The FIG Story

Cast of Characters

Founding Fellows

 

Fellows

Michael Fonstein
Yakov Kogan
Andrei Osterman
Ross Overbeek
Veronika Vonstein
  Rob Edwards
Sveta Gerdes
Bruce Parrello
Gordon Pusch
Olga Vassieva
Olga Zagnitko

FIG Fellows have known one another and influenced each other’s scientific views for over three decades: their relationships as friends, students, supervisors, and colleagues have matured into this unique fellowship we call FIG.

Timeline

1971 Professor Ross Overbeek teaches programming to high-school student Bruce Parrello at Northern Illinois University (DeKalb, IL). Parrello came to the attention of Overbeek as a result of a manuscript in mathematical logic he authored while in high school. During this time, they develop a relationship with Argonne National Laboratory.
1972
1973  
1974  
1975  
1976  
1977 Parrello returns to NIU. He and Overbeek work on a methodology for turning Entity-Relationship models into physical database designs.
1978
1979  
1980 Overbeek begins a long-term working relationship with the Applied Mathematics division at Argonne National Laboratories.
1981  
1982  
1983 Michael Fonstein, a young geneticist, and Andrei Osterman, a young biochemist, begin their scientific careers in neighboring labs at VNII Genetica, Institute of Microbial Genetics, Moscow, Russia
1984  
1985 Sveta Gerdes (nee Lashina) works on her MS degree at VNII Genetika. Under the supervision of Fonstein she develops new tools for the construction and analysis of gene libraries using phagemids.
1986 Osterman and Olga Zagnitko, working in a traditional protein chemistry lab, use vectors developed by Fonstein for their first molecular cloning projects. Fonstein and his co-workers apply Pulse Field Gel Electrophoresis (PFGE) for chromosomal mapping of several gram-positive and gram-negative organisms. Veronika Vonstein, an exchange scientist from Humboldt University, Berlin, Germany, joins Fonstein's team.
1987
1988
1989

Carl Woese invites Overbeek to participate in the computational support for Woese’s alignments of rRNA. Overbeek begins devoting all his time to the support of biological research.Overbeek becomes an initial member of the Ribosomal Database Project and works with Gary Olsen in the development and maintenance of the phylogenetic trees distributed by the RDP.

1990 Osterman, Fonstein and Vonstein help co-found Diagnosticum, Moscow. Diagnosticum is one of the first private biotech service companies in Russia under the new philosophy of perestroika.
1991 Yakov Kogan, an undergraduate student of Moscow State University joins Osterman’s group at VNNII Genetica.
1992 Overbeek works with a number of biologists on software for integrating genomic data. One application—GenoGraphics—offers visual displays of colinear maps; another supports a pidgin English interface for querying E. coli data.
1993 Overbeek leads a team that develops GenoBase, a system that supports complex queries against integrated of biological data. The system uses data from proteins, structure, 2D-gel databases, and genomic sequence data.
1994 Overbeek's team at Argonne develops PUMA, an integrated database of sequence data, alignments, and metabolic overviews. Fonstein and Overbeek begin collaboration on the annotation of Rhodobacter capsulatus. They are eventually joined by Kogan.
1995
1996 Overbeek is involved in the annotation of Methanococcus jannaschii, Archaeoglobus fulgidus, and Aquifex aeolicus. To better support this work, his team at Argonne, in collaboration with scientists from the University of Illinois, develop the WIT system. Gordon Pusch joins this effort and participates in the design and implementation of WIT. Vonstein uses the WIT system for the annotation of Thermus flavus genome.
1997 Fonstein, Vonstein and Overbeek join forces to found Intergated Genomics. Under their leadership, the vision of comparative genome analysis supported by sequencing of a phylogenetically diverse set of microbes opens new ways for in silico analysis and prediction of gene functionality.
1998 Pusch joins the team as developer of the new comparative genomics environment ERGO. Kogan joins as team leader for the core sequencing functions. Rob Edwards begins collaboration with Overbeek and uses the WIT system for the annotation of multiple Salmonella genomes.
1999 Osterman, Olga Vassieva and Gerdes join the research team. Osterman applies his skills as protein chemist to the verification of in silico predictions of functional roles of genes, Vassieva participates in the development of metabolic reconstructions of microbial genomes from their genome sequence, and Gerdes participates in the development of techniques and their application for whole genome essentiality analysis.
2000 The team pioneers the use of genome context analysis and metabolic reconstruction technology to predict previously uncharacterized genes in metabolic pathways. Many of these functional predictions are verified by direct biochemical and genetic experiments, changing forever the perception of the value of comparative genomics. Over 30 scientific publications are living evidence of this effort.
2001
2002
2003

Fonstein, Kogan, Osterman, Overbeek and Vonstein found the non-profit Fellowship for Interpretation of Genomes (FIG) to follow their vision of seeking advances in understanding through comparative analysis of the growing body of genomic data. The team at FIG begins a new open source comparative genomics environment, the SEED. The Project to Annotate 1000 Genomes becomes a central goal of FIG.

2004 Parrello and Pusch become FIG fellows. After FIG receives an award from the National Institute of Allergy and Infectious Diseases to participate in the development of the National Microbial Pathogen Data Resource, Gerdes, Zagnitko, Edwards and Vassieva join the fellowship. The Project to Annotate 1000 Genomes gathers steam and the encoding of Subsystems begins. Teams of scientists from various institutions support FIG’s initiatives and very close collaborations begin.
2005  

Partial List of Papers

  1. Melnick J, Lis E, Park JH, Kinsland C, Mori H, Baba T, Perkins J, Schyns G, Vassieva O, Osterman A, Begley TP. (2004) Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase. J Bacteriol. 186(11):3660-2.
  2. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Goltsman E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P. (2004) Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol. 22(12):1554-8. Epub 2004 Nov 14.
  3. Farahi K, Pusch GD, Overbeek R, Whitman WB. (2004) Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method. J Mol Evol. 58(5):615-31.
  4. Overbeek, R., Devine, D., and Vonstein, V. (2003) TARGETS2, 138-146.Curation Is Forever:Comparative Genomics Approaches to Functional Annotation.
  5. Osterman A, Overbeek R. (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol.7(2):238-51. Review.
  6. Kurnasov O, Goral V, Colabroy K, Gerdes S, Anantha S, Osterman A, Begley TP. (2003) NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria. Chem Biol. 10(12):1195-204.
  7. Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A, Chu L, Mazur M, Goltsman E, Larsen N, D'Souza M, Walunas T, Grechkin Y, Pusch G, Haselkorn R, Fonstein M, Dusko Ehrlich S, Overbeek R, Kyrpides N. (2003) Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 423(6935):87-91.
  8. Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 185(19):5673-84.
  9. Kazakov AE, Vassieva O, Gelfand MS, Osterman A, Overbeek R. (2003) Bioinformatics classification and functional analysis of PhoH homologs. In Silico Biol. 3(1-2):3-15. Epub 2002 Dec 30.
  10. Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov E Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vassieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N. (2003). The ERGO (TM) genome analysis and discovery system. Nucleic Acids Res. 31(1): 164-71.
  11. Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL. (2002). From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways. J Bacteriol. 184(16):4555-72.
  12. Kurnasov, O.V., Polanuyer, B.M., Ananta, S., Sloutsky, R., Tam, A., Gerdes, S.Y., Osterman, A.L. (2002). Ribosylnicotinamide kinase domain of NadR protein: Identification and implications in NAD biosynthesis. J Bacteriol. 184:6906-17.
  13. Bhattacharyya A, Stilwagen S, Reznik G, Feil H, Feil WS, Anderson I, Bernal A, D'Souza M, Ivanova N, Kapatral V, Larsen N, Los T, Lykidis A, Selkov E Jr, Walunas TL, Purcell A, Edwards RA, Hawkins T, Haselkorn R, Overbeek R, Kyrpides NC, Predki PF. (2002) Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights. Genome Res. 12(10):1556-63.
  14. Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vassieva O, Chu L, Kogan Y, Chaga O, Goltsman E, Bernal A, Larsen N, D'Souza M, Walunas T, Pusch G, Haselkorn R, Fonstein M, Kyrpides N, Overbeek R. (2002). Genome sequence and analysis of the oral bacterium F. nucleatum strain ATCC 25586. J Bacteriol. 184(7):2005-18.
  15. Daugherty M; Vonstein V; Overbeek R; Osterman A, (2001) Archaeal shikimate kinase, a new member of the GHMP-kinase family. J Bacteriol. 183(1):292-300.
  16. Haselkorn R., A. Lapidus, Y. Kogan, C. Vlcek, J. Paces, P. Ulbrich, T. Pacenkova, D. Rebrikov, A. Milgram, M. Mazur, R. Cox, N. Kyrpides, N. Ivanova, V. Kapatral, T. Los, A. Lykidis, N. Mikhailova, G. Reznik, O. Vassieva, M. Fonstein. (2001). “ The Rhodobacter capsulatus genome”. Photosynthesis Research 70: 43-52.
  17. Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M. (2000). Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans. Proc Natl Acad Sci U S A. 97(7):3509-14.
  18. Kyrpides, N. C., C. A. Ouzounis, I. Iliopoulos, V. Vonstein, and R. Overbeek. (2000) Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools. Nucleic Acids Res. 28(22):4573-6.
  19. Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28(1):123-5.
  20. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A. 96(6):2896-901.
  21. Fonstein M., T. Nikolskaya, Y. Kogan, and R. Haselkorn. (1998) Genome encyclopedias and their use for comparative analysis of Rhodobacter capsulatus strains. Electrophoresis. 19(4): 469-77.
  22. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N. (1998) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1(2):93-108.
  23. Nikolsky, Y, M. Fonstein, V. Goering (Vonstein), Y. Rostova and N. Yankovsky. ( 1992) Mapping of genetic markers of Corynebacterium glutamicum ATCC 13032 on its physical map. Genetica ( Moscow ) 28(12):38-47.
  24. Osterman AL , Grishin NV, Smulevitch SV, Matz MV, Zagnitko OP, Revina LP, Stepanov VM. (1992) Primary structure of carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family. J Protein Chem. 11(5):561-70 .
  25. Teplyakov A, Polyakov K, Obmolova G, Strokopytov B, Kuranova I, Osterman A, Grishin N, Smulevitch S, Zagnitko O, Galperina O. (1992) Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris. Eur J Biochem. 208(2):281-8.
  26. Smulevitch SV, Osterman AL, Shevelev AB, Kaluger SV, Karasin AI, Kadyrov RM, Zagnitko OP,Chestukhina GG, Stepanov VM. (1991) Nucleotide sequence of a novel delta-endotoxin gene cryIg of Bacillus thuringiensis ssp. galleriae. FEBS Lett. 18;293(1-2):25-8.
  27. Smulevitch SV, Osterman AL, Galperina OV, Matz MV, Zagnitko OP, Kadyrov RM, Tsaplina IA, Grishin NV, Chestukhina GG, Stepanov VM. Molecular cloning and primary structure of Thermoactinomyces vulgaris carboxypeptidase T. (1991) A metalloenzyme endowed with dual substrate specificity. FEBS Lett. 7;291(1):75-8.
  28. Yankovsky, N., Fonstein, M., Lashina-Ermakova (Gerdes) S., Bukanov, N., Yakubovich, N., Ermakova, L., Rebentish, B., Janulaitis, A., Debabov, V. (1989) Phagemids as effective and simple tools for construction and analysis of gene libraries. Gene 81, 203-210.
  29. Lusk, E. L., R. A. Overbeek, and B. Parrello, (1985) General ledger systems and the design of entity-relationship models, Journal of Data and Knowledge Engineering, 1, pp. 155-180, North-Holland.