Print Version
ANDREI OSTERMAN, PH.D.
Associate Professor
Bioinformatics & Systems Biology
858.646.3100 x5296 (phone)
858.795.5249 (fax)
RESEARCH FOCUS, BIOGRAPHY, STAFF, PUBLICATIONS
Research Focus
The main focus of Dr. Osterman’s research team is on fundamental and applied aspects of the key metabolic subsystems in a variety of species, from bacteria to human. This group uses a Systems Biology approach to reconstruct and explore metabolic and transcriptional regulatory networks. This approach combines comparative genomics and other bioinformatic techniques with biochemical and genetic experiments for pathway, gene and target discovery. Using this approach this group predicted and experimentally verified numerous enzyme families in the metabolism of cofactors, carbohydrates, and amino acids. Recent breakthroughs included prediction and characterization of novel transporters, transcriptional regulators and carbohydrate utilization pathways in a number of model bacterial systems. Applications in the field of infectious disease include identification of novel drug targets and structure-based development of novel antiinfective agents. New directions in cancer research are based on application of metabolic profiling technology for identification of novel diagnostic and therapeutic targets. Other directions of the on-going research include bioinformatics of regulatory proteolysis and applications of structural modeling for exploration of metabolic networks and gene discovery.
Biography
Andrei Osterman is an Associate Professor in the Bioinformatics and Systems Biology Program at the Infectious and Inflammatory Disease Center of the Burnham Institute for Medical Research (since August 2003). He received his doctorate from Moscow State University in 1983, did postdoctoral work UT Southwestern Medical Center, and held the position of the Director and then Vice President of Research at Integrated Genomics in 1999-2003. Dr. Osterman is one of the founders of the Fellowship for Interpretation of Genomes (FIG), a nonprofit research organization that launched the Project to Annotate 1,000 Genomes in 2003. FIG provides the open-source integration of all publicly available genomes and tools for their comparative analysis, annotation, and metabolic reconstruction.
SELECTED RECENT PEER-REVIEWED ARTICLES
1. Gerdes, S. Y., O. V. Kurnasov, K. Shatalin, B. Polanuyer, R. Sloutsky, V. Vonstein, R. Overbeek, and A. L. Osterman (2006). Comparative genomics of NAD biosynthesis in cyanobacteria. J Bacteriol 188:3012-23.
2. Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Y. Obraztsova, K. H. Nealson, and A. L. Osterman. (2006). Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem 281:29872-85
3. Yang, C., Richardson, A. D., Smith, J. W., Osterman, A. (2007). Comparative metabolomics of breast cancer. In " Biocomputing Pac Symp Biocomput. 2007;:181-92.
4. **Dmitry A. Rodionov, Oleg V. Kurnasov, Boguslaw Stec, Yan Wang, Mary F. Roberts, and Andrei L. Osterman (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. . Proc Natl Acad Sci U S A. Mar 13;104(11):4279-84.
5. Igarashi Y, Eroshkin A, Gramatikova S, Gramatikoff K, Zhang Y, Smith JW, Osterman AL, Godzik A. (2007), CutDB: a proteolytic event database. Nucleic Acids Res 35 (Database issue):D546-9.
6. Richardson AD, Yang C, Osterman A, Smith JW. (2007) Central carbon metabolism in the progression of mammary carcinoma. Breast Cancer Res Treat. 2007 Sep 19; [Epub ahead of print]
7. Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2008) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. J Bacteriol. Mar;190(5):1773-82.
8. Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H. (2008) Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism. Structure. Feb;16(2):196-209.
9. Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N. (2008) Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res. Apr;36(6):2047-59.
10. Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL. (2008) Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res. Apr;36(6):2032-46.
11. Igarashi Y, Heureux E, Doctor KS, Talwar P, Gramatikova S, Gramatikoff K,, Zhang Y, Blinov M, Ibragimova SS, Boyd S, Ratnikov B, Cieplak P, Godzik A, Smith JW, Osterman AL, Eroshkin AM. (2008) “PMAP: databases for analyzing proteolytic events and pathways” Nucleic Acids Res. 2008 Oct 8. [Epub ahead of print] PMID: 18842634
12. **Rodionov DA, Hebbeln P, Eudes A, Ter Beek J, Rodionova IA, Erkens GB, Slotboom, DJ, Gelfand MS, Osterman AL, Hanson AD, Eitinger T. (2008) “A Novel Class of Modular Transporters for Vitamins in Prokaryotes.” J Bacteriol. 2008 Oct 17. [Epub ahead of print]
13. **Sorci L, Martynowski D, Rodionov DA, Eyobo Y, Zogaj X, Klose KE, Nikolaev EV, Magni G, Zhang H, Osterman AL. (2009) Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis. Proc Natl Acad Sci U S A. 2009 Feb 9. [Epub ahead of print] PMID: 19204287
14. Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, Beliaev AS. (2009) Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A. 2009 Feb 5. [Epub ahead of print] PMID: 19196979
(** Cited by Faculty of 1,000)
BOOK CHAPTERS AND REVIEWS
1. Osterman, A. & Overbeek R. (2003) “Missing genes in metabolic pathways: A comparative genomics approach.” Current Opin. Chem. Biol. 7, 1-14.
2. Osterman, A. (2006). A hidden metabolic pathway exposed. Proc Natl Acad Sci U S A 103:5637-8.
3. Gerdes, S., R. Edwards, M. Kubal, M. Fonstein, R. Stevens, and A. Osterman. (2006). Essential genes on metabolic maps. Curr Opin Biotechnol 17:448-56
4. Osterman, A., and T. Begley. (2007). A Subsystems-based approach to the identification of drug targets in bacterial pathogens, p. 132-170. In H.Boshoff and C.Barry (ed.), Progress in Drug Research, vol. 64.
5. Yates JR III, Osterman AL. (2007) Introduction: advances in genomics and proteomics. Chem Rev. Aug;107(8):3363-6. Epub 2007 Jul 21
6. Osterman AL, Gerdes SY. (2008) Comparative approach to analysis of gene essentiality. Methods Mol Biol.;416:459-66.
7. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS,, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini, DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. (2008) “Towards environmental systems biology of Shewanella.” Nature Reviews Microbiol. 2008 Aug;6(8):592-603. Epub 2008 Jul 7
8. Osterman, A. (2009) Chapter 3.6.3.10, Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide. In A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch, and C. L. Squires, and D. Ussery (ed.), EcoSal—Escherichia coli and Salmonella: cellular and molecular biology. http://www.ecosal.org. ASM Press, Washington, DC.
