A motif is a short DNA or protein sequence that contributes to the biological function of the
sequence in which it resides. Over the past several decades, many computational methods …

Shotgun proteomics uses liquid chromatography–tandem mass spectrometry to identify
proteins in complex biological samples. We describe an algorithm, called Percolator, for …

The field of machine learning, which aims to develop computer algorithms that improve with
experience, holds promise to enable computers to assist humans in the analysis of large, …

The prediction of regulatory elements is a problem where computational methods offer great
hope. Over the past few years, numerous tools have become available for this task. The …

Motivation: During the past decade, the new focus on genomics has highlighted a particular
challenge: to integrate the different views of the genome that are provided by various types …

A common question within the context of de novo motif discovery is whether a newly discovered,
putative motif resembles any previously discovered motif in an existing database. To …

We introduce a new sequence-similarity kernel, the spectrum kernel, for use with support
vector machines (SVMs) in a discriminative approach to the protein classification problem. Our …

Motivation: Despite advances in high-throughput methods for discovering protein–protein
interactions, the interaction networks of even well-studied model organisms are sketchy at best…

Automated methods for assigning peptides to observed tandem mass spectra typically return
a list of peptide−spectrum matches, ranked according to an arbitrary score. In this article, …

We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin
data from multiple experiments, including positions of histone modifications, transcription-factor …