Publications

Molecular cloning : a laboratory manual

Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, ...

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individu...

Fast and accurate short read alignment with Burrows–Wheeler transform

Abstract Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A...

Highly accurate protein structure prediction with AlphaFold

Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort ...

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...

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB...

KEGG: Kyoto Encyclopedia of Genes and Genomes

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional informatio...

QIIME allows analysis of high-throughput community sequencing data

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

fastp: an ultra-fast all-in-one FASTQ preprocessor

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for e...

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

HTSeq—a Python framework to work with high-throughput sequencing data

Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from stand...