Discover, rate, and verify biology preprints.

Arrest-associated transcriptional programmes outweigh apoptosis-associated programmes in treatment-naive pancreatic ductal adenocarcinoma

The paper examines the balance between apoptosis and arrest-associated transcriptional programs in untreated PDAC, finding a consistent bias toward arrest programs.

Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea

The paper shows that during infection, Botrytis cinerea reallocates its transcriptome, altering synonymous codon demand across different host systems.

Hide and seek in a rainforest canopy : when a fruit-eating carnivore (almost) met its top predator carnivore

The paper describes a rare observation of a nocturnal arboreal kinkajou being followed by a puma in a rainforest canopy.

Toward space-optimal approximate colored indexes at scale

This paper introduces Zindex, a space-efficient indexing framework for large-scale sequence repositories, achieving compact storage and fast query performance with novel interleaved filters and merging mechanisms.

spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

Isocaloric restriction of a high-fat diet under TAK-242 administration: metabolic and gut microbial responses in mice

This study examines the effects of isocaloric high-fat diet restriction with TAK-242 on metabolic and gut microbial responses in mice, finding limited normalization of adiposity and microbial community.

Inferring gene regulatory networks from single-cell perturbation data by optimizing causal reach of latent mediator dynamics

CausalODE infers gene regulatory networks from single-cell perturbation data by optimizing causal reach, capturing transient dynamics, and modeling latent protein levels, outperforming existing methods on real datasets.

Measuring neuronal input-output operations in vivo with random access projection microscopy

This paper introduces SLAP2, a high-speed microscope for measuring submicron synapses and dendritic voltage in behaving mice, revealing nonlinear input-output amplification in neurons.

RPFace: From biased structural benchmarks to generalizable RNA-protein interface prediction

RPFace predicts RNA-protein interfaces directly from sequence, outperforming existing methods on RNA interfaces and generalizing to in vivo data without pretraining.

Regenerative epithelial spike cells instruct immune niche homeostasis in zebrafish fin epidermis

The paper identifies a novel epithelial cell type in zebrafish fins, spike cells, and shows their role in maintaining immune cell niche homeostasis through interactions with mpeg1+ immune cells.

Persistent hippocampal traces of lifelong spatial memory

The paper shows that mice retain spatial memory in the hippocampus after long absences, with neural patterns persisting despite changes in individual neuron activity.

Monounsaturated fatty acid depletion is a metabolic pattern of pathogenesis surveilled to activate p38 MAPK innate immunity

The paper identifies oleate depletion as a metabolic signal sensed by C. elegans to activate innate immunity against bacterial infection.

Energetic and functional development of soil food webs along secondary succession

This study examines energy flux changes in soil food webs during secondary succession, finding shifts from herbivory to detritivory and differences between plantation and natural forest types.

scCircaSim: A Circadian Simulator for Single-Cell and Spatial Transcriptomics

scCircaSim generates circadian single-cell and spatial transcriptomic data with known ground truth to evaluate analysis methods.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

No Evidence of an Effect of a Single Mirror Visual Feedback Session on Subsequent Motor Imagery

This study finds that a single session of mirror visual feedback does not significantly alter subsequent motor imagery-related neural activity.

RNA-targeted aminopyridine compounds provide a new antifungal strategy

The paper identifies aminopyridine compounds that target fungal group I introns, showing antifungal activity and synergy with amphotericin B.

Global Data Fitting Enables Kinetic Dissection of Cullin-RING Ligase-Catalyzed Ubiquitylation: From Substrate Priming to Poly-ubiquitin Chain Formation

This study uses pre-steady state kinetics and global data fitting to analyze CRL-dependent ubiquitylation, revealing kinetic parameters and catalytic efficiencies across different CRL systems and substrate contexts.

Circuit and cell-type mechanisms of the spectrolaminar motif of cortical oscillations

The paper uses a bio-realistic model of mouse primary visual cortex to show that cortical oscillations follow a spectrolaminar motif, with gamma in superficial layers and alpha/beta in deep layers, driven by specific cell types and synaptic properties.

Cross-excitation in dorsal root ganglia redistributes coding capacity from stimulus intensity to stimulus location

The paper models cross-excitation in dorsal root ganglia to show it improves spatial localization at the cost of intensity encoding, leveraging the Weber-Fechner law.