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- Timothy L. Bailey, Mikael Bodén, +6 authors William Stafford Noble
- Nucleic Acids Research
- 2009
The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains. The popular… (More)
- Charles E. Grant, Timothy L. Bailey, William Stafford Noble
- Bioinformatics
- 2011
UNLABELLED
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 have… (More)
- Ewan Birney, John A. Stamatoyannopoulos, +308 authors Pieter J de Jong
- Nature
- 2007
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data… (More)
- Christina S. Leslie, Eleazar Eskin, William Stafford Noble
- Pacific Symposium on Biocomputing
- 2002
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 kernel is… (More)
- Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey, William Stafford Noble
- Genome Biology
- 2006
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 answer this… (More)
- Martin Tompa, Nan Li, +22 authors Zhou Zhu
- Nature Biotechnology
- 2005
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 purpose of the… (More)
- Li Liao, William Stafford Noble
- Journal of Computational Biology
- 2003
One key element in understanding the molecular machinery of the cell is to understand the structure and function of each protein encoded in the genome. A very successful means of inferring the… (More)
- Lukas Käll, Jesse D. Canterbury, Jason Weston, William Stafford Noble, Michael J. MacCoss
- Nature Methods
- 2007
Shotgun proteomics uses liquid chromatography–tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of… (More)
- Gert R. G. Lanckriet, Tijl De Bie, Nello Cristianini, Michael I. Jordan, William Stafford Noble
- Bioinformatics
- 2004
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 of experimental… (More)
- Zhijun Duan, Mirela S Andronescu, +7 authors William Stafford Noble
- Nature
- 2010
Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes. Interphase… (More)