/03/2026
It turns out that some of them are pipeline artifacts! If we rerun the same dataset with a different aligner, many of these outliers disappear. Can you guess what these reads really are? 6/
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