mixed model

Prediction of Accurate Binding Modes using Combination of classical and accelerated Molecular dynamics and Free Energy Perturbation Calculations: An Application to Toxicity Studies

The paper predicts accurate binding modes of PFCAs in PPARγ using combined docking, MD simulations, and FEP+ to improve toxicity studies.

Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index

This paper introduces a mixed integer program to find optimal search schemes for approximate string matching using bidirectional FM-index, significantly improving speed over previous methods.

Maize GO Annotation - Methods, Evaluation, and Review (maize-GAMER)

This paper provides a high-coverage, high-confidence GO annotation for maize genes, outperforming existing annotations in accuracy using a mixed-method pipeline.

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

The paper introduces lme4qtl, an R package extending lme4 to enable flexible covariance structures and parameter constraints for QTL mapping in genetic studies of related individuals.

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

LiMMBo enables efficient joint genetic analysis of high-dimensional phenotypes using linear mixed models and bootstrapping, showing power advantages and scalability.

Intraclass correlation: improved modeling approaches and applications for neuroimaging

The paper improves ICC modeling for neuroimaging by introducing four new approaches and recommends their use based on data characteristics.

Accuracies Of Univariate And Multivariate Genomic Prediction Models In African Cassava.

This study compares univariate and multivariate genomic prediction models for cassava traits, finding that multivariate models improve prediction accuracy in both single and multi-environment evaluations.

Modelling isoscapes using mixed models

This paper introduces mixed models for modeling isoscapes, showing higher predictive power than alternative methods for hydrogen isotope composition in European precipitation.

Dissecting HIV Virulence: Heritability Of Setpoint Viral Load, CD4+ T Cell Decline And Per-Parasite Pathogenicity

The paper estimates heritability of HIV virulence traits using donor-recipient regression and phylogenetic models, finding moderate heritability for CD4+ T cell decline and per-parasite pathogenicity.

Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes cis-Regulatory Elements

The paper models how DNA methylation affects CRX binding to regulatory elements of RHO and PDE6B genes in human ocular tissues, showing inverse correlations and structural changes in DNA grooves.

The Influence Of Study Characteristics On Coordinate-Based fMRI Meta-Analyses

This study evaluates how different factors affect the reliability and balance of false and true positives in coordinate-based fMRI meta-analyses.

Mindboggling morphometry of human brains

Open source Mindboggle pipeline extracts cortical folds, sulci and fundi and computes diverse shape measures, yielding normative morphometry for 101 manually labeled healthy human brains.

Factors contributing to the accumulation of reproductive isolation: a mixed model approach

This paper introduces phylogenetic linear mixed models to analyze factors contributing to reproductive isolation, demonstrating their flexibility and ability to test complex hypotheses.

Mixed Model Association with Family-Biased Case-Control Ascertainment

This paper introduces LT-Fam, a family-based association statistic that is robust to family-biased case-control ascertainment, showing improved calibration and power compared to existing methods.

MTG2: An efficient algorithm for multivariate linear mixed model analysis based on genomic information

The paper introduces MTG2, an efficient algorithm for multivariate linear mixed model analysis using genomic data, showing speeds up to 1000 times faster than standard REML software.

A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data

The paper introduces MACAU, a binomial mixed model for analyzing bisulfite sequencing data, showing improved power to detect differentially methylated sites in structured populations.

Two variance component model improves genetic prediction in family data sets

This paper introduces a two variance component model that improves genetic prediction in family data by jointly modeling IBS sharing and pedigree structure, achieving higher prediction accuracy and correcting inflated test statistics.

Mixed Models for Meta-Analysis and Sequencing

The paper introduces a mixed model method for meta-analysis that nearly matches the power of pooled studies without sharing individual-level data, with potential gains in effective sample size for height and BMI studies.

Efficient Bayesian mixed model analysis increases association power in large cohorts

BOLT-LMM improves genetic association power in large cohorts by using a Bayesian mixture prior to model non-infinitesimal genetic architectures more realistically.