Publications

<i>Ab initio</i>molecular dynamics for liquid metals

We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-d...

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Abstract Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics a...

XGBoost

Tree boosting is a highly effective and widely used machine learning method.\nIn this paper, we describe a scalable end-to-end tree boosting system called\nXGBoost, which is use...

Three Approaches to Qualitative Content Analysis

Content analysis is a widely used qualitative research technique. Rather than being a single method, current applications of content analysis show three distinct approaches: con...

CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP

The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, w...

Highly accurate protein structure prediction with AlphaFold

Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort ...

limma powers differential expression analyses for RNA-sequencing and microarray studies

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. limma is an R/Bioconductor software package that provides an integrated solution ...

Support-vector networks

Multiple regression: testing and interpreting interactions

Introduction Interactions between Continuous Predictors in Multiple Regression The Effects of Predictor Scaling on Coefficients of Regression Equations Testing and Probing Three...

Preferred Reporting Items for Systematic Reviews and Meta-Analyses: The PRISMA Statement

Systematic reviews and meta-analyses have become increasinglyimportant in health care. Clinicians readthem to keep up to date with their field (1, 2), and they areoften used as ...

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation o...

Adaptation in Natural and Artificial Systems

Genetic algorithms are playing an increasingly important role in studies of complex adaptive systems, ranging from adaptive agents in economic theory to the use of machine learn...