Affiliation: Stanford University
- MotifCut: regulatory motifs finding with maximum density subgraphsEugene Fratkin
Department of Computer Science, Stanford University, California 94305, USA
Bioinformatics 22:e150-7. 2006....
- A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sitesBrian T Naughton
Department of Biochemistry, Stanford University, CA 94305, USA
Nucleic Acids Res 34:5730-9. 2006..We elucidate the reasons why we expect graph-based methods to perform well on motif data. Our MotifScan algorithm shows greatly improved performance over the prevalent PSSM-based method for the detection of eukaryotic motifs...
- Effect of genetic divergence in identifying ancestral origin using HAPAAAndreas Sundquist
Department of Computer Science, Stanford University, Stanford, California 94305, USA
Genome Res 18:676-82. 2008..Using HAPAA, we explore the limits of ancestry inference in closely related populations...