Many scientists use artificial intelligence in their work, but agents are increasingly soliciting researchers for collaborations.

In this Journal Club, Camille Berthelot highlights a 2011 paper by Brawand et al. that used early RNA-sequencing data across several mammalian species to determine how gene expression evolves, identif...

Top artificial-intelligence models failed to predict the biological consequences of rewriting a virus's entire DNA code.

A dynamic atlas of gene regulation was generated by perturbing every expressed gene across 22 million primary human CD4+ T cells under resting conditions and following re-stimulation. The resulting ma...

The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

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.

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.

Databases and submission systems are often inflexible. Can’t publishers do more on author names?

New science may explain mysterious gap before oxygen flooded our planet billions of years ago

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...

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...

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...

Silhouette score is unsuitable as a metric for single-cell data integration.

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.

The case against AI hype with Cory Doctorow

A disease that was once a death sentence is increasingly treatable

Arc Institute’s “MULTI-evolve” learns a classical additive model, not epistasis.

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

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...

A scientific journal designed for ease and ethics. Publishing open-access articles, Special Issues, and entire journals.

Fully documented source code for Elite on the 6502 (BBC Micro, Acorn Electron, Commodore 64, Apple II, NES), with more than 100 deep dive articles explaining how every aspect of this iconic game works...