statistical model

Identification of Kinome Biomarkers and Therapeutic Rescue in cGMP-Linked Retinal Degeneration

This study identifies kinome biomarkers and shows therapeutic rescue in cGMP-linked retinal degeneration using LP-CN03 in mouse models.

Frequency-Dependent Structural Responses of Amyloid-β Fibrils to Terahertz Pulses: A Nonequilibrium Molecular Dynamics Study

This study uses nonequilibrium molecular dynamics to show frequency-dependent structural changes in amyloid fibrils under terahertz pulses, identifying two electric-field thresholds for disruption.

Fatty Acid Synthase Binds Cellular mRNAs and its Depletion Reduces Translational Efficiency

This study identifies FASN's RNA binding sites and shows its depletion reduces translational efficiency of associated mRNAs.

Epidermal Langerhans Cells Act as Neuroimmune Regulators of Pain and Itch

This study identifies Langerhans cells as immune-derived amplifiers of cutaneous sensory signaling and identifies semaphorin 7A as a mediator of LC-induced itch potentiation.

The MarR-family regulator TilR links biosynthesis of enterotoxin tilimycin with physiologic adaptation in Klebsiella oxytoca

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

Multi-omics integration reveals candidate genes and molecular mechanisms associated with resistance to sugarcane smut

The paper integrates association mapping and transcriptomics to identify candidate genes and molecular mechanisms associated with sugarcane resistance to smut.

Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics

This paper introduces SSAF-T, a segmentation-free framework for cell-type inference in spatial transcriptomics that avoids cell segmentation and enables accurate cell-type-guided segmentation.

Massive inter-animal horizontal gene transfer contributes to stress tolerance in the fungus gnat Bradysia coprophila

This study identifies extensive horizontal gene transfer in the fungus gnat Bradysia coprophila, showing these genes contribute to stress tolerance and ecological adaptation.

Label-free flow operators and stability operators from single-cell time courses: what local dynamical operators can and cannot identify

This paper introduces scJDO2, a method to separate score and flow operators from single-cell time courses, evaluating their ability to identify unstable cells and bifurcations in hematopoiesis.

Functional Data Clustering of Filopodia Dynamics

The paper clusters filopodia dynamics using functional data analysis to identify distinct temporal patterns linked to Notch signaling in fruit fly development.

Genomic signatures of positive selection and relaxed selective constraints associated with convergent dietary specialisation

The paper identifies genomic signatures of positive selection and relaxed constraints in Dysdera spiders with convergent dietary specialisation on woodlice.

A Framework for SPICE MRSI Reconstruction Posterior Uncertainty Quantification

The paper introduces a framework to quantify uncertainty in SPICE MRSI reconstructions using Laplace approximation and Hessian-vector products, validated with in vivo experiments.

Network analysis of mouse brain proteomes resolves molecular and cellular endophenotypes of aging and Aβ pathology

This study uses proteomics to identify aging and Aβ-related molecular changes in mouse brains and finds they are conserved in human AD proteomes.

Maximum Likelihood Localization Maps

This paper introduces a non-iterative method to create molecular probability maps from single-molecule localization data, preserving positional likelihood without coordinate-based rendering.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

Learning interpretable compositional features associated with continuous covariates

This paper introduces IsoVita, a framework for learning interpretable compositional features from continuous covariates, showing improved detection of temporal isoform variation in human brain RNA-seq data.

SARDINE unlocks EWAS summary statistics for large-scale epigenetic biomarker analysis

SARDINE uses EWAS summary statistics to estimate epigenetic clock-phenotype associations without individual-level data, revealing heterogeneity in biomarker associations with aging and diseases.

Temporal changes in genetic variation during the invasion of Lygodium japonicum in North America

This study uses herbarium specimens to analyze genetic variation in Lygodium japonicum during its invasion of North America, identifying Asia as the source and finding evidence of rapid adaptation and reduced non-coding diversity.

TestNet-PA: Sampling-Zero-Aware Inference of Microbial Presence-Absence Networks

TestNet-PA addresses sampling zeros in microbial presence-absence networks by modeling them as structural or sampling zeros, improving FDR control and sensitivity compared to Fisher's exact test.

Single-cell multi-omics identify OTP and NOVA1 as regulators of leptin action in hypothalamic feeding circuits

This study uses single-cell multi-omics to identify OTP and NOVA1 as key regulators of leptin action in hypothalamic feeding circuits, revealing cell-type-specific transcriptional and regulatory changes.

Endothelial protein C receptor is an entry receptor for Langya virus

This study identifies the endothelial protein C receptor (EPCR) as the entry receptor for Langya virus and reveals the molecular basis of its interaction with the viral attachment glycoprotein.

Epigenome-informed Polymer Modeling Reveals Chromosome Folding Landscapes across Distinct Genetic and Epigenetic Contexts

This study uses epigenome-informed polymer modeling to generate chromosomal conformational ensembles from epigenomic data, revealing how genetic and epigenetic contexts shape chromosome folding landscapes.

Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

The paper assesses genetic load and structural variation in American black bear populations, finding elevated levels in an isolated population.

A hierarchical Bayesian model for dynamic phenotypes in multi-environment trials with genotype by environment interaction

The paper develops a hierarchical Bayesian model to analyze dynamic phenotypes in multi-environment trials, quantifying genotype, environment, and G x E effects on growth parameters.

Concussion decreases brain signal variability

This study shows that concussion reduces BOLD signal variability in specific brain networks, linking it to symptom severity and cognitive decline.

TailEnrich enables discovery of dysregulated genes through disease sample enrichment testing

TailEnrich identifies dysregulated genes in patient subsets by testing expression distribution tails, outperforming DESeq2 and edgeR in simulated data and uncovering novel genes in Alzheimer's disease.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

Starve, stress, and mate: Activation of the CCAAT-Binding complex overrides sterility of mating-type heterozygous Candida albicans

The paper identifies the CCAAT-binding complex (CBC) as a key regulator that overrides genetic sterility in Candida albicans by integrating environmental stress signals to enable mating.

Quantum Entanglement as a Physical Determinant of Genomic Instability in TP53

The paper explores whether quantum entanglement, measured via von Neumann Entropy, influences TP53 mutation patterns, finding elevated entropy at known mutational hotspots but cautioning about limited validation.