Valentine Svensson
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nxn.se
Valentine Svensson
@nxn.se
870 followers 80 following 98 posts
Molecular cell biology and stats / ML, mostly scRNA-seq.
Principal Scientist at Tahoe Tx.
https://www.nxn.se/archive
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nxn.se
We still can’t predict much of anything in biology - blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
November 12, 2025 at 9:10 PM
nxn.se
The Truth Is Out There, Part 4: The Downside of Belief - www.filfre.net/2024/10/the-...
» The Truth Is Out There, Part 4: The Downside of Belief The Digital Antiquarian
www.filfre.net
November 12, 2025 at 5:35 PM
nxn.se
Hollywood Archaeology: The Super Mario Bros. Movie - grantland.com/features/the...
» Hollywood Archaeology: The Super Mario Bros. Movie
grantland.com
November 11, 2025 at 5:18 AM
Reposted by Valentine Svensson
scverse.bsky.social
🧬 Tahoe Workshop at scverse conference 2025 🧬

Disease Biology and Therapeutics in the Age of Frontier Datasets

@tahoetherapeutics.bsky.social

#scverse2025 #ComputationalBiology #DrugDiscovery #TahoeTherapeutics #SingleCell #PerturbationBiology
October 15, 2025 at 2:28 PM
Reposted by Valentine Svensson
natmethods.nature.com
MrVI, based on deep generative modeling, is a unified framework for integrative, exploratory, and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets. @justjhong.bsky.social @canergen.bsky.social @elhamazizi.bsky.social

www.nature.com/articles/s41...
Deep generative modeling of sample-level heterogeneity in single-cell genomics - Nature Methods
MrVI, based on deep generative modelling, is a unified framework for integrative, exploratory and comparative analyses of large-scale (multi-sample) single-cell RNA-seq datasets.
www.nature.com
October 14, 2025 at 4:44 PM
nxn.se
Training SCVI — Differential expression over epochs - www.nxn.se/p/training-s...
Training SCVI — Differential expression over epochs
With a trained SCVI model you can perform differential expression analysis to learn which genes are increased and decreased in gene expression as cells change their states.
www.nxn.se
October 14, 2025 at 6:14 AM
nxn.se
A lymphocyte chemoaffinity axis for lung, non-intestinal mucosae and CNS - www.nature.com/articles/s41...
A lymphocyte chemoaffinity axis for lung, non-intestinal mucosae and CNS - Nature
GPR25 and its ligand define the core chemoaffinity axis GPR25–CXCL17 of the integrated extraintestinal mucosal immune system, regulating how immune responses disseminate to non-intestinal barrier tissues and with implications for understanding and manipulating immunity and inflammation.
www.nature.com
October 9, 2025 at 5:41 AM
nxn.se
A single-cell spatial chart of the airway wall reveals proinflammatory cellular ecosystems and their interactions in health and asthma - www.nature.com/articles/s41...
A single-cell spatial chart of the airway wall reveals proinflammatory cellular ecosystems and their interactions in health and asthma - Nature Immunology
Here, the authors use single-cell spatial transcriptomics to profile the airway wall landscape in health and during asthma. Discrete proinflammatory ecosystems containing alarmins, chemokines and a unique combination of stromal cells were identified in healthy individuals, and these were spatially dysregulated in asthma.
www.nature.com
October 7, 2025 at 6:10 AM
nxn.se
Causal temperatures - www.nxn.se/p/causal-tem...
Causal temperatures
Time is special.
www.nxn.se
October 5, 2025 at 8:31 AM
nxn.se
Negative binomial regression and inference using a pre-trained transformer - www.nxn.se/p/negative-b...
Negative binomial regression and inference using a pre-trained transformer
I wanted to speed up negative binomial regression with a novel transformer model, but it actually turns out that a classical method of moments is a better solution.
www.nxn.se
September 23, 2025 at 5:54 AM
nxn.se
Hanseatic League - en.wikipedia.org/wiki/Hanseat...
Hanseatic League - Wikipedia
en.wikipedia.org
September 18, 2025 at 5:06 AM
nxn.se
The immunology of asthma and chronic rhinosinusitis - www.nature.com/articles/s41...
The immunology of asthma and chronic rhinosinusitis - Nature Reviews Immunology
In this Review, Kato and Kita discuss the complex interactions between airway epithelial cells and immune cells that contribute to the development of asthma and chronic rhinosinusitis. They highlight ...
www.nature.com
September 16, 2025 at 5:12 AM
nxn.se
Alien: Earth (2025) - www.themoviedb.org/tv/157239-al...
Alien: Earth
When the mysterious deep space research vessel USCSS Maginot crash-lands on Earth, Wendy and a ragtag group of tactical soldiers make a fateful discovery that puts them face-to-face with the planet's ...
www.themoviedb.org
September 9, 2025 at 3:04 AM
nxn.se
The Truth Is Out There, Part 3: The Game of Belief - www.filfre.net/2024/10/the-...
» The Truth Is Out There, Part 3: The Game of Belief The Digital Antiquarian
www.filfre.net
September 7, 2025 at 3:32 AM
nxn.se
THE LOTTERY OF FASCINATIONS - slatestarcodex.com/2013/06/30/t...
The Lottery of Fascinations
I. Suppose I were to come out tomorrow as gay. I have amazing and wonderful friends, and I certainly wouldn’t expect them to hate me forever or tell me to burn in Hell or anything like that. …
slatestarcodex.com
September 7, 2025 at 12:11 AM
nxn.se
How pour-over coffee got good - worksinprogress.co/issue/how-po...
How pour-over coffee got good - Works in Progress Magazine
Pour-over coffee has long been popular with coffee enthusiasts, but it frustrated coffee shops because it takes so long to make. That’s changing.
worksinprogress.co
September 1, 2025 at 12:34 AM
nxn.se
A Visual Guide to Gene Delivery - press.asimov.com/articles/gen...
A Visual Guide to Gene Delivery
There are at least 10,000 known monogenic diseases. When attempting to cure them, how do clinicians decide which gene-therapy delivery method is best?
press.asimov.com
August 25, 2025 at 12:47 AM
nxn.se
The Day Novartis Chose Discovery - www.alexkesin.com/p/the-day-no...
The Day Novartis Chose Discovery
How a Swiss pharma giant built the last great corporate research skunkworks - and why that model may never work again.
www.alexkesin.com
August 17, 2025 at 4:58 AM
nxn.se
What's going on with gene therapies? (Part one) - nehalslearnings.substack.com/p/whats-goin...
What's going on with gene therapies? (Part One)
Cell and gene therapies are treating previously untreatable diseases and saving tens of thousands of lives. So why are companies shutting down?
nehalslearnings.substack.com
August 16, 2025 at 11:18 PM
nxn.se
The immunology of asthma - www.nature.com/articles/s41...
The immunology of asthma - Nature Immunology
In this Review, the authors update us on the immunology and clinical options for treating asthma.
www.nature.com
August 16, 2025 at 8:56 PM
nxn.se
Animals as chemical factories - worksinprogress.co/issue/animal...
Animals as chemical factories - Works in Progress Magazine
Horses bled for antivenom, crabs drained for endotoxin tests, and silkworms boiled for silk. Science can now replace these practices with synthetic alternatives — but we need to find ways to scale the...
worksinprogress.co
August 16, 2025 at 6:12 PM
nxn.se
The therapeutic potential of stem cells - royalsocietypublishing.org/doi/10.1098/...
The therapeutic potential of stem cells | Philosophical Transactions of the Royal Society B: Biological Sciences
In recent years, there has been an explosion of interest in stem cells, not just within the scientific and medical communities but also among politicians, religious groups and ethicists. Here, we summ...
royalsocietypublishing.org
August 12, 2025 at 5:47 AM
nxn.se
The pharma industry from Paul Janssen to today: why drugs got harder to develop and what we can do about it - atelfo.github.io/2023/12/23/b...
The pharma industry from Paul Janssen to today: why drugs got harder to develop and what we can do about it
Personal site for posts about my interests: the biotech industry, medicine, molecular biology, neuroscience, biorisk, science, consciousness, AI, innovation, decision making, philosophy, games, sci-fi...
atelfo.github.io
August 9, 2025 at 3:15 AM
Reposted by Valentine Svensson
arxiv-stat-ml.bsky.social
Valentine Svensson
Negative binomial regression and inference using a pre-trained transformer
https://arxiv.org/abs/2508.04111
August 7, 2025 at 4:16 AM
nxn.se
Negative binomial regression and inference using a pre-trained transformer - arxiv.org/abs/2508.04111
Negative binomial regression and inference using a pre-trained transformer
Negative binomial regression is essential for analyzing over-dispersed count data in in comparative studies, but parameter estimation becomes computationally challenging in large screens requiring mil...
arxiv.org
August 7, 2025 at 1:31 AM