Prokka: rapid prokaryotic genome annotation
Abstract Summary: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent d...
Publications
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2,500 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...
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
Abstract Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allo...
Object recognition from local scale-invariant features
An object recognition system has been developed that uses a new class of local image features. The features are invariant to image scaling, translation, and rotation, and partia...
Regularization Paths for Generalized Linear Models via Coordinate Descent
We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nom...
Normalized cuts and image segmentation
We propose a novel approach for solving the perceptual grouping problem in vision. Rather than focusing on local features and their consistencies in the image data, our approach...
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
Abstract For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure ...
Ten Lectures on Wavelets
Mathematics of Computing -- Miscellaneous.
Regularization Paths for Generalized Linear Models via Coordinate Descent.
We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multinomia...
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood....
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 ...