Gennady Gorin @goringennady.bsky.social · 11/10/2026bsky.app/profile/gori... A great deal has changed since 1959. 000
Gennady Gorin @goringennady.bsky.social · 11/10/2026pretty 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. 110
Gennady Gorin @goringennady.bsky.social · 10/10/2026There are many drugs with unknown mechanisms of action. But I am not so sure today's pharma culture has much appetite for that. 110
Gennady Gorin @goringennady.bsky.social · 09/10/2026My wife @rileyisyelling.bsky.social wrote another book! Join us for the release party! 111
Reposted by Gennady GorinHanbin Lee @epigenci.bsky.social · 06/10/2026We 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. 15423
Reposted by Gennady GorinRiley E. Smith @rileyisyelling.bsky.social · 04/10/2026The Last Meeting of the Henchmen's Union, Citadel Branch. Are you Team Henchmen or Team Cardinal? Watch to find out: youtu.be/R5JtUoSgu7k #bookreleaseyoutu.beThe Last Meeting of the Henchmen's Union, Citadel BranchYouTube video by Riley E. Smith - Writer // Comedian 012
Reposted by Gennady GorinHanbin Lee @epigenci.bsky.social · 21/09/2026This in JASA is quite funny. How should we evaluate statistical significance when the parties involved have stakes on the results? arxiv.org/pdf/2205.06812arxiv.org 021
Gennady Gorin @goringennady.bsky.social · 15/09/2026could be. the risk profile of one or another model seems like a wide open hypothetical. the risk profile of centralization, however, sure seems worse 001
Reposted by Gennady GorinNick Stroustrup @nstroustrup.bsky.social · 05/09/2026Did 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 621185
Gennady Gorin @goringennady.bsky.social · 28/07/2026Check out one of mine, which will be direly counterproductive to learning how cryptics work!puzzleme.amuselabs.comPlay this Crossword - A Comedy of ErrorsA Comedy of Errors 030
Gennady Gorin @goringennady.bsky.social · 20/06/2026coincidentally, also the name of 2027's most popular Lin-Manuel Miranda musical 130
Reposted by Gennady GorinPierre-Paul Axisa @ppaxisa.bsky.social · 01/06/2026Also #singlecell RNaseq for sure 🧪🧬💻 061
Reposted by Gennady GorinReese Richardson @reeserichardson.bsky.social · 28/05/2026TL;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.blogHow 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 23591312
Reposted by Gennady GorinCeleste Labedz @celestelabedz.bsky.social · 27/05/2026I'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. 33310
Reposted by Gennady GorinbioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 08/05/2026Efficient Stochastic Trace Generation for Transcription www.biorxiv.org/content/10.64898/20… 011
Reposted by Gennady GorinPiper @the-pied-piper.bsky.social · 20/05/2026they should invent software updates that make the software better over time instead of worse 892931279
Reposted by Gennady GorinWilliam DeWitt @wsdewitt.github.io · 29/04/2026Arc 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.ioAdditivity is all you need?Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis. 37927
Reposted by Gennady GorinNicholas Mancuso @nmancuso.bsky.social · 06/05/2026Super 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 34516
Gennady Gorin @goringennady.bsky.social · 03/05/2026Vivek Murthy just finished off his second term 000
Gennady Gorin @goringennady.bsky.social · 30/04/2026AI: the premier solution for automating making up vacuous numbers 000
Reposted by Gennady GorinA. Murat Eren (Meren) @merenbey.bsky.social · 16/04/2026How 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.orgUnfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism StudyThe myth of open data, reproducibility, responsibility, and accountability in science, and your role in it 1216380
Gennady Gorin @goringennady.bsky.social · 13/04/2026I am holding out for measure theory in Vol. VII 110
Reposted by Gennady GorinLior Pachter @lpachter.bsky.social · 13/04/2026If 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/🧵 13912
Reposted by Gennady GorinJay Shendure @jshendure.bsky.social · 10/04/2026Latest 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). 14116
Reposted by Gennady GorinMichael "Shapes Dude" Betancourt @betanalpha.bsky.social · 05/04/2026Friendly 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.ioOrdinal Modeling 2376
Gennady Gorin @goringennady.bsky.social · 05/04/2026Oh, 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.comMonod: model-based discovery and integration through fitting stochastic transcriptional dynamics to single-cell sequencing data - Nature MethodsMonod fits biophysically motivated models to single-cell transcriptomics data, empowering multifaceted and integrative insights of gene expression dynamics, stochasticity and regulation. 020
Reposted by Gennady GorinMichael "Shapes Dude" Betancourt @betanalpha.bsky.social · 03/04/2026You know what's better than inflating the variation of your observational model to heuristically accommodate "outliers"? Actually modeling the contaminating data generating process. 0155
Reposted by Gennady GorinStephen Turner @stephenturner.us · 21/03/2026Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes academic.oup.com/nargab/artic... 🧬💻🧪 github.com/BFL-lab/eukan 0115
Reposted by Gennady GorinThe 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... 06213
Gennady Gorin @goringennady.bsky.social · 17/03/2026As 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. 000
Gennady Gorin @goringennady.bsky.social · 17/03/2026Sure. 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. 110
Gennady Gorin @goringennady.bsky.social · 16/03/2026Sure. 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. 100
Gennady Gorin @goringennady.bsky.social · 16/03/2026I 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. 100
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 compellingformatmypaper.comFormatMyPaper - The End of Manuscript FormattingPaste your paper, choose your journal, and let our AI handle the tedious rest. Get back to the science. 000
Gennady Gorin @goringennady.bsky.social · 12/03/2026Every 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) 040
Gennady Gorin @goringennady.bsky.social · 11/03/2026Einstein AI C&D charging bsky.app/profile/gori... 110
Reposted by Gennady Gorinhoffsbeefs.bsky.social @hoffsbeefs.bsky.social · 10/03/2026RIP ishmael you would have loved this 🐋 093
Reposted by Gennady GorinLior Pachter @lpachter.bsky.social · 09/03/2026Ambient 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/ 25815
Reposted by Gennady GorinReese Richardson @reeserichardson.bsky.social · 09/03/2026New COSIG update! 3️⃣4️⃣ 021
Gennady Gorin @goringennady.bsky.social · 09/03/2026I 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. 13/13gennadygorin.github.ioGennady Gorin, Ph.D.Senior Scientist applying stochastic models for therapeutic discovery 001
Gennady Gorin @goringennady.bsky.social · 09/03/2026This 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/ 100
Gennady Gorin @goringennady.bsky.social · 09/03/2026But 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.govRNA trafficking and local protein synthesis in dendrites: an overview - PubMedIt 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 … 110
Gennady Gorin @goringennady.bsky.social · 09/03/2026Yet 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/ 100
Gennady Gorin @goringennady.bsky.social · 09/03/2026Adjust 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/ 100
Gennady Gorin @goringennady.bsky.social · 09/03/2026Feature 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/ 100
Gennady Gorin @goringennady.bsky.social · 09/03/2026Some 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/ 100
Gennady Gorin @goringennady.bsky.social · 09/03/2026It 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/ 100