Gennady Gorin
@goringennady.bsky.social
🦠🧬📊bioinformatics, statistics, and stochastic processes.
"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
Reposted by Gennady Gorin
Hungarian writer László Krasznahorkai, known for philosophical and bleakly funny novels, has won the Nobel Prize in literature.
Hungarian writer László Krasznahorkai wins the Nobel Prize in literature
Hungarian writer László Krasznahorkai has won the Nobel Prize in literature for what the Nobel committee called his compelling and visionary work.
bit.ly
October 9, 2025 at 11:31 AM
Hungarian writer László Krasznahorkai, known for philosophical and bleakly funny novels, has won the Nobel Prize in literature.
Reposted by Gennady Gorin
"We're going to create superintelligence" How about making outlook search work first. How about that
October 3, 2025 at 5:18 PM
"We're going to create superintelligence" How about making outlook search work first. How about that
A new revision is out! Lots of interesting cross-species data analysis, all of it pointing to the same conclusion: male XIST expression in the heart really is only detectable in humans!
October 1, 2025 at 9:53 PM
A new revision is out! Lots of interesting cross-species data analysis, all of it pointing to the same conclusion: male XIST expression in the heart really is only detectable in humans!
Reposted by Gennady Gorin
scFLUENT-seq reveals that individual cells—lymphocytes to stem cells—transcribe only ∼0.02%–3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
September 27, 2025 at 5:43 PM
scFLUENT-seq reveals that individual cells—lymphocytes to stem cells—transcribe only ∼0.02%–3.1% of the genome, versus >80% in bulk, revealing limited genome engagement and profound cell-type and cell-to-cell heterogeneity @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
the lengths Apple will go to to avoid making consumer software are amazing. hope we get some good scientific software out of it
a performant model without protein specific architecture.
One comment: they trained on 9M structures, >95% generated by deep learning models that DO use protein specific architecture.
I’d call this knowledge distillation and challenge the core claim of the paper. Will read more deeply
One comment: they trained on 9M structures, >95% generated by deep learning models that DO use protein specific architecture.
I’d call this knowledge distillation and challenge the core claim of the paper. Will read more deeply
Apple is entering the protein folding arena.
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
September 26, 2025 at 12:17 AM
the lengths Apple will go to to avoid making consumer software are amazing. hope we get some good scientific software out of it
sperm is stored in the female visceral fat, of course, everybody knows this
September 26, 2025 at 12:15 AM
sperm is stored in the female visceral fat, of course, everybody knows this
Reposted by Gennady Gorin
don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code
use preprint servers to share your science, not advertisements
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code
use preprint servers to share your science, not advertisements
September 21, 2025 at 5:41 PM
don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code
use preprint servers to share your science, not advertisements
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code
use preprint servers to share your science, not advertisements
Reposted by Gennady Gorin
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 11:07 AM
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
Reposted by Gennady Gorin
There's been a recent explosion in shoddy, cookie-cutter analysis of large, widely-available public health datasets (think NHANES, the UK Biobank, FAERS, etc). Matt Spick and I offer some advice in our new Viewpoint in European Science Editing:
doi.org/10.3897/ese....
More reading material below!
doi.org/10.3897/ese....
More reading material below!
![Figure 1 of the commentary with caption:
igure 1. Artificial intelligence–assisted workflows enable rapid acceleration in publications.
(A) Illustrative workflow schematic. (B) PubMed search using the following search string:
“nhanes[tiab] OR uk biobank[tiab] OR finngen[tiab] OR global burden of disease study[tiab] OR
faers[tiab].” The estimate for the publication count in the remainder of 2025 is derived by
applying the same ratio of H2 2024 / H1 2024 publication count to the H1 2025 publication count
and assumes a similar seasonal pattern of higher publication rates in the first 6 months of the year.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:zksiuknephxzeyvlzbcbpbbb/bafkreidlopucqq4yszbusbxdfar4iz3hsox7epmmizaein6qwvvl7pfksq@jpeg)
September 19, 2025 at 3:38 PM
There's been a recent explosion in shoddy, cookie-cutter analysis of large, widely-available public health datasets (think NHANES, the UK Biobank, FAERS, etc). Matt Spick and I offer some advice in our new Viewpoint in European Science Editing:
doi.org/10.3897/ese....
More reading material below!
doi.org/10.3897/ese....
More reading material below!
Reposted by Gennady Gorin
Fundamental Limits of Inferring Dynamical Gene Regulatory Models from Single-Cell Data https://www.biorxiv.org/content/10.1101/2025.09.12.674509v1
September 13, 2025 at 5:47 AM
Fundamental Limits of Inferring Dynamical Gene Regulatory Models from Single-Cell Data https://www.biorxiv.org/content/10.1101/2025.09.12.674509v1
Reposted by Gennady Gorin
mega this, mega that. some of you computer people need to be more worried about charismatic MEGAfauna. i'm saying you're going to be eaten by tigers if you keep being confusing like this
September 11, 2025 at 3:44 AM
mega this, mega that. some of you computer people need to be more worried about charismatic MEGAfauna. i'm saying you're going to be eaten by tigers if you keep being confusing like this