Biology Department photograph montage

Christopher Smith

Faculty in Faculty, Cell and Molecular Biology
Assistant Professor
University of California, San Francisco
At SFSU Since: 
2007
Office: 
Hensill Hall 518
Office Hours: 
Mondays & Wednesdays 10-11am
Office Phone: 
(415) 405-2505
Specialties: 
Bioinformatics, Heterochromatin, Behavioral Genetics, Epigenetics, Biodiversity

 

 

 

Projects

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, the our approach and tools will be applicable to other behavioral disorders including autism and schizophrenia. 

2) Studying the role of RNA structures in regulation of 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.

4) Heterochromatin genomics.  The centromeres and telomeres of our genome are essential for cell division and chromosome stability.  Long dismissed as 'junk DNA' these regions harbor hundreds of genes that play roles in everything from cell division to controlling invading viruses.

 

Publications

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

15.  Drosophilid Comparative Genomics Consortium. Twelve flies: Evolution of genes and genomes in the genus Drosophila. Nature. 2007; Nov 8; 450(7167):25-40

16.      Lopatto, D., … Smith, CD,…Elgin, SCR. Using Genomics to Bring Undergraduates into the Research Community. Science. 2008, Oct 31; 322(5902).