- We worked on collaborative projects on identification of motifs of RNA binding proteins and their target genes with Dr. M. Gorospe of LCMB. In the last fiscal year, we published 3 peer-reviewed papers in the projects (Andersen JB et al. 2009;Mazan-Mamczarz K et al. 2009;Rudi et al. submitted). We also worked on more RNA-binding proteins in this regard, including HuD, GR, and Nucleolin. - We worked on collaborative projects of transcriptomic studies on aging in flies with Dr. S. Zou of LEG. In particular, we implemented new algorithms for identifying conserved and divergent pathways between normal and longevity mutant. We are currently drafting manuscripts to report the findings by the studies. - We worked on collaborative projects on gene regulatory pathways controlling stem cell pluripotency with Dr. Ken Boheler of LCS and on pathways related to hypoxia with Dr. Rui-Ping Xiao of LCS. In addition, we completed a collaborative project of proteomics studies on osteoarthritis with Dr. S Ling of CRB;the first paper has been published (Ling et al. 2009), and the second paper is under progress. - We have developed a new algorithm for cross-species identification of evolutionarily conserved and divergent transcriptional programs by two-stage matrix decomposition. The paper has been published (Li &Zhan, 2009). We have also developed a new algorithm for deciphering gene regulatory network based on sparse matrix analysis, and we are in progress of drafting a manuscript to report the new method. Moreover, we have been working on new algorithms for comparative omics studies across multiple species and tissues by integrating data from heterogeneous sources,and on systems biology methods for studying regulatory pathways.
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