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.