statistical model

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

Integrative Multiomics Analysis of the Angiogenesis-EMT Interface in Head and Neck Squamous Cell Carcinoma

This study identifies coordinated angiogenesis-EMT gene programs in OSCC using multi-omic analysis and validates candidate genes through external datasets and protein-level confirmation.

Visual surfaceomics reveals the substrate-scavenging cell surface of Asgard archaea

This study identifies surface proteins in Asgard archaea using visual surfaceomics, revealing a peptidophilic cell surface involved in peptide capture and symbiotic interactions.

Genomic signatures distinguish isolates of Salmonella Typhimurium from humans and livestock

The paper distinguishes human and livestock-associated Salmonella Typhimurium isolates using genomic signatures and machine learning.

Isoform diversity as a complementary dimension of gene expression

The paper shows isoform diversity is a distinct dimension of gene expression, complementary to gene-level abundance, and changes with age and tissue-specific processes.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

LinearRaccess: linear-time approximation of RNA accessibility without base-pair span limits

LinearRaccess computes RNA accessibility for long windows in linear time without base-pair span limits, achieving high accuracy and efficiency.

Interspecific social contacts spread gut microbiota in wild rodent communities

This study shows that social interactions between different rodent species can spread gut microbiota, with stronger transmission from wood mice to yellow-necked mice.

Development of a Pan-Proteome Multi-Epitope Vaccine Candidate Against Nipah Virus Using Reverse Vaccinology and Immunoinformatics Approaches

This paper designs a multi-epitope vaccine candidate against Nipah virus using immunoinformatics and reverse vaccinology, identifying VC033_V6_BD_L03 as a lead candidate with high global and regional population coverage.

Microscale nonrandomness revisited: An overlooked predictor of ecological change

The paper introduces a framework using microscale nonrandomness to predict short-term ecological changes across diverse systems, showing improved predictive performance compared to macroscale variables.

A three-factor model can explain symmetry breaking and the n-1 rule during X-chromosome inactivation

This paper introduces a three-factor mathematical model to explain symmetry breaking and the n-1 rule in X-chromosome inactivation by integrating Xist, an X-linked activator, and SPEN.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

QRAFT: Scaling coalescent-based species tree inference to one million taxa

QRAFT efficiently infers species trees for up to a million taxa using coalescent-based methods, outperforming existing tools in speed and memory usage.

Targeting REV1 Exposes Context-Dependent Therapeutic Responses in Colorectal Cancer

This study shows that targeting REV1 in colorectal cancer enhances chemotherapy sensitivity in a context-dependent manner and inhibits organoid growth.

MOCHI enables systematic identification of candidate independent intronic transcriptional signals from short-read RNA-seq data

MOCHI identifies candidate independent intronic transcripts from short-read RNA-seq data, revealing novel transcripts associated with cancer survival.

Hub labeling makes exact distance calculation practical for large human pangenome graphs

The paper introduces a hub labeling method to reduce the space required for distance indexing in large pangenome graphs, improving query support and reducing storage needs.

Brief visual oddball events evoke CSF flow in the spinal canal

The paper measures CSF flow in the spinal canal using fMRI and finds it correlates with BOLD activity decreases and is provoked by visual oddball stimuli.

Continental scale genetic diversity supports geo-clustered ecoregions connectivity

The paper examines genetic diversity and connectivity between ecoregions, finding a divide between eastern and western regions with restricted gene flow in the west.

2'-O-Methylated ncRNA condensates form a recombination center for IgH synapsis

This study shows that FBL-mediated 2'-O-methylation of GLTs forms condensates that drive IgH synapsis and CSR in B cells.

Genomic and Epigenomic Relationships Capture Different Patterns of Genotype-by-Environment Interaction in Grapevine Clones

This study compares how genomic and epigenomic relationships contribute to genotype-by-environment interaction in grapevine clones, finding that epigenomic factors capture more GEI variance than genomic factors.

Active site electrostatic effects modulate DBO inhibitor potency against OXA-48 variants

This paper investigates how electrostatic effects in the active site influence the potency of DBO inhibitors against OXA-48 variants using computational simulations.

Tools for genetic mapping and gene identification in Caenorhabditis briggsae

The paper updates a toolkit for genetic studies in C. briggsae by identifying indel variants and mapping mutations to genes using high-throughput sequencing.

Coarse-graining genome-scale metabolic models for dynamic, multi-scale simulations of Pseudomonas aeruginosa in gel environments

This paper introduces GEM-CM, a computational framework that couples reaction-diffusion models with genome-scale metabolic models to simulate Pseudomonas aeruginosa growth and pyocyanin production in agar gels.

Evaluating non-oxidative glycolysis using 13C metabolic flux analysis

This study evaluates the precision of 13C metabolic flux analysis using different glucose tracers to estimate non-oxidative glycolysis fluxes in E. coli.

Body size cascades from Neodiprion sawfly hosts to Perilampid parasitoids: An investigation of sequential divergence

The paper investigates whether parasitoid body size and morphology diverge in response to host species differences in Neodiprion sawflies, supporting sequential divergence.

Phase-locked dual-band vibration bursts strengthen anti-kindling by vibrotactile coordinated reset stimulation in a spiking network model

The paper shows that a dual-band vibration burst improves anti-kindling in a spiking network model compared to single-frequency stimulation.

Amyloid stability and condensate material properties independently govern the hnRNPA2 condensate to fibril transition

This study shows that amyloid structure and condensate stability independently influence the hnRNPA2 condensate-to-fibril transition, revealing a structural framework for this process.

Widespread Saccharomyces hybridization in agave fermentations arises repeatedly from asymmetric parental diversity

The paper identifies widespread Saccharomyces hybridization in agave fermentations, showing multiple independent origins and asymmetric parental genetic diversity.

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

Multi-Criteria Evaluation of Hibiscus mutabilis Cultivars for Food Development Using Delphi and Analytic Hierarchy Process

This study evaluates 11 Hibiscus mutabilis cultivars for food use using Delphi and AHP, identifying three top cultivars for food development.