As of Fall 2011, Dr. Smith will be on leave and the lab will not be accepting students.
We use bioinformatic methods to compare the structure of genes, genomes, and explore the role of genes in social behavior. We are also interested in using molecular tools to study the biodiversity of the San Francisco Bay Area and beyond. Specific projects include:
1) Developing social insects (ants and bees) as a model system to study the mechanism of genes implicated in human neurological disease. Our current focus is on the ~30 genes implicated in the hemizygous deletion on human chromosome 7 that results in William's Bueren Syndrome. However, our approach and tools will be applicable to other behavioral disorders including autism and schizophrenia. We are recently completed several ant genomes to meet this goal and are developing RNAi and other molecular tools to study these genes. We are also investigating the role(s) or DNA methylation and serotonin metabolism in social insect behavior.
2) Studying the role of RNA structures in dicistronic genes. Most eukaryote protein coding genes have only one protein encoded, but dicistronic genes have two. We are using comparative genomics of 12 fruitfly species to find candidate RNA structures that regulate these special genes and then test our predictions in live cells.
3) Biodiversity of San Francisco. How many species live in San Francisco? Are we gaining or losing species? Does habitat restoration actually help promote species diversity? We are using DNA barcoding to catalog the biodiversity of San Francisco starting on the green rooftop of the California Academy of Sciences.
24. Suen G, et al. (Smith CD 46th of 49 authors, group leader). The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle. PLoS Genetics 2011, February 11 7(2):e1002007.
23. Smith CD et al. The Draft Genome of the Globally Widespread and Invasive Argentine ant (Linepithema humile). PNAS 2011, January 31; doi/10.1073/pnas.1008617108.
22. Smith CR & Smith CD et al. A draft genome of the red harvester ant, Pogonomyrmex barbatus: a model for reproductive division of labor and social complexity. PNAS 2011, January 31; doi/10.1073/pnas.1007901108.
21. Sharakhova MV, George P, Brusentsova IV, Leman SC, Bailey JA, Smith CD, Sharakhov IV. Genome mapping and characterization of the Anopheles gambiae heterochromatin. BMC Genomics, 2010; Aug 4; 11:459.
20. Xia A, Sharakhova MV, Lehman SC, Tu Z, Bailey JA, Smith CD, and Sharakhov IV. Genome Landscape and Evolutionary Plasticity of Chromosomes in Malaria Mosquitoes. PLoSONE. 2010; May; 5(5):e10592, 1-13.
19. The Genomics Education Partnership. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions" CBE-LSE. 2010; Spring; (9)55-69.
18. Nasonia Genome Consortium** (Smith CD 15th of 209 authors, 2 student authors). Insights from Three Genomes of Nasonia: Insect Natural Enemies and Emerging Genetic Model. Science. 2009; Jan 15; 327(343): 343-348.
17. Smith CD, Smith CR, Mueller U, Gadau J. Ant genomics: strength and diversity in numbers. Molecular Ecology. 2009; Nov 30; 19(1):31-35.
16. The Genomics Education Partnership (Smith CD 26th of 38 authors). Using Genomics to Bring Undergraduates into the Research Community. Science. 2008, Oct 31; 322(5902):684-685.
15. Drosophilid Comparative Genomics Consortium. Twelve flies: Evolution of genes and genomes in the genus Drosophila. Nature. 2007; Nov 8; 450(7167):25-40
14. Smith CD, Shu S, Mungall CJ, Karpen GH. The Release 5.1 Annotation of D. melanogaster heterochromatin. Science. 2007; June 15:316(5831):1586-91.
13. Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers GW, Karpen GH. Improved transposable element identification and repeat masking in Dipterans. Gene. 2007; Mar 1;389(1):1-9.
12. Mark Yandell, Chris J. Mungall, Christopher Smith, Simon Prochnik, Joshua Kaminker, George Hartzell, Suzanna Lewis & Gerald M. Rubin. Large-Scale Trends in the Evolution of Gene Structures within 11 Animal Genomes. PLoS Comput Biol. 2006; Mar;2(3):e15.
11. Smith CD, Smith DL, DeRisi JL, Blackburn EH. Telomeric Protein Distributions and Remodeling Through the Cell Cycle in Saccharomyces cerevisiae. Mol Biol Cell. 2003; 14(2):556-70.
10. Smith CD, Hoskins RA, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen GH. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biology. 2002; 3(12):RESEARCH0085-5.
9. Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology. 2002; 3(12):RESEARCH0083-3.
8. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, Richter J, Wiel C, Bayraktaroglir L, Birney E, Crosby MA, Kaminker JS, Matthews BB, Prochnik SE, Smith CD, Tupy JL, Rubin GM, Misra S, Mungall CJ, Clamp ME. Apollo: a sequence annotation editor. Genome Biology 2002, 3(12):RESEARCH0082-2
7. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, Smith CD, Smith E, Tupy JL, Wiel C, Rubin GM, Lewis SE. An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biol 2002; 3(12):RESEARCH0081-1.
6. Blackburn, E.H., S. Chan, J. Chang, T.B. Fulton, A. Krauskopf, M.J. McEachern, J. Prescott, J. Roy, C.D. Smith, and H.E. Wang. Molecular manifestations and molecular determinants of telomere capping. Cold Spring Harbor Symposia on Quantitative Biology: Biological Responses to DNA Damage 2000 Vol. LXV 253-263.
5. R.L. Chevalier, C.D. Smith, J. Wolstenholme, S. Krajewski, and J.C. Reed. Chronic ureteral obstruction in the rat suppresses renal tubular BCL-2 and stimulates apoptosis. Exp Nephrol 2000, Mar-Apr;8(2):115-22.
4. C.D. Smith and E.H. Blackburn. Detrimental cellular phenotypes are caused by telomere deregulation, rather than elongation. Journal of Cell Biology 1999;145(2): 203-214.
3. R.L. Chevalier, K.H. Chung, C.D. Smith, M. Ficenec, and R.A. Gomez. Renal apoptosis and clusterin following ureteral obstruction: The role of maturation. Journal of Urology 1996, 156:1474-9.
2. C.D. Smith, L.A. Baglia, S.C. Curristin, and A. Ruddell. The VBP and a1/EBP leucine zipper factors bind overlapping subsets of avian retroviral LTR CCAAT/enhancer elements. Journal of Virology 1994, 68:6232-42.
1. W.J. Bowers, J.F. Petrosino, C.D. Smith, and A. Ruddell. Transcription regulation of ALV bursal lymphomagenesis. 1993, Journal of the International Association of Comparative Research on Leukemia and Related Diseases, Montreal Canada.