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  1. Osterman A, Overbeek R.  Missing Genes in Metabolic Pathways: A Comparative Genomics Approach.  Curr Opin Chem Biol. 2003 Apr; 7(2): 238-51
  2. Overbeek R, Devine D, and Vonstein V.   Curation Is Forever: Comparative Genomics Approaches to Functional Annotation.   Targets (2003) in press
  3. Overbeek R, Larsen N, Walunas T, D'Souza M, Pusch G, Selkov Jr, Liolios K, Joukov V, Kaznadzey D, Anderson I, Bhattacharyya A, Burd H, Gardner W, Hanke P, Kapatral V, Mikhailova N, Vasieva O, Osterman A, Vonstein V, Fonstein M, Ivanova N, Kyrpides N.  The ERGO™ genome analysis and discovery system.   Nucleic Acids Res. 31(1):164-71 (2003)
  4. Baytaluk MV, Gelfand MS, Mironov A.A.  Exact mapping of prokaryotic gene starts.   Brief Bioinform 3(2):181-94 (2002)
  5. Mironov AA, Novichkov PS, Gelfand MS  Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.   Bioinformatics 17(1):13-5 (2001)
  6. Bernal A, Ear U, Kyrpides N.  Gene recognition in eukaryotic DNA by comparison of genomic sequences.  Bioinformatics 17(11):1011-8 (2001)
  7. Bernal A, Ear U, Kyrpides N.  Genomes OnLine Database (GOLD): a monitor of genome projects world-wide.   Nucleic Acids Res. 29(1):126-7 (2001)
  8. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO.  Metabolic modeling of microbial strains in silico.  Trends Biochem Sci. 26(3):179-86 (2001)
  9. Mironov AA, Fickett JW, Gelfand MS.  Frequent alternative splicing of human genes.  Genome Res. 9(12):1288-93 (1999)
  10. Overbeek R.  Genomics: what is realistically achievable?  Genome Biol. 1(2): COMMENT (2002)
  11. Overbeek R, Larsen N, Pusch GD, D'Souza M, Selkov E Jr, Kyrpides N, Fonstein M, Maltsev N, Selkov E.  WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction.  Nucleic Acids Res. 28(1):123-5 (2000)
  12. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N  Use of contiguity on the chromosome to predict functional coupling.  In Silico Biol. 1(2):93-108 (1999)
  13. Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N.  The use of gene clusters to infer functional coupling.   Proc Natl Acad Sci U S A. 96(6):2896-901 (1999)
  14. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA.  Protein interaction maps for complete genomes based on gene fusion events.   Nature. 402(6757):86-90 (1999)

 

  1. Anderson I, Sorokin A, Kapatral V, Reznik G, Bhattacharya A, Mikhailova N, Burd H, Joukov V, Kaznadzey D, Walunas T, Markd'Souza, Larsen N, Pusch G, Liolios K, Grechkin Y, Lapidus A, Goltsman E, Chu L, Fonstein M, Ehrlich SD, Overbeek R, Kyrpides N, Ivanova N.  Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis.  FEMS Microbiol Lett. 2005 Sep 15;250(2):175-84.
  2. Ivanova, N., Sorokin, A. Galleron, N., Candelon B., Kapatral V., Anderson, I., Reznik, G., Bhattacharyya, A., Gardner, W., Goltsman, E., Larsen, N., DSouza, M., Walunas, T., Pusch, G., Haselkorn, R., Fonstein, M., Ehrlich, S.D., Kyrpides, N., Overbeek, R.  Complete genome sequence of the opportunistic pathogen B. cereus ATCC 14579  Nature. 2003 May 1; 423(6935): 87-91
  3. Kapatral, V., Ivanova, N., Anderson I., Reznik, G., Bhattacharyya, A., Gardner W., Mikhailova, N., Larsen, N., D Souza, M., Walunas, T., Haselkorn, R., Overbeek, R. and Kyrpides, N.   The genome analysis of Fusobacterium nucleatum spp. vincentii and comparison with F. nucleatum subspecies.  Genome Res. 2003 Jun; 13(6A): 1180-9
  4. DelVecchio, V.G., Kapatral, V., Elzer, P., Patra, G., Mujer, C.V.  The genome of Brucella melitensis.  Vet Microbiol 90:587-92 (2002)
  5. Jenkins, C., Samudrala, R., Anderson, I., Hedlund, B.P., Petroni, G., Michailova, N., Pinel, N., Overbeek, R., Rosati, G., Staley, J.T.  Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter.  Proc. Natl. Acad. Sci. U.S.A., 99:17049-54 (2002)
  6. Raymond, J., Zhaxybayeva, O., Gogarten, J.P., Gerdes, S.Y., Blankenship, R.E.  Whole genome analysis of photosynthetic prokaryotes.  Science 298:1616-20 (2002)
  7. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS.  Comparative genomics of thiamin biosynthesis in procaryotes: new genes and regulatory mechanisms.  J Biol Chem. 277(50):48949-59 (2002)
  8. Rodionov, D.A., Mironov A.A., Gelfand, M.S.  Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea.  Genome Res. 12:1507-16 (2002)
  9. Bhattacharyya, A., Stilwagen, S., Reznik, G., Feil, H., Feil, W.S., Anderson, I., Bernal, A., DSouza, M.,  Ivanova, N., Kapatral, V., Los, T., Lykidis, A., Pusch, G.D., Selkov Jr., E., Walunas, T.L., Purcell, A.H., Edwards, R.A., Hawkins, T., Overbeek, R., Kyrpides, N.C., P.F. Predki  Draft sequencing and comparative genomics of Xylella fastidiosa strains reveal novel biological insights.  Genome Research, 12:1556-63 (2002)
  10. Bhattacharyya, A., Stilwagen, S., Lykidis, A., Anderson, I., Bernal, A., DSouza, M., Ivanova, N., Kapatral, V., Larsen, N., Los, T., Reznik, G., Selkov Jr., E., Walunas, T.L., Feil, H., Feil, W.S., Purcell, A.H., Edwards, R.A., Hawkins, T.L., Haselkorn, R., Overbeek, R., Predki, P.F. and Kyrpides, N.C.  Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains  Proc. Natl. Acad. Sci. U.S.A., 99:12403-8 (2002)
  11. Deppenmeier U., Johann, A., Hartsch, T., Rainer, R., Schmitz, R.A., Martinez-Arias, R., Henne, A., Wiezer, A., Bäumer, S., Jacobi, C., Brüggemann, H., Lienard, T., Christmann, A., Bömeke, M., Steckel, S., Bhattacharyya, A., Lykidis, A., Overbeek, R., Klenk, H.-P., Gunsalus, R.P., Fritz, H.-J., and Gottschalk, G.   The genome of Methanosarcina mazei: Evidence for lateral gene transfer between Bacteria and Archaea.  Journal of Molecular Microbiology and Biotechnology 4:453-61 (2002)
  12. Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O'Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.   Discovering lactic acid bacteria by genomics.   Van Leeuwenhoek 82(1-4):29-58 (2002)
  13. Kapatral V, Anderson I, Ivanova N, Reznik G, Los T, Lykidis A, Bhattacharyya A, Bartman A, Gardner W, Grechkin G, Zhu L, Vasieva 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.  Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586.  J Bacteriol. 184(7):2005-18 (2002)
  14. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R.  The genome sequence of the facultative intracellular pathogen Brucella melitensis  Proc Natl Acad Sci U S A. 99(1):443-8 (2002)
  15. Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB.  Comparative approach to analysis of regulation in complete genomes: multi-drug resistance systems in gamma-proteobacteria.  J Mol Microbiol Biotechnol 3(2):319-2 (2001)
  16. Graham DE, Kyrpides N, Anderson IJ, Overbeek R, Whitman WB.   Genome of Methanocaldococcus (Methanococcus) jannaschii.  Methods Enzymol 330:40-123 (2001)
  17. Robert Haselkorn, Alla Lapidus, Yakov Kogan, Cestmir Vlcek, Jan Paces , et al.  The Rhodobacter capsulatus genome.  Photosynthesis Research 70: 4352, (2001)
  18. Selkov E, Overbeek R, Kogan Y, Chu L, Vonstein V, Holmes D, Silver S, Haselkorn R, Fonstein M.  Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans.  Proc Natl Acad Sci U S A. 97(7):3509-14 (2000)
  19. Graham DE, Overbeek R, Olsen GJ, Woese CR.  An archaeal genomic signature   Proc Natl Acad Sci USA.  97(7):3304-8 (2000)
  20. Kyrpides NC, Ouzounis CA, Iliopoulos I, Vonstein V, Overbeek R.  Analysis of the Thermotoga maritima genome combining a variety of sequence similarity and genome context tools.  Nucleic Acids Res, 28(22):4573-6 (2000)

 

  1. Zhang X, Kurnasov OV, Karthikeyan S, Grishin NV, Osterman AL, Zhang H.  Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis.  J Biol Chem 2003 Feb 6 [epub ahead of print]
  2. Kurnasov OV, Polanuyer BM, Ananta S, Sloutsky R, Tam A, Gerdes SY, Osterman AL.  Ribosylnicotinamide Kinase Domain of NadR Protein: Identification and Implications in NAD Biosynthesis.  J Bacteriol. 184(24):6906-17 (2002)
  3. Daugherty, M,  Polanuyer, B, Farrell, M, Lykidis, A, de Crécy-Lagard, V, and Osterman, A.  Human Coenzyme A Biosynthesis: Complete Pathway Reconstitution Via Comparative Genomics.  J Biol Chem. 277(24):21431-9 (2002)
  4. Zhou T, Kurnasov O, Tomchick DR, Binns DD, Grishin NV, Marquez VE, Osterman AL, Zhang H.  Structure of Human Nicotinamide/Nicotinic Acid Mononucleotide Adenylyltransferase.  Basis for the Dual Substrate Specificity and Activation of the Oncolytic Agent Tiazofuran.  J Biol Chem. 277(15):13148-13154 (2002)
  5. Singh SK, Kurnasov OV, Chen B, Robinson H, Grishin NV, Osterman AL, Zhang H.  Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities.   J Biol Chem. 277(36):33291-9 (2002)
  6. Gerdes, SY, Scholle, MD, DSouza, M, Bernal, A,  Baev, MV, Farrell, M, Kurnasov, OV, Daugherty, MD, Mseeh, F, Polanuyer, BM, Campbell, J, Anantha, S, Shatalin, KY, Chowdhury, SAK, Fonstein, M, and Osterman, AL  From Genetic Footprinting to Antimicrobial Drug Targets: Examples in Cofactor Biosynthetic Pathways.  J. Bacteriology 184: 4555-72 (2002)
  7. Permina EA, Mironov AA, Gelfand MS.  Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements.  Gene 293(1-2):133-40 (2002)
  8. Vitreschak AG, Rodionov DA, Mironov AA,  Gelfand MS.  Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.  Nucleic Acids Res  30(14):3141-51 (2002)
  9. Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H.   Structural basis for the catalysis and substrate specificity of homoserine kinase.  Biochemistry 40(36):10810-8 (2001
  10. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E  Sensing small molecules by nascent RNA. A mechanism to control transcription in bacteria.  Cell 111:747-756 (2002)
  11. Begley TP, Kinsland C, Mehl RA, Osterman A, Dorrestein P.  The biosynthesis of nicotinamide adenine dinucleotides in bacteria.   Vitam Horm. 61:103-19
  12. Daugherty M, Vonstein V, Overbeek R, Osterman A.  Archaeal shikimate kinase, a new member of the GHMP-kinase family.   J Bacteriol. 183(1):292-300
  13. Panina EM, Mironov AA, Gelfand MS.  Comparative analysis of FUR regulons in gamma-proteobacteria.  Nucleic Acids Res 29(24):5195-206 (2001)
  14. Laikova ON, Mironov AA, Gelfand MS.  Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria.   FEMS Microbiol Lett 205(2):315-22 (2001)
  15. Rodionov DA, Mironov AA, Gelfand MS.  Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.  FEMS Microbiol Lett 205(2):305-14 (2001)
  16. Tavernarakis N, Everett JK, Kyrpides NC, Driscoll M.   Structural and functional features of the intracellular amino terminus of DEG/ENaC ion channels.   Curr Biol. 11(6):R205-8. (2001)
  17. Sianidis G, Karamanou S, Vrontou E, Boulias K, Repanas K, Kyrpides N, Politou AS, Economou A.  Cross-talk between catalytic and regulatory elements in a DEAD motor domain is essential for SecA function.  EMBO J. 20(5):961-70
  18. Tavernarakis N, Driscoll M, Kyrpides NC.  The SPFH domain: implicated in regulating targeted protein turnover in stomatins and other membrane-associated proteins.   Trends Biochem Sci24(11):425-7 (1999)

 

  1. Kapatral V, Campbell JW, Minnich SA, Thomson NR, Matsumura P, Pruss BM.  Gene array analysis of Yersinia enterocolitica FlhD and FlhC: regulation of enzymes affecting synthesis and degradation of carbamoylphosphate.  Microbiology. 2004 Jul;150(Pt 7):2289-300.
  2. Luke, K, Radek, A, Liu, X, Campbell, J,  Uzan, M,  Haselkorn, R, and Kogan, Y   Microarray Analysis of Gene Expression During Bacteriophage T4 Infection   Virology 299:182 (2002)
  3. Prüß, B., Campbell, J.W., Van Dyk, T.K., Zhu, C., Kogan, Y., Matsumura, P.   FlhD/FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer.   J. Bact. 185:534-543 (2003)

 
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