Publications

Scalable molecular dynamics with NAMD

Abstract NAMD is a parallel molecular dynamics code designed for high‐performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high‐end par...

UPARSE: highly accurate OTU sequences from microbial amplicon reads

A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity

Ditching Invading DNA Bacteria and archaea protect themselves from invasive foreign nucleic acids through an RNA-mediated adaptive immune system called CRISPR (clustered regular...

Capitalism, Socialism and Democracy

Introduction. Part I: The Marxian Doctrine. Prologue. I. Marx the Prophet. II. Marx the Sociologist. III. Marx the Economist. IV Marx the Teacher. Part II: Can Capitalism Surviv...

Community structure in social and biological networks

A number of recent studies have focused on the statistical properties of networked systems such as social networks and the Worldwide Web. Researchers have concentrated particula...

UCHIME improves sensitivity and speed of chimera detection

Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

Functional analysis of large gene lists, derived in most cases from emerging high-throughput genomic, proteomic and bioinformatics scanning approaches, is still a challenging an...

Dendritic cells and the control of immunity

PhysioBank, PhysioToolkit, and PhysioNet

Abstract —The newly inaugurated Research Resource for Complex Physiologic Signals, which was created under the auspices of the National Center for Research Resources of the Nati...

Finding and evaluating community structure in networks

We propose and study a set of algorithms for discovering community structure in networks-natural divisions of network nodes into densely connected subgroups. Our algorithms all ...

Reflecting on reflexive thematic analysis

Since initially writing on thematic analysis in 2006, the popularity of the method we outlined has exploded, the variety of TA approaches have expanded, and, not least, our thin...

Social Cognitive Theory: An Agentic Perspective

▪ Abstract The capacity to exercise control over the nature and quality of one's life is the essence of humanness. Human agency is characterized by a number of core features tha...