- We have wrapped up our collaborative project on human-mouse comparative transcriptomic studies of embryonic stem cells with Drs. M. Mattson and M. Rao of LNS. The collaboration has yielded 9 peer-reviewed papers since then, with four papers published during 2007-2008 (Zhan 2007; Sun et al. 2007; Sun et al. 2008, Shin et al. 2007).? ? - We are continuing our collaborative project on identification of motifs of RNA binding proteins with Dr. M. Gorospe of LCMB. The collaboration has yielded 5 peer-reviewed papers since then. In the last fiscal year, we continued working on the identification of motifs of RNA-binding proteins, paying a closer attention on their relationships with microRNA bindings. Three papers were published from this project during the time (Mazan-Mamczarz et al. 2008; van der Brug et al. 2008; Kim et al. 2007). ? ? - We are continuing our collaborative project on transcriptomic studies of aging in flies with Dr. S. Zou of LEG. Two peer-reviewed papers were published during the fiscal year (Norgate et al. 2007; Zhan et al 2008). We have finished drafting the third manuscript at the time, and the forth publication is under progress.? ? - We completed a collaborative project on transcriptomic studies on brain aging with Dr. M. Mattsons group; the paper has been published (Xu et al. 2008).? ? - We completed a collaborative project on proteomics studies on osteoarthritis with Dr. S Ling of CRB; the paper has been published (Ling et al. 2008).? ? - We have been working developing on new algorithms for deciphering gene regulatory networks. In the last fiscal year, we published a manuscript, describing a two-stage matrix decomposition algorithm (Li & Zhan, 2007). Another paper, describing a sparse matrix analysis based algorithms, is under progress? ? - We have been working on developing new algorithms for cross-species identification of evolutionarily conserved and divergent transcriptional programs of cells. In the last fiscal year, two papers, both describing applications of the matrix decomposition algorithm, have been published (Li & Zhan, 2008a) or submitted (Li & Zhan, 2008b). A new algorithm is also under development, which is based on joint or generalized independent component analysis for comparative omics studies across multiple species and tissues, and by integrating data from heterogeneous sources.
