Contact Information
Building 38A, Room 3S314C
8600 Rockville Pike MSC 3830
Bethesda, MD 20894-6075
Tel: 301-594-6889
[email protected]
Dapeng Zhang, PhD
Computational Biology Branch
NCBI, NLM, NIH
Research Interests
I use computational methods and evolutionary principles/strategy to understand molecular pathways of biological systems.
- Defining new biochemical activities and biosystems from comparative sequence and genomic analysis
- Characterization of novel protein families and domains
- Protein function and structure evolution
- Development of bioinformatics methods and strategies
- Functional genomics of physiological and neuroendocrine systems
Education
- 8/2009 - present: Postdoctoral fellow in NCBI, USA
- 9/2004 - 7/2009: Ph.D. in Biology, University of Ottawa, Canada
- 9/2001 - 6/2004: M.Sc. in Biochemistry, Nanjing University, China
- 9/1997 - 7/2001: B.Sc. in Bioengineering, Northeast Normal University, China
Selected Publications
My publications in PubMed.
- Iyer LM, Zhang D , Rogozin IB, Aravind L. Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. Nucleic Acid Research 2011. ( NAR’s Featured Article )
- Zhang D , Iyer LM, Aravind L. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Nucleic Acid Research 2011, 39(11):4532-4552. ( NAR’s Featured Article )
- Zhang D , Aravind L. Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes. Gene 2010, 469(1-2):18-30.
- Anantharaman V, Zhang D , Aravind L. OST-HTH: a novel predicted RNA-binding domain. Biology Direct 2010, 5:13.
- Zhang D , Duarte-Guterman P, Langlois VS, Trudeau VL. Temporal expression and steroidal regulation of piRNA pathway genes (mael, piwi, vasa) during Silurana (Xenopus) tropicalis embryogenesis. Comparative Biochemistry and Physiology - Part C: Toxicology & Pharmacology 2010, 152(2): 202-206.
- Zhao E, Grey CL, Zhang D , Mennigen JA, Basak A, Chang JP, Trudeau VL. Secretoneurin (SN) is a paracrine factor from lactotrophs stimulating gonadotropin release in the goldfish pituitary. The American Journal of Physiology - Regulatory, Integrative and Comparative Physiology 2010, 299(5):R1290-7.
- Langlois VS, Zhang D , Cooke G, Trudeau VL. Evolution of steroid 5-alpha-reductases and comparison of their function with 5-beta-reductase. General and Comparative Endocrinology 2010, 166(3): 489-497.
- Zhang D , Xiong H, Mennigen JA, Popesku JT, Marlatt VL, Martyniuk CJ, Crump K, Xia X, Cossins AR, Trudeau VL. Defining neuroendocrine gene expression patterns associated with reproductive seasonality in fish. PLoS ONE 2009, 4(6): e5816.
- Zhang D , Popesku JT, Martyniuk CJ, Xiong H, Duarte-Guterman P, Yao L, Xia X, Trudeau VL. Profiling neuroendocrine gene expression changes following fadrozole-induced estrogen decline in the female goldfish. Physiological Genomics 2009, 38: 351-361.
- Zhang D . Homology between DUF784, DUF1278 domains and the plant prolamin superfamily typifies evolutionary changes of disulfide bonding patterns. Cell Cycle 2009, 8(20): 3428-3430.
- Zhao E, Zhang D , Basak A, Trudeau VL. New insights into granin-derived peptides: evolution and endocrine roles. General and Comparative Endocrinology 2009, 164(2-3): 161 - 174.
- Zhang D , Xiong H, Shan J, Xia X, Trudeau VL. Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3’-5’ exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch. Biology Direct 2008, 3:48.
- Popesku JT, Martyniuk CJ, Mennigen JA, Xiong H, Zhang D , Cossins AR, Xia X, Trudeau VL. The goldfish (Carassius auratus) as a model for neuroendocrine signaling. Molecular and Cellular Endocrinology 2008, 293(1-2):43-56.
- Zhang D , Trudeau VL. The XS domain of a plant specific SGS3 protein adopts a unique RNA recognition motif (RRM) fold. Cell Cycle 2008, 7(14):2268-2270. ( Evaluated on Faculty of 1000 Biology
) - Xiong H, Zhang D , Martyniuk CJ, Trudeau VL, Xia X. Using generalized Procrustes analysis for normalization of cDNA microarray data. BMC Bioinformatics 2008, 9:25.
- Marlatt VL, Martyniuk CJ, Zhang D , Xiong H, Watt J, Xia X, Moon T, Trudeau VL. Auto-regulation of estrogen receptor subtypes and gene expression profiling of 17beta-estradiol action in the neuroendocrine axis of male goldfish. Molecular and Cellular Endocrinology 2008, 283(1-2):38-48.
- Zhang D , Martyniuk CJ, Trudeau VL. SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation. Bioinformatics 2006, 22 (20):2459-2462.
- Zhang D , Trudeau VL. Integration of membrane and nuclear estrogen receptor signaling. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology 2006, 144 (3):306-315. ( TOP (1-20) hottest article of the journal during 2006-2010 )