- 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.

Agency
National Institute of Health (NIH)
Institute
National Institute on Aging (NIA)
Type
Scientific Cores Intramural Research (ZIC)
Project #
1ZICAG000619-02
Application #
7969901
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2009
Total Cost
$1,438,740
Indirect Cost
Name
National Institute on Aging
Department
Type
DUNS #
City
State
Country
Zip Code
Swistowska, Anna Maria; da Cruz, Alexandre Bettencourt; Han, Yi et al. (2010) Stage-specific role for shh in dopaminergic differentiation of human embryonic stem cells induced by stromal cells. Stem Cells Dev 19:71-82
Yang, Ruiqing; Zhan, Ming; Nalabothula, Narasimha Rao et al. (2010) Functional significance for a heterogenous ribonucleoprotein A18 signature RNA motif in the 3'-untranslated region of ataxia telangiectasia mutated and Rad3-related (ATR) transcript. J Biol Chem 285:8887-93
Chang, Na; Yi, Jie; Guo, Gaier et al. (2010) HuR uses AUF1 as a cofactor to promote p16INK4 mRNA decay. Mol Cell Biol 30:3875-86
Wang, Chen; Xuan, Jianhua; Li, Huai et al. (2010) Knowledge-guided gene ranking by coordinative component analysis. BMC Bioinformatics 11:162
Kuwano, Yuki; Pullmann Jr, Rudolf; Marasa, Bernard S et al. (2010) NF90 selectively represses the translation of target mRNAs bearing an AU-rich signature motif. Nucleic Acids Res 38:225-38
Ling, S M; Patel, D D; Garnero, P et al. (2009) Serum protein signatures detect early radiographic osteoarthritis. Osteoarthritis Cartilage 17:43-8
Li, Huai; Sun, Yu; Zhan, Ming (2009) Exploring pathways from gene co-expression to network dynamics. Methods Mol Biol 541:249-67
Han, Yi; Miller, Aaron; Mangada, Julie et al. (2009) Identification by automated screening of a small molecule that selectively eliminates neural stem cells derived from hESCs but not dopamine neurons. PLoS One 4:e7155
Mazan-Mamczarz, Krystyna; Kuwano, Yuki; Zhan, Ming et al. (2009) Identification of a signature motif in target mRNAs of RNA-binding protein AUF1. Nucleic Acids Res 37:204-14
Zhang, Bai; Li, Huai; Riggins, Rebecca B et al. (2009) Differential dependency network analysis to identify condition-specific topological changes in biological networks. Bioinformatics 25:526-32

Showing the most recent 10 out of 18 publications