Publications

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...

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,...

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existi...

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Abstract We present the latest version of the Molecular Evolutionary Genetics Analysis (M ega ) software, which contains many sophisticated methods and tools for phylogenomics a...

Optimization by Simulated Annealing

There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and mul...

<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...

Gene Ontology: tool for the unification of biology

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 ...

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools

CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system...

Applied logistic regression

From the reviews of the First Edition. An interesting, useful, and well-written book on logistic regression models... Hosmer and Lemeshow have used very little mathematics, have...

Fully convolutional networks for semantic segmentation

Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, ex...

Emergence of Scaling in Random Networks

Systems as diverse as genetic networks or the World Wide Web are best described as networks with complex topology. A common property of many large networks is that the vertex co...