Publications

Maximum Likelihood from Incomplete Data Via the <i>EM</i> Algorithm

Summary A broadly applicable algorithm for computing maximum likelihood estimates from incomplete data is presented at various levels of generality. Theory showing the monotone ...

STATISTICAL METHODS FOR ASSESSING AGREEMENT BETWEEN TWO METHODS OF CLINICAL MEASUREMENT

In clinical measurement comparison of a new measurement technique with an established one is often needed to see whether they agree sufficiently for the new to replace the old. ...

UCSF Chimera—A visualization system for exploratory research and analysis

Abstract The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic se...

Going deeper with convolutions

We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Sca...

Qualitative Data Analysis: An Expanded Sourcebook

MUSCLE: multiple sequence alignment with high accuracy and high throughput

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting,...

<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...

Coefficient Alpha and the Internal Structure of Tests

A general formula ( α ) of which a special case is the Kuder-Richardson coefficient of equivalence is shown to be the mean of all split-half coefficients resulting from differen...

<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...

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...

Comparison of simple potential functions for simulating liquid water

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for t...