Gennady Gorin
@goringennady.bsky.social
🦠🧬📊bioinformatics, statistics, and stochastic processes.
Reposted by Gennady Gorin
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
www.cell.com/cell-genomic... @ucirvine.bsky.social
January 2, 2026 at 1:22 AM
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
www.cell.com/cell-genomic... @ucirvine.bsky.social
Reposted by Gennady Gorin
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
December 26, 2025 at 12:11 PM
Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏
Batch Effects Remain a Fundamental Barrier to Universal Embeddings in Single-Cell Foundation Models https://www.biorxiv.org/content/10.64898/2025.12.19.695371v1
December 27, 2025 at 1:02 AM
Reposted by Gennady Gorin
No contest. Just read the first two sentences of the abstract. www.nature.com/articles/s41...
All right it’s time for the annual “please tell us about one (or a few if you are ambitious) paper from 2025 that really impressed you and why we should all read it“! Go! If you tell us how it changed your view of the world and what makes it so powerful and consequential It would be excellent.
December 21, 2025 at 8:31 PM
No contest. Just read the first two sentences of the abstract. www.nature.com/articles/s41...
Reposted by Gennady Gorin
New #ebook at Project Gutenberg: Pan's garden by Algernon Blackwood https://www.gutenberg.org/ebooks/77472
December 15, 2025 at 11:20 PM
New #ebook at Project Gutenberg: Pan's garden by Algernon Blackwood https://www.gutenberg.org/ebooks/77472
Reposted by Gennady Gorin
The mechanics and physics of tofu: Understanding hydrated soft solids through feature networks https://www.biorxiv.org/content/10.64898/2025.12.10.693552v1
December 13, 2025 at 10:46 PM
The mechanics and physics of tofu: Understanding hydrated soft solids through feature networks https://www.biorxiv.org/content/10.64898/2025.12.10.693552v1
Reposted by Gennady Gorin
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 Gennady Gorin
A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics https://www.biorxiv.org/content/10.1101/2025.11.25.690568v1
November 29, 2025 at 4:46 PM
A Comparison of Computational Methods for Modeling Stochastic Collaborative DNA Methylation Dynamics https://www.biorxiv.org/content/10.1101/2025.11.25.690568v1
Reposted by Gennady Gorin
November 27, 2025 at 8:03 PM
Reposted by Gennady Gorin
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...
"Move fast with stable infrastructure" is when both your website and your messaging app are so unreliable as to be practically unusable
Let’s talk about “Move fast and break things.” First of all, Facebook itself changed its motto to “Move fast with stable infrastructure” in 2014. So much for breaking things, at least if you’re a soulless corporate behemoth.
1/12
1/12
November 25, 2025 at 12:24 AM
"Move fast with stable infrastructure" is when both your website and your messaging app are so unreliable as to be practically unusable
Reposted by Gennady Gorin
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: http://buff.ly/2p3UZIt
November 22, 2025 at 8:45 PM
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: http://buff.ly/2p3UZIt
Reposted by Gennady Gorin
The challenges of single cell transcriptomics on difficult human tissue: the placenta #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
November 16, 2025 at 8:01 AM
The challenges of single cell transcriptomics on difficult human tissue: the placenta #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
https://www.biorxiv.org/content/10.1101/2025.11.14.688483v1
Reposted by Gennady Gorin
Joint Biophysical Modeling of Paired Single-Cell RNA and Protein Measurements https://www.biorxiv.org/content/10.1101/2025.11.14.688548v1
November 16, 2025 at 3:47 AM
Joint Biophysical Modeling of Paired Single-Cell RNA and Protein Measurements https://www.biorxiv.org/content/10.1101/2025.11.14.688548v1
Reposted by Gennady Gorin
Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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.
www.nature.com
November 11, 2025 at 5:35 PM
Monod fits biophysically motivated models to single-cell transcriptomics data, providing insights into gene expression dynamics. @goringennady.bsky.social @lpachter.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Tech Innovation from Google (An Alphabet Company), Powered By AI one assumes
November 12, 2025 at 12:36 AM
Tech Innovation from Google (An Alphabet Company), Powered By AI one assumes
Reposted by Gennady Gorin
This is one of the most remarkable academic debacles I've ever seen.
A large RCT got published in BMJ. There are currently 44 Pubpeer comments, mostly about the data, including...well. Read for yourself.
pubpeer.com/publications...
A large RCT got published in BMJ. There are currently 44 Pubpeer comments, mostly about the data, including...well. Read for yourself.
pubpeer.com/publications...
PubPeer - Prevention of acute myocardial infarction induced heart fail...
There are comments on PubPeer for publication: Prevention of acute myocardial infarction induced heart failure by intracoronary infusion of mesenchymal stem cells: phase 3 randomised clinical trial (P...
pubpeer.com
November 11, 2025 at 1:19 AM
This is one of the most remarkable academic debacles I've ever seen.
A large RCT got published in BMJ. There are currently 44 Pubpeer comments, mostly about the data, including...well. Read for yourself.
pubpeer.com/publications...
A large RCT got published in BMJ. There are currently 44 Pubpeer comments, mostly about the data, including...well. Read for yourself.
pubpeer.com/publications...
Reposted by Gennady Gorin
We publish *imaginary* research abstracts!
The Journal of Imaginary Research is now accepting submissions of new short fictional pieces. Click to read:
Why Abstract fiction?
The theme
How to get started
What to submit to us
What *not* to submit
journalofimaginaryresearch.home.blog/2025/10/28/c...
The Journal of Imaginary Research is now accepting submissions of new short fictional pieces. Click to read:
Why Abstract fiction?
The theme
How to get started
What to submit to us
What *not* to submit
journalofimaginaryresearch.home.blog/2025/10/28/c...
Call for Abstracts – Journal Of Imaginary Research Volume 11
The Journal of Imaginary Research is now accepting submissions of new short fictional pieces for our annual volume produced each November to celebrate Global Academic Writing Month. We pu…
journalofimaginaryresearch.home.blog
October 29, 2025 at 9:38 AM
We publish *imaginary* research abstracts!
The Journal of Imaginary Research is now accepting submissions of new short fictional pieces. Click to read:
Why Abstract fiction?
The theme
How to get started
What to submit to us
What *not* to submit
journalofimaginaryresearch.home.blog/2025/10/28/c...
The Journal of Imaginary Research is now accepting submissions of new short fictional pieces. Click to read:
Why Abstract fiction?
The theme
How to get started
What to submit to us
What *not* to submit
journalofimaginaryresearch.home.blog/2025/10/28/c...
Reposted by Gennady Gorin
the unfortunate truth re: data visualisation is that you really do gotta hand it to bar charts
November 3, 2025 at 8:47 AM
the unfortunate truth re: data visualisation is that you really do gotta hand it to bar charts
Reposted by Gennady Gorin
I know I posted this on Twitter ages ago, but I came across it again last night and thought some may not have seen it yet.
(From the Not the Nine O'Clock News spin-off book, 1980.)
(From the Not the Nine O'Clock News spin-off book, 1980.)
October 19, 2025 at 10:59 AM
I know I posted this on Twitter ages ago, but I came across it again last night and thought some may not have seen it yet.
(From the Not the Nine O'Clock News spin-off book, 1980.)
(From the Not the Nine O'Clock News spin-off book, 1980.)
I have found the candles
October 28, 2025 at 1:45 AM
I have found the candles
Reposted by Gennady Gorin
Programming skill is just a set of rules you've inferred via personal suffering
October 27, 2025 at 10:36 PM
Programming skill is just a set of rules you've inferred via personal suffering
To achieve good velocity embeddings, test on training data
velotest: Statistical assessment of RNA velocity embeddings reveals quality differences for reliable trajectory visualizations https://www.biorxiv.org/content/10.1101/2025.10.26.683064v1
October 27, 2025 at 5:49 AM
To achieve good velocity embeddings, test on training data
iCloud has a fun Easter egg where it deletes all your books from the local device at random intervals so you can't use Apple Books when you get on a plane
So somehow the AWS outage destroyed my ability to listen to my audible book download even offline? How on earth does that work? Just had to connect to the internet to listen to an already downloaded book on the plane -_-
October 21, 2025 at 6:04 AM
iCloud has a fun Easter egg where it deletes all your books from the local device at random intervals so you can't use Apple Books when you get on a plane