mixed model

The land-use dynamics of potato agrobiodiversity in the highlands of central Peru: a case study of spatial-temporal management across farming landscapes

The paper examines land-use dynamics and conservation of potato diversity in two Peruvian highland regions, finding that landrace diversity is unevenly distributed and influenced by socio-economic factors.

Ghost QTL and hotspots in experimental crosses - novel solution by mixed model with nonzero mean

The paper addresses ghost QTL and hotspots in QTL mapping by introducing an extended mixed model with nonzero mean random effects to improve detection accuracy.

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

The paper uses simulations to show that the inactive ternary complex of AC5, Golf, and Gi enables synergistic cAMP production in response to coincident neuromodulatory signals.

SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble

SAME-clustering improves single-cell RNA-seq clustering by combining multiple methods to produce a more accurate and diverse ensemble solution.

A Bayesian Non-parametric Mixed-Effects Model of MicrobialPhenotypes

This paper introduces a Bayesian non-parametric model to analyze microbial growth data, accounting for random effects and improving accuracy in estimating biological effects.

The Prevalence and Impact of Model Violations in Phylogenetics

Permutation-based maximal matched-pairs symmetry tests show 40.8% of 3,572 partitions from 35 published phylogenetic datasets reject stationary, reversible, homogeneous evolution, frequently altering inferred tree topologies.

OSCA: a tool for omic-data-based complex trait analysis

OSCA provides a tool for omic-data-based complex trait analysis using the MOMENT method, showing improved robustness and lower false positive rates in simulations.

Understanding the molecular mechanism of umami recognition by T1R1-T1R3 using molecular dynamics simulations

This study uses molecular dynamics simulations to investigate how different umami ligands affect the structural dynamics of the T1R1-T1R3 taste receptor, identifying key residues and binding sites involved in ligand recognition.

Mendelian Randomization Analysis Using Mixture Models (MRMix) for Genetic Effect-Size-Distribution Leads to Robust Estimation of Causal Effects

The paper introduces MRMix, a mixture model-based method for Mendelian randomization that provides robust causal effect estimates, showing improved performance in simulations and identifying several genetic risk factors for diseases.

ETFL: A formulation for flux balance models accounting for expression, thermodynamics, and resource allocation constraints

The paper introduces ETFL, a new metabolic model formulation that integrates expression, thermodynamics, and resource allocation constraints, showing improved accuracy over traditional FBA in simulating proteome-limited growth.

Alarm tones, music and their elements: A mixed methods analysis of reported waking sounds for the prevention of sleep inertia.

This study investigates how melodic elements of waking sounds affect sleep inertia using self-reported data from 50 participants.

Consolidation alters motor sequence-specific distributed representations

In human fMRI, consolidated finger sequences are more discriminable than new ones in sensorimotor putamen, premotor and prefrontal cortices, but less so in hippocampus and caudate.

Structural basis of internal peptide recognition by PDZ domains using molecular dynamics simulations

The paper uses molecular dynamics simulations to study how PDZ domains recognize internal peptides and how adjacent domains modulate this recognition.

Bcl-xL dynamics and cancer-associated mutations under the lens of protein structure networks and biomolecular simulations

The paper investigates Bcl-xL's allosteric communication between binding sites and evaluates how cancer mutations affect this mechanism using molecular dynamics and protein structure networks.

Determinants of Minimum Acceptable Diet among 6-23 Months Age Children in Ethiopia: A Multilevel Analysis of The Ethiopian Demographic Health Survey

Only 6.1% of Ethiopian 6-23-month-olds received a minimum acceptable diet (EDHS 2016); child age, paternal education, maternal employment, water access, media exposure and region were associated with it.

Fast and flexible linear mixed models for genome-wide genetics

This paper introduces Grid-LMM, a fast and flexible linear mixed model framework for genome-wide genetics, improving computational efficiency and accuracy in genetic association analyses.

Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole genome sequencing studies

The paper introduces SMMAT, a variant-set mixed model association test for continuous and binary traits in large-scale WGS studies, showing it controls type I error rates and applies to population structured and related samples.

Study of the binding mechanisms between palytoxin and its aptamer by docking and molecular simulation

This paper models and simulates the interaction between palytoxin and its aptamer, showing strong hydrogen-bonding and electrostatic interactions in the DNA groove.

Movement responses to environment: fast inference of variation among southern elephant seals with a mixed effects model

The paper uses a mixed effects model to rapidly infer individual variation in southern elephant seal movement responses to environmental factors.

A linear mixed model approach to study multivariate gene-environment interactions

This paper introduces StructLMM, a linear mixed model for analyzing multivariate gene-environment interactions, demonstrating its effectiveness in detecting GxE signals in BMI and eQTL data.

Optimizing the identification of causal variants across varying genetic architectures in crops

This study evaluates statistical methods for GWAS in crops with varying genetic architectures, finding that different approaches are optimal for different trait complexities.

Substrate binding and specificity appear as major forces in the functional diversification of eqolisins.

The paper identifies substrate binding and specificity as key drivers of functional diversification in eqolisins through molecular dynamics simulations and phylogenetic analysis.

The design, analysis and application of mouse clinical trials in oncology drug development

This study provides guidelines for designing, analyzing, and applying mouse clinical trials in oncology, showing that LMMs and frailty models improve statistical power and biomarker discovery.

Meta-analysis of genome-wide association studies for body fat distribution in 694,649 individuals of European ancestry

Meta-analysis of waist-to-hip ratio adjusted for BMI in 694,649 European-ancestry individuals identifies 463 signals in 346 loci, roughly one-third sexually dimorphic and mostly stronger in women.

Genome-Wide Control of Population Structure and Relatedness in Genetic Association Studies via Linear Mixed Models with Orthogonally Partitioned Structure

This paper introduces LMM-OPS, a linear mixed model method that improves calibration and power in genetic association studies with ancestry heterogeneity, demonstrating its effectiveness in a GWAS of white blood cell count in Hispanic/Latino women.

Comparative Network Reconstruction using Mixed Integer Programming

This paper introduces a computational method to reconstruct signaling networks from incomplete perturbation data and identify differences between networks in sensitive and resistant cells.

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies

This paper introduces a new method for detecting marginal epistasis in case-control studies and demonstrates its improved power and type I error control compared to existing approaches.

Software update: Moving the R package sommer to multivariate mixed models for genome-assisted prediction

The sommer R package gains a multivariate solver: several random effects at once, with covariance structures set per effect and between traits, for genome-assisted breeding prediction.

An ODE-based mixed modelling approach for B- and T-cell dynamics induced by Varicella-Zoster Virus vaccines in adults shows higher T-cell proliferation with Shingrix compared to Varilrix

This paper uses ODE-based mixed models to analyze T-cell and B-cell dynamics from a vaccine trial, finding Shingrix induces greater T-cell proliferation than Varilrix.

A fast mrMLM algorithm for multi-locus genome-wide association studies

FASTmrMLM swaps mrMLM's numerical gradients and Hessians for analytic ones, cutting runtime by more than 50% while matching or slightly beating its simulated power and accuracy.