Publications

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

A Simple Sequentially Rejective Multiple Test Procedure

This paper presents a simple and widely ap- plicable multiple test procedure of the sequentially rejective type, i.e. hypotheses are rejected one at a tine until no further reje...

<i>Ab initio</i>molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-tem...

Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation

Generalized gradient approximations (GGA’s) seek to improve upon the accuracy of the local-spin-density (LSD) approximation in electronic-structure calculations. Perdew and Wang...

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

Search and clustering orders of magnitude faster than BLAST

Abstract Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. Results: UBLAS...

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

MODELTEST: testing the model of DNA substitution.

Abstract SUMMARY: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, includin...

The Evolution of Cooperation

Cooperation in organisms, whether bacteria or primates, has been a difficulty for evolutionary theory since Darwin. On the assumption that interactions between pairs of individu...

When to use and how to report the results of PLS-SEM

Purpose The purpose of this paper is to provide a comprehensive, yet concise, overview of the considerations and metrics required for partial least squares structural equation m...

Very high resolution interpolated climate surfaces for global land areas

We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The c...