Simon Anders
@s-anders.bsky.social
physicist, bioinformatics / biostats researcher at University of Heidelberg
Corruption. Election fraud. Billionaires. Dictators. America: Trump & Musk. Russia: Putin. Britain: #Brexit Referendum fraud, Farage, UKIP / ReformUK, Tories, fascism. This is democracy manipulated and destroyed. Are people stupid enough to waste their votes on this deception? #SocialistSunday
Google replaced pushing Git tags for certain source code with obtaining source code via Google Drive after making a request through Google Forms. It's completely ridiculous and they've gradually become very slow at handling requests. They're in clear violation of the GPLv2 now.
Nature research paper: An expanded codebook of human transcription factor DNA-binding specificity go.nature.com/4wMUZ15
An expanded codebook of human transcription factor DNA-binding specificity - Nature
Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.
go.nature.com
⬇️ Check out this new postdoctoral fellowship to be jointly hosted by Mathew Garnett's lab and our lab! lnkd.in/p/eZUYhWmz
Thrilled to share that our scE2G paper is now published in Nature Genetics! www.nature.com/articles/s41... scE2G predicts enhancer-gene regulatory interactions from single-cell data with state-of-the-art performance. Amazing work led by @mayayayas.bsky.social and @613weilin.bsky.social!
Mapping enhancer–gene regulatory interactions from single-cell data - Nature Genetics
scE2G is a family of models that predict enhancer–gene regulatory interactions from single-cell datasets and enable mapping of these interactions across diverse cell types and tissues.
nature.com
Jesse Engreitz@jengreitz.bsky.social · 2w agoUpdate: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/
˚⋆đźŹđź§ŞAlliance Industry Program 🧪⚙️⋆˚ The Health + Life Science Alliance Heidelberg Mannheim is inviting applications for collaborative projects between companies and Alliance partners. 👉Deadline: 10/15/26 https://www.health-life-sciences.de/opportunities/industry/
The publishing system often asks authors to reshape one of the most personal parts of their identity: their name go.nature.com/4wCIdSz
James Bond, not Bond James: why scientific publishing must respect name order
Databases and submission systems are often inflexible. Can’t publishers do more on author names?
go.nature.com
My take on p-values: 1. p-values do what they are designed to do, which is not what most people using them imagine them to do. 2. Trying to fix p-values is a trap, because no single-number summary can do what people want p-values to do! 3. Trying to explain p-values is also a trap, because...
Julia M. Rohrer@dingdingpeng.the100.ci · last wk.“A p-value is the most widespread statistical concept that is not definable in a single sentence“ CHECKMATE
New mineral analyses may explain the mysterious gap that was present before oxygen flooded our planet billions of years ago. https://scim.ag/4hQ0lUo
What triggered one of the most dramatic changes in Earth’s history?
New science may explain mysterious gap before oxygen flooded our planet billions of years ago
scim.ag
Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n
New blog post! Odds ratios are...a bit weird. Here I explain two problems (interpretation, non-collapsibility) and provide some simple recommendations for improved reporting. www.the100.ci/2026/07/30/r...
Reviewer notes: Odds ratios are really odd
When psychological researchers investigate binary outcomes, they routinely report odds ratios to quantify the strength of an effect or an association. This is quite understandable given that psycholog...
the100.ci
Our manuscript on the co-option of TEs as cerebellar CREs is now officially published in @natcomms.nature.com! Huge thanks to @kaessmannlab.bsky.social @marisepp.bsky.social, and @ioansarr.bsky.social for the fantastic collaboration throughout this project! www.nature.com/articles/s41...
Gene regulatory innovations from transposable elements in primate cerebellum development - Nature Communications
The roles of transposable elements in primate brain development remain underexplored. Here, the authors identify transposable elements with ancestral regulatory potential that have been co-opted as ci...
nature.com
Kaessmann Lab@kaessmannlab.bsky.social · 10mo agoDid transposable elements shape brain evolution — and if so, which ones, and in which cell states and lineages? Led by @tyamadat.bsky.social, we explored this question in cerebellum development using sequence-based deep learning models! www.biorxiv.org/content/10.1...
RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...
Analog intrinsic recoding measures RNA dynamics without chemical conversion
Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...
biorxiv.org
This is a real image. Taken by Voyager 1 in 1979, the icy moon Europa floats above Jupiter's swirling Red Spot maelstrom. The shadow is from Io, another of Jupiter's large inner moons, which is out of frame. Oh to see this view with my own eyes (safely shielded from the lethal radiation fields)
Silhouette score is unsuitable as a metric for single-cell data integration go.nature.com/4fcQzZr rdcu.be/fpOKP
Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology
Silhouette score is unsuitable as a metric for single-cell data integration.
go.nature.com
A biology journal trialled paying their reviewers and found it led to faster first editorial decisions – and increased review quality. go.nature.com/446SaLu
Why paying peer reviewers works, according to a journal’s editor-in-chief
A biology journal which paid peer reviewers found that the approach cut the time to a first editorial decision by 85% and maintained high-quality reviews.
go.nature.com
I still think this is one of the most egregious acts of Treason ever committed….
It is always worth your while to listen to @doctorow.pluralistic.net.
How to Think About AI Before It’s Too Late
The case against AI hype with Cory Doctorow
theatlantic.com
Cell segmentation for spatial transcriptomics isn’t so easy, right? We thought so too. A wonderful group lead by @garybader.bsky.social and @rgottardo.bsky.social put together a perspectives piece on where things stand, the challenges, and what’s next. Check it out: arxiv.org/pdf/2606.09675
arxiv.org
I'm alive *AND* I wrote a blog post?! Unheard of! Much đź’– to @abbycabs.dev, and @grafana.bsky.social's David Allen and Amanda Wagner whose FOSDEM talk's were a huge source of inspo!
stdlib@stdlib.io · 2mo agoFor years, open source communities relied on visible friction: people got stuck, asked questions in public, and became part of a community. AI is changing that. What happens when newcomers are no longer visible—and neither side knows the other is there? blog.stdlib.io/ai-and-the-i...
Fascinating footage of a human white blood cell chasing a bacterium captured through a microscope. 📽️: David Rogers
Interesting post about a breakthrough in the treatment of pancreatic cancer. I had some vague idea that pancreatic cancer was really bad, but no idea why -- happy I could fill in some gaps in my understanding. www.worksinprogress.news/p/pancreatic...
Pancreatic cancer just met its match
A disease that was once a death sentence is increasingly treatable
worksinprogress.news
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...
Additivity is all you need?
Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.
dewitt-lab.github.io
Exciting news 📣 The first preprint from @grandlab.bsky.social is out 🧬 How are essential genes controlled? By rapid degradation and recovery of TFs alone or in combination, we show that essential genes rely on a single dominant TF, despite dense co-binding. www.biorxiv.org/content/10.6...
Essential genes are dominantly activated by single transcription factors
Cell viability depends on the precise expression of essential genes, which are controlled by CpG-island (CGI) promoters densely bound by transcription factors (TFs). This has led to the prevailing model that TFs cooperate to ensure ubiquitous expression. Here, using rapid and reversible single and combinatorial degradation in murine stem cells, we systematically dissect the regulatory interactions between five key TFs. We uncover an unexpectedly specific architecture in which regulatory dominance, rather than cooperation, is the prevailing mode, where individual TFs autonomously drive chromatin opening and gene activation at largely distinct promoters. Cooperative regulation occurs at a minority of sites with antagonistic or synergistic outcomes modulated by the interplay between nucleosome positioning and TF sensitivity to chromatin. This logic is recapitulated at synthetic sequences and reflected in human genetic variation. These findings reveal that single TFs dominantly activate distinct sets of CGI-linked genes, including essential genes, across development, homeostasis, and disease. ### Competing Interest Statement The authors have declared no competing interest. DFG, GR 6341/2-1, 556634773
biorxiv.org
Our publication on 3D models for drug discovery is out! In the primer, we discuss the role of organoid models in drug discovery and development. Full article: www.sciencedirect.com/science/arti... @dkfz.bsky.social @uniheidelberg.bsky.social @hlsalliance.bsky.social @sfb1324.bsky.social
If you're as paranoid as I am about tidyverse *_join and pivot_* functions pretending to succeed but secretly introducing unnamed horrors into your data set, you'll probably like {tidylog} github.com/elbersb/tidylo… which adds a nice debriefing comment saying what just happened after each one.
GitHub - elbersb/tidylog: Tidylog provides feedback about dplyr and tidyr operations. It provides wrapper functions for the most common functions, su…
Tidylog provides feedback about dplyr and tidyr operations. It provides wrapper functions for the most common functions, such as filter, mutate, select, and group_by, and provides detailed output f...
github.com
This a very important, and extremely well-executed study from Ralph Grand’s group @uniheidelberg.bsky.social. Congrats to all the authors! www.biorxiv.org/content/10.6...
Just found out about the new science journal "Stacks". The editorial board includes the legendary @elisabethbik.bsky.social. Publication costs are what they should be. Moreover, it has an interesting peer-review where reviewers interact, agree and vote for publications. stacksjournal.org
Stacks Journal | Create better science, together.
A scientific journal designed for ease and ethics. Publishing open-access articles, Special Issues, and entire journals.
stacksjournal.org
Oligarchs have always been a threat, but tech oligarchs represent a new level of danger. Their wealth dwarfs historical tycoons and their control over algorithms allows them to curate human reality. They own the digital infrastructure of thought
