Discover, rate, and verify biology preprints.

Red and blue light cues drive contrasting remodeling of lipophilic metabolites and photophysiology in natural benthic diatom biofilms

Within 30 minutes, red light remodeled natural benthic diatom lipids and pigments more than blue; blue high light most altered photophysiology; de-epoxidation was similar at equal incident intensity.

Gene Regulatory Network Inference reveals tcf4 as a key a player in neuroblastoma gene expression circuitry

Mechanistic stochastic gene regulatory network inference on neuroblastoma tumoroid scRNA-seq predicts TCF4 as a hub whose loss slows chromaffin-to-sympathoblast progression, supported by JQ1 treatment ex vivo.

AlphaFold3 and Intrinsically Disordered Proteins: Reliable Monomer Prediction, Unpredictable Multimer Performance

AlphaFold3 pLDDT matches AlphaFold2 at calling disordered residues (Matthews correlation 0.693 vs 0.701); on disorder-containing complexes mean DockQ is similar, but interface features explain less variance (42% vs 58%).

MtbAIM: AI/ML-guided endpoint-specific prediction of small-molecule activity across drug-susceptible and drug-resistant Mycobacterium tuberculosis

Tree models on RDKit/Morgan features predict M.tb activity and MIC endpoints for drug-susceptible and resistant isolates, slightly beating pretrained embeddings; released as a Colab tool.

Neural prediction decorrelation reveals that adversarial robustness substantially improves DNN prediction accuracy across the entire human auditory cortex

Sounds synthesized to decorrelate model predictions across human auditory cortex show an adversarially robust CochResNet50 predicts fMRI responses far better than its standard counterpart, a gap hidden with natural sounds.

A base-modifying enzyme extends the range of anti-phage defense provided by DNA glycosylases

Brig3, a DNA glycosylase from a soil metagenome, excises 5-hydroxymethylcytosine from T-even phage DNA; the glucose hydrolase BapA extends defense to glucosylated genomes such as wild-type T4.

Unraveling phenotypic variation in multiscale behavioral dynamics

Comparing coarse-grained dynamics across resolutions, weighted by sampling uncertainty, yields phenotypic spaces linking E. coli run speed to CheB and showing paramecia experience narrows zebrafish variability.

Mapping the Trade-Offs That Shape Mammalian Brain Network Architecture

Across 25,000 generative-model networks scored on 29 properties, 635 human and 224 mammalian connectomes cluster in one narrow niche, trading wiring economy for computational capability and robustness.

Structural Basis of Human Kinetochore-Microtubule Coupling by the Ndc80 and Ska Complexes

Cryo-EM shows human Ndc80 and Ska complexes bound to adjacent microtubule protofilaments, linked by a SKA3 tether that passes Ska's preference for GTP-like lattice and tip tracking to Ndc80.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

KAS-CUT&Tag for direct mapping of transcription bubbles

N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.

Hyperosmotic stress induces rewiring of 3D chromatin interactions

One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Two Comparators May Be All We Need

Random forests on sequence and 2D chemistry pick the favored protein for a molecule, or the favored molecule for a protein, at 0.71 to 0.78 accuracy on unseen compounds.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

The Central Coupler of ClpXP Controls Intersubunit Communication and Couples Intrasubunit Chemical Energy with Force Generation

Q208A mutations in up to four subunits of the ClpX central coupler barely slow unfolded-substrate translocation but raise ATP spent per step, weaken force generation and can abolish GFP unfolding.

PTEN Subcellular Localization Dictates Function

Nuclear-excluded PTEN rescued all knockout overgrowth phenotypes in mouse dentate granule neurons; nuclear-restricted PTEN rescued only spine head area and partly soma size, so localization shapes function.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.