Tregwiki:People working on transcription regulation


 * Vingron group Max Planck, Berlin, Germany:
 * Stefan Roepke: reg database, matrix comparison
 * Szymon Kielbasa: Matrix comparison, motif discovery


 * Michael Q. Zhang group
 * lot's of good software: matrix comparison (matcompare), (DME) motif discovery, chip-chip analysis, regulatory database, etc. etc.


 * Eisen Lab, Berkeley, CA:
 * Daniel Pollard (pubs) is working on evolution of binding sites. He did a benchmark on alignment programs for noncoding seqs and an algorithm that searches matrices in multiple alignments.
 * These people are part of the berkeley drosophila trascnription network project


 * Sladek lab, Riverside, CA;
 * HNF4 research.


 * Fraenkel lab
 * Yeast (science 2003), motif discovery, TAMO, very good software


 * Ian Holmes Lab
 * more like conservation and alignments, not too much about binding sites


 * Miller Lab
 * Whole Genome alignments and search of alignments for conserved sites (blastz, pipmaker, etc)


 * David Haussler Group, UCSC:
 * Gill Bejerano: Ultraconserved Region


 * Jacques van Helden: Motif Discovery with (spaced) words


 * Jim Kadonaga coauthor of about 100 articles about transcription factors and interactions


 * Students:
 * Jonathan Carlson adds another motif discovery algorithm and is confident that it outperforms others.