statistical model

Heterogeneous self-couplings enable scale-invariant memory and cognitive flexibility without criticality

This paper introduces a recurrent neural network model with heterogeneous self-interactions that generates scale-invariant memory and cognitive flexibility without requiring criticality.

DeepPhage: leveraging the power of NGS phage display data, an in-depth analysis for the identification of Eu3+-binding peptides

DeepPhage identifies Eu3+-binding peptides from NGS phage display data by analyzing sequence biases and comparing multiple experimental conditions.

Mechanoadaptive focal adhesion-actomyosin coupling organizes diverse modes across ECM stiffness

The paper develops a dynamical model to show how ECM stiffness and mechanoadaptive processes generate diverse focal adhesion modes and influence their stability.

GolgiFold: A Structural Predictome of Human Golgi Protein Complexes

The paper develops GolgiFold, a structure-based PPI map of human Golgi proteins, identifying over 1,800 interactions and confirming new protein contacts through experimental validation.

Torsion in motion: the visual system as a three-axis gimbal

This study estimates eye torsion during walking using head-mounted technology and shows its role in altering retinal flow for self-motion parameter extraction.

Distinct gradients of cortical architecture capture visual representations and behavior across the lifespan

The paper shows two architectural gradients in human visual cortex that correlate with structural, functional, and behavioral traits across the lifespan.

Towards a complete diploid chicken genome

This paper presents a nearly complete haplotype-resolved chicken genome using trio-sequencing and long-read data, identifying gaps and structural variants in dot chromosomes.

A droplet-to-data workflow for antimicrobial screening of complex matrices

The paper presents a droplet-based workflow for antimicrobial screening in complex matrices, showing it can detect MICs at lower concentrations and reveal extract-specific aggregation effects.

Brain and kidney Extracellular Vesicle Morphology and Complementary Brain proteomics after Inflammatory Challenge

The paper compares brain and kidney extracellular vesicle morphology and proteomics after inflammatory challenge, identifying significant protein changes but noting limitations in causal conclusions.

Mobile genetic elements accompany the emergence of clonal crop lineages from weed-associated populations of Xanthomonas campestris

The paper analyzes Xanthomonas campestris strains from weed and crop hosts to show that mobile genetic elements accompany the emergence of clonal crop lineages and are present in diverse weed-associated strains.

Genome-wide fluctuating selection under demographic cycling in Icelandic rock ptarmigan

The paper identifies genomic signatures of fluctuating selection in rock ptarmigan populations over an 11-year period, showing allele frequency changes correlated with demographic cycles.

Comparative analysis of protease-inhibitor gene family counts under different counting units and genome annotations

The paper compares protease-inhibitor gene family counts across species, showing how annotation methods and counting units affect results.

Cognitive Control in Pediatric Cancer Survivors: A task-fMRI study

This study uses fMRI to compare brain activation during a cognitive task between pediatric cancer survivors exposed to chemotherapy and healthy controls, finding altered neural activation and cognitive control deficits in the chemo-exposed group.

Molecule-resolved inference reveals the spatial organization of transcriptional programs

The paper introduces FICTURE2, a statistical model that infers transcriptional programs from individual RNA molecules in spatial transcriptomics data, revealing spatial organization and cellular identity without segmentation.

Serum nutritional-metabolic recovery during tuberculosis treatment across BMI-defined undernutrition strata: A longitudinal proteomic reanalysis

This study reanalyzes longitudinal serum proteomics data from tuberculosis patients to assess how nutritional-metabolic recovery during treatment varies by baseline BMI, finding no significant BMI-dependent trajectories but an overall increase in a 36-protein summary axis.

Shepherding by biased diffusion organizes diffusible proteins on microtubules

The paper demonstrates that motors can shepherd diffusive proteins on microtubules through biased diffusion, revealing a mechanism for spatial patterning without direct binding.

How many mutations does it take to evolve a new function?

The paper investigates how many mutations are needed to evolve a new function using a Boolean-network model of genotype-phenotype maps, showing a power-law scaling with network size.

Knockdown of the long non-coding RNA DNAAF3-AS1 activates the p53 pathway and remodels the H3K36me3 landscape

This study shows that knocking down DNAAF3-AS1 reduces gene-body H3K36me3, activates the p53 pathway, and alters promoter usage in apoptosis-related genes.

Comparing pest survey methods through detection probability: seasonal and abundance-dependent detection of spotted lanternfly (Lycorma delicatula, Hemiptera: Fulgoridae)

The paper evaluates three pest survey methods for spotted lanternflies, finding seasonal and abundance-dependent detection probabilities, with traps performing better on larger trees and preferred hostplants.

Hippocampal replay repairs the cognitive map for flexible planning

This paper proposes that hippocampal replay repairs the cognitive map by updating it for new goals and maintaining abandoned ones, supported by rat foraging experiments.

Lexical surprisal drives pupil dilation during continuous story listening

This study shows that pupil dilation during story listening reflects lexical surprisal, indicating cognitive processing costs in naturalistic language comprehension.

Assessing the Operational Feasibility of Evolutionary Therapy in Metastatic Non-Small Cell Lung Cancer

This study evaluates the clinical feasibility of evolutionary therapy for NSCLC by simulating its performance under real-world constraints like measurement error and appointment delays.

ARG-PASS v2.0 expands global resistome surveillance to reveal previously unrecognized antibiotic resistance genes reaching the human gut

ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

Degeneracy in neuronal bifurcation landscapes: equivalent bifurcation sequences across distinct parameter sets

The paper shows that different biophysical parameters can produce equivalent bifurcation sequences in neuronal models, revealing degeneracy in neuronal dynamics.

Repeatability of adaptation in interacting species

This study investigates how intergenomic epistasis affects endpoint repeatability in coevolving species, finding high repeatability within landscapes but varying fitness outcomes across landscapes.

SVEP1 enables efficient binding of Angiopoietin-2 to the TIE1 receptor, allowing receptor phosphorylation and downstream signaling

This study identifies SVEP1 as a mediator of ANG2-TIE1 binding, leading to TIE1 phosphorylation and downstream signaling in lymphatic endothelial cells.

Agentic cryo-EM structure determination with CryoPilot

CryoPilot uses two language model agents to automate cryo-EM structure determination, improving resolution and model accuracy through adaptive decision-making.

Mapping chromothripsis across human cancer cell lines reveals genome evolution and therapeutic vulnerabilities

This study maps chromothripsis in 1,646 human cancer cell lines, showing its conservation with tumors, higher prevalence, and therapeutic vulnerabilities to HDAC inhibitors.

GaussF: An Unbiased Gaussian Framework for High-Precision Transcript Quantification with a Programmable Self-Benchmark Model

GaussF improves isoform quantification by using a theoretical Gaussian model to correct sequencing biases without empirical data, outperforming existing tools.

Tissue-specific transcriptomic responses to early Toxoplasma gondii infection in sheep during congenital toxoplasmosis

This study examines early transcriptomic responses to Toxoplasma gondii infection in pregnant sheep, identifying tissue-specific immune and stress pathways linked to fetal loss.