Tregwiki:People working on transcription regulation
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- 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.
