Topic 123

statistical methods method data propose proposed bioinformatics problem simulation linear regression framework real power false often algorithm when approach performance estimate variables application null sample set datasets confounding analysis simulated test approaches studies estimation procedure dimensional introduce inference simulations issues tests apply variance estimates illustrate paper standard existing where based multiple correlation covariance interest can use neuroimaging such latent common powerful examples each large detecting gaussian testing number address multivariate it associations error sets account using noise available demonstrate analyzing feature empirical many used widely model sparse because problems algorithms hypothesis variable do applied neuroscience bias analyses parameters modeling scenarios

173 items. Top items listed below.

Using a supervised principal components analysis for variable selection in high-dimensional datasets reduces false discovery rates 123 83 4

Controlling for Human Population Stratification in Rare Variant Association Studies 145 123 19 4

Permutation tests for hypothesis testing with animal social data: problems and potential solutions 123 83 4

Probabilistic index models for testing differential expression in single cell RNA sequencing data 43 4

Power analysis of transcriptome-wide association study: implications for practical protocol choice 145 123 19 4

A deep learning framework for characterization of genotype data 26 4

Sparse latent factor regression models for genome-wide and epigenome-wide association studies 123 19 4

Testing monotonic trends among multiple group means against a composite null 123 4

Robust point-process Granger causality analysis in presence of exogenous temporal modulations and trial-by-trial variability in spike trains. 123 38 2

Differential Transcript Usage Analysis Incorporating Quantification Uncertainty Via Compositional Measurement Error Regression Modeling 175 123 83 4

Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring 43 4

Finding associations in a heterogeneous setting: Statistical test for aberration enrichment 123 112 4

Analyzing matched sets of microbiome data using the LDM and PERMANOVA 123 4

On set-based association tests: insights from a regression using summary statistics 123 19 4

On stability of Canonical Correlation Analysis and Partial Least Squares with application to brain-behavior associations 123 4 2

A Rarefaction-Based Extension of the LDM for Testing Presence-Absence Associations in the Microbiome 123 4

Incorporating Prior Knowledge into Regularized Regression 123 4

A Fast and Scalable Framework for Large-scale and Ultrahigh-dimensional Sparse Regression with Application to the UK Biobank 123 19 4

Multi-tissue transcriptome-wide association studies 19 4

Testing for Dependence on Tree Structures 123 83 4

A rigorous method for integrating multiple heterogeneous databases in genetic studies 123 4

Bayes Estimate of Primary Threshold in Cluster-wise fMRI Inferences 123 83 59 4 2

Heterogeneous Mediation Analysis for Causal Inference 123 83 4

A simple permutation-based test of intermodal correspondence 123 59 22 2

Subpopulation identification for single-cell RNA-sequencing data using functional data analysis 43 4

To pool or not to pool: Can we ignore cross-trial variability in FMRI? 123 83 59 38 4 2

Inferring Causal Direction Between Two Traits in the Presence of Horizontal Pleiotropy with GWAS Summary Data 123 83 19 4

A classification-based approach to estimate the number of resting fMRI dynamic functional connectivity states 123 22 4 2

Analysis of variance when both input and output sets are high-dimensional 123 4

A Sparse Additive Model for High-Dimensional Interactions with an Exposure Variable 123 4

Application of the hierarchical bootstrap to multi-level data in neuroscience 123 83 4 2

A latent variable approach to decoding neural population activity 123 38 4 2

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics 19 4

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

A bivariate zero-inflated negative binomial model for identifying underlying dependence with application to single cell RNA sequencing data 123 43 4

Improving the sensitivity of cluster-based statistics for fMRI data 123 4

Statistical analysis of no observed effect concentrations or levels in eco-toxicological assays with overdispersed count endpoints 123 83 4

A convex optimization framework for gene-level tissue network estimation with missing data and its application in understanding disease architecture 123 19 4

Joint estimation of neuralsources and their functional connections from MEG data 123 59 38 4 2

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data 123 83 38 4 2

Hyperbolic geometry of gene expression 123 43 4

Naught all zeros in sequence count data are the same 123 4

Estimation of Non-null SNP Effect Size Distributions Enables the Detection of Enriched Genes Underlying Complex Traits 19 4

Robust Estimation of Noise for Electromagnetic Brain Imaging with the Champagne Algorithm 123 59 4 2

graphsim: An R package for simulating gene expression data from graph structures of biological pathways 13 4

Detection of the changes in dynamical structures insynchronous neural oscillations from a viewpoint of probabilistic inference 123 38 2

A Model Selection Approach to Hierarchical Shape Clustering with an Application to Cell Shapes 123 4

Gene Expression of Functionally-Related Genes Coevolves Across Fungal Species: Detecting Coevolution of Gene Expression Using Phylogenetic Comparative Methods 123 4

ComBat-Seq: batch effect adjustment for RNA-Seq count data 123 43 4

Longitudinal ComBat: A Method for Harmonizing Longitudinal Multi-scanner Imaging Data 123 59 4 2

A Bayesian inference tool for identifying artifactual calls from differential transcript abundance analyses 83 4

A Generalized Robust Allele-based Genetic Association Test 123 19 4

Confound modelling in UK Biobank brain imaging 123 59 19 4 2

An empirical comparison of univariate versus multivariate methods for the analysis of brain-behavior mapping 123 59 4 2

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity 19 13 4

Leveraging expression from multiple tissues using sparse canonical correlation analysis (sCCA) and aggregate tests improves the power of transcriptome-wide association studies (TWAS) 19 4

A novel single-cell based method for breast cancer prognosis 43 26 4

Large-Scale Sparse Regression for Multiple Responses with Applications to UK Biobank 123 13 4

Model-based Feature Selection and Clustering of RNA-seq Data for Unsupervised Subtype Discovery 123 4

Combining multiple functional connectivity methods to improve causal inferences 123 22 2

Statistical Integration of Multiple Omics Datasets Using GO2PLS 123 112 4

A genome-wide case-only test for the detection of digenic inheritance in human exomes 145 19 4

Understanding interactions between risk factors, and assessing the utility of the additive and multiplicative models through simulations 182 123 112 38 4

Two-Step Mixed Model Approach to Analyzing Differential Alternative RNA Splicing 43 4

A statistical nonparametric method for identifying consistently important features across samples 147 13 4

Wavelet Screening: a novel approach to analysing GWAS data 19 4

Extracting Brain Disease-Related Connectome Subgraphs by Adaptive Dense Subgraph Discovery 123 59 4 2

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 123 112 4

Common datastream permutations of animal social network data are not appropriate for hypothesis testing using regression models 123 30 4

Microbial trend analysis for common dynamic trend, group comparison and classification in longitudinal microbiome study 123 4

Tensor decomposition based unsupervised feature extraction in big data analytics applied to prostate cancer multiomics data 123 4

Shrinkage improves estimation of microbial associations under different normalization methods 123 4

Unified methods for feature selection in large-scale genomics data with censored survival outcomes 123 112 4

A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes 7 4

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets 26 4

New gene association measures by joint network embedding of multiple gene expression datasets 43 4

Partitioning gene-based variance of complex traits by gene score regression 19 13 4

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment 83 4

Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics. 19 4

Efficient approaches for large scale GWAS studies with genotype uncertainty 145 83 4

Opportunities and limits of combining microbiome and genome data for complex trait prediction 19 4

Bootstrap aggregating improves the generalizability of Connectome Predictive Modelling 123 7 4 2

Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits 19 4

Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays 4 2

Valid and powerful group statistics for decoding accuracy: Information Prevalence Inference using the i-th order statistic (i-test) 123 83 59 2

Boundary-Forest Clustering: Large-Scale Consensus Clustering of Biological Sequences 145 4

Controlling for effects of confounding variables on machine learning predictions 123 26 4 2

A quick and easy way to estimate entropy and mutual information for neuroscience 123 38 4 2

A powerful subset-based gene-set analysis method identifies novel associations and improves interpretation in UK Biobank 19 4

Scalable and accurate automated method for neuronal ensemble detection in spiking neural networks 123 50 4 2

Removal of Scanner Effects in Covariance Improves Multivariate Pattern Analysis in Neuroimaging Data 123 59 4 2

On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data 43 4

Identifying signal and noise structure in neuralpopulation activity with Gaussian process factormodels 123 100 2

DNN-Assisted Statistical Analysis of a Model of Local Cortical Circuits 38 26 4 2

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement 43 26 4

Nonparametric Anomaly Detection on Time Series of Graphs 123 59 4 2

A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics 123 13 4

Compositional knockoff filter for high-dimensional regression analysis of microbiome data 123 4

Graph of graphs analysis for multiplexed data with application to imaging mass cytometry 26 4