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Last updated 7 December 2009.
Ochman, H. and R. Raghavan. (2009) Excavating the functional landscape of bacterial cells (Perspective). Science 326:1200-1.
Jarvik, T., C. Smillie, E.A. Groisman, H. Ochman (2009) Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J. Bacteriol. 2009 Nov 6. [Epub ahead of print]
Kuo, C.H., H. Ochman. (2009) Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct. 4:35.
Stavrinides, J., A. No, H. Ochman (2009) A single genetic locus in the phytopathogen Pantoea stewartii enables gut colonization and pathogenicity in an insect host. Environ. Microbiol. 2009 Sep 24. [Epub ahead of print]
Ochman, H. (2009) Afterword: Genomics Update update. Environ. Microbiol. 11:2193.
Kunin, V., A. Engelbrektson, H. Ochman, P. Hugenholtz (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 2009 Aug 27. [Epub ahead of print]
Kuo, C.H., N.A. Moran, H. Ochman (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-4.
Ochman, H. (2009) Radical views of the Tree of Life. Environ. Microbiol. 11:731-2.
Stavrinides, J., J.K. McCloskey, H. Ochman (2009) The pea aphid as both host and vector for the phytopathogenic bacterium, Pseudomonas syringae. Appl. Environ. Microbiol. 75:2230-5.
Kuo, C.H., H. Ochman (2009) Deletional bias across the three domains of life. Genome Biol. Evol. 1:145-152.
Kuo C.H., H. Ochman (2009) The fate of new bacterial genes. FEMS Microbiol. Rev. 33:38-43.
Narra, H.P., M.H. Cordes, H. Ochman (2008) Structural features and the persistence of acquired proteins. Proteomics. 8:4772-81.
Marri, P.R., L.K. Harris, K. Houmiel, S.C. Slater, and H. Ochman (2008) The effect of chromosome geometry on genetic diversity. Genetics. 179:511-516.
van Passel, M.W., P.R. Marri, and H. Ochman (2008) The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput. Biol. 4:e1000059.
van Passel, M.W. and H. Ochman (2007) Selection on the genic location of disruptive elements. Trends Genet. 23:601-4.
Liu, R. and H. Ochman (2007) Origins of flagellar gene operons and secondary flagellar systems. J. Bacteriol. 189:7098-104.
Liu, R. and H. Ochman (2007) Stepwise formation of the bacterial flagellar system. Proc. Natl. Acad. Sci. U S A 104:7116-21. Erratum 104:11507
H. Ochman (2007) Single-cell genomics. Environ. Microbiol. 9:7.
van Passel, M.W., C.S. Smillie, and H. Ochman (2007) Gene decay in Archaea. Archaea. 2:137-143.
Ochman, H., R. Liu and E.P.C. Rocha (2007) Erosion of interaction networks in reduced and degraded genomes. J. Exp. Zool. (Mol. Dev. Evol.) 308B:97-103.
Narra, H.P., Ochman, H. (2006) Of what use is sex to bacteria? Curr. Biol. 16:R705-R710.
Wirth, T., D. Falush, R. Lan, F. Colles, P. Mensa, L.H. Wieler, H. Karch, P.R. Reeves, M.C. Maiden, H. Ochman, and M. Achtman. (2006) Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60:1136-1151.
Ochman, H. and L.M. Davalos (2006) The nature and dynamics of bacterial genomes. Science 311:1730-1733.
Moran, N.A., P.H. Degnan, S.R. Santos, H.E. Dunbar, and H. Ochman (2005) The players in a mutualistic symbiosis: insects, bacteria, viruses and virulence genes. Proc. Natl. Acad. Sci. U S A 102:16919-16926.
Ochman, H. (2005) Genomes on the shrink. Proc. Natl. Acad. Sci U S A 102:11959-11960.
Lerat, E. and H. Ochman (2005) Recognizing pseudogenes in bacterial genomes. Nucleic Acids Research, 33(10):3125-32.
Lerat, E., V. Daubin, H. Ochman and N.A. Moran (2005) Evolutionary origins of genomic repertoires in bacteria. PloS Biology, 3(5):e130.
Ochman, H., E. Lerat and V. Daubin (2005) Examining bacterial species under the specter of gene transfer and exchange. Proc. Natl. Acad. Sci. U S A, 3;102 Suppl 1:6595-9.
Ochman, H., V. Daubin and E. Lerat (2005) A bunch of fun-guys: the whole-genome view of yeast evolution. Trends Genet. 21(1):1-3.
Ochman, H. and S.R. Santos. (2005) Exploring microbial microevolution with microarrays. Infect. Genet. Evol. 5:103-108.
Dale, C., Dunbar, H., Moran, N.A. and H. Ochman (2005) Extracting single genomes from heterogenous DNA samples: A test case with Carsonella ruddii, the bacterial symbiont of psyllids (Insecta). J. Insect Science, 5:3.
Daubin, V. and H. Ochman (2004) Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res. 14: 1036-1042.
Daubin, V. and H. Ochman (2004) Start-up entities in the evolution of new genes. Curr. Opin. Genet. Devel. 14: 616-619.
Lerat, E. and H. Ochman (2004) Y-F: Exploring the outer limits of bacterial pseudogenes. Genome Research 14: 2273-2278.
Daubin, V. and H. Ochman (2004) Recognizing lateral gene transfer by quartet mapping. Molec. Biol. Evol. 21: 48-51.
Santos, S. R. and H. Ochman (2004) Identification and phylogenetic sorting of bacterial lineages using universally conserved genes and proteins. Environ. Microbiol. 6: 754-759.
Dale, C., B. Wang, N. A. Moran and H. Ochman (2003) Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration in mutualistic bacterial endosymbionts. Molec. Biol. Evol. 20: 1188-1194.
Daubin, V., N. A. Moran, and H. Ochman (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
Francino, M. P., S. R. Santos, and H. Ochman (2003) Phylogenetic relationships of bacteria with special reference to enteric and endosymbiotic species. In M. Dworkin (ed.) The Prokaryotes 3rd edition, a Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. Springer-Verlag, NY.
Hudson, R. E., U. Bergthorsson, and H. Ochman (2003) Transcription increases a broad spectrum of spontaneous mutations in bacteria. Nucleic Acids Res. 31: 4517-4522.
Moran, N. A., H. Dunbar, C. Dale, W. Smith and H. Ochman (2003) Intracellular symbionts of sharpshooters (Insecta: Hemiptera: Cicadellinae) form a distinct clade with a small genome. Environ. Microbiol. 5: 116-126.
Ochman, H. (2003) Neutral mutations and neutral substitutions in bacterial genomes. Molec. Biol. Evol. 20: 2091-2096.
Ochman H., and C. Dale (2003) Type III secretion systems and the conversion from parasitism to mutualism. Nova Acta Leopoldina NF 88, nr. 333, 61-63.
Ochman, H. and S. R. Santos (2003) Eyeing bacterial genomes. Curr. Op. Microbiol. 6: 109-113.
Dale, C., G. Plague, B. Wang, H. Ochman, and N. A. Moran (2002) Type III secretion systems and the evolution of mutualistic endosymbiosis. Proc. Natl. Acad. Sci USA 99: 12397-12402.
Dale, C., W. Smith, and H. Ochman (2002) Physical analysis of chromosome size variations in bacteria. In M. Blot (ed.) Methods and Tools in Biosciences and Medicine, Birkhauser Verlag.
Hudson, R. E., U. Bergthorsson, J. R. Roth, and H. Ochman (2002) Effect of chromosome location on bacterial mutation rates. Molec. Biol. Evol. 19: 85-92.
Lawrence, J. G. and H. Ochman (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10: 1-4.
Mira, A. and H. Ochman (2002) Gene location and bacterial sequence divergence. Molec. Biol. Evol. 19: 1350-1358.
Ochman, H. (2002) Chromosome arithmetic and geometry. Curr. Biol. 12: R427-R428.
Ochman, H. (2002) Distinguishing the ORFS from the ELFs: Short bacterial genes and the over-annotation of genomes. Trends Genet. 18: 335-337.
Ochman, H. (2002) Side-stepping genetics. (Book review) Nature Cell Biol. 4: E158.
Ochman, H. and M. P. Francino (2002) Isochores. In T. Creighton (ed.) Wiley Encyclopedia of Molecular Medicine, Academic Press, NY, pp. 1830-1831.
Francino, M. P. and H. Ochman (2001) Deamination as the basis of mutational strand asymmetry in Escherichia coli. Molec. Biol. Evol. 18: 1147-1150.
Mira, A., H. Ochman and N. A. Moran (2001) Deletional bias and the evolution of bacterial genomes. Trends Genet. 10: 589-596.
Morgan, U., H. Ochman, F. Renaud and M. Tibayrenc (2001) Population genetics and population biology: what did they bring to the epidemiology of transmissible diseases? An e-debate. Infect. Genet. Evol. 1: 161-166.
Ochman, H. (2001) Lateral and oblique gene transfer. Curr. Opin. Genet. Devel. 11: 616-619.
Ochman, H. (2001) The origins of bacterial virulence. (In Valenciano) Metode 28: 44-46.
Ochman, H. and N. A. Moran (2001) Genes lost and genes found: the molecular evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-1098.
Francino, M. P. and H. Ochman (2000) Strand symmetry around the ß-globin origin of replication in primates. Molec. Biol. Evol. 17: 416-422.
Groisman, E. A. and H. Ochman (2000) The path to Salmonella. ASM News 65: 21-27.
Houndt, T. and H. Ochman (2000) Shifts in patterns of antibiotic resistance in natural populations of enteric bacteria. Appl. Environ. Microbiol. 66: 5406-5409.
Ochman, H. (2000) The evolution of bacterial pathogens. In E. A. Groisman (ed.) Principles of Bacterial Pathogenesis. Academic Press, NY, pp. 1-41.
Ochman, H. and I. B. Jones (2000) Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19: 6637-6643.
Ochman, H., J. G. Lawrence and E. A. Groisman (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-305.
Wernegreen, J. J., H. Ochman, I. B. Jones and N. A. Moran (2000) Decoupling of genome size and sequence diversity in endosymbiotic bacteria. J. Bacteriol. 182: 3867-3869.
Bergthorsson, U. and H. Ochman (1999) Chromosomal changes during experimental evolution in laboratory populations of Escherichia coli. J. Bacteriol. 181: 1360-1363.
Francino, M. P. and H. Ochman (1999) A comparative genomics approach to DNA asymmetries. Ann. NY Acad. Sci. 870: 428-431.
Francino, M. P. and H. Ochman (1999) Isochores result from mutation not selection. Nature 400: 30-31.
Ochman, H. (1999) Bacterial evolution: Jittery genomes. Curr. Biol. 9: 485-486.
Ochman, H. (1999) Editorial Overview. Curr. Opin. Microbiol. 2: 517-518.
Ochman, H., S. Elwyn and N. A. Moran (1999) Calibrating bacterial evolution. Proc. Natl.Acad.Sci. USA 96: 12638-12643.
Ochman, H. and E. A. Groisman (1998) Seeking the genetic basis of phenotypic differences among bacterial species. In B. Schierwater and R. DeSalle (eds.) Molecular Ecology and Evolution: Approaches and Applications. Volume 2. Birkhauser Verlag, NY.
Bergthorsson, U. and H. Ochman (1998) Distribution of chromosome length variation in natural isolates of Escherichia coli. Molec. Biol. Evol. 15: 6-16.
Bergthorsson, U. and H. Ochman (1998) Evolution of the E. coli genome. In F. J. de Bruijn et al. (eds.) Bacterial Genomes: Physical Structure and Analysis. Chapman and Hall, NY.
Lawrence, J. G. and H. Ochman (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95: 9413-9417.
Ochman, H. and U. Bergthorsson (1998) Rates and patterns of chromosome evolution in enteric bacteria. Curr. Opin. Microbiol. 1: 580-583.
Boyd, E. F., J. Li, H. Ochman and R. K. Selander (1997) Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica. J. Bacteriol. 179: 1985-1991.
Francino, M. P. and H. Ochman (1997) Strand asymmetries in DNA evolution. Trends in Genetics 13: 240-245.
Groisman. E. A. and H. Ochman (1997) How Salmonella became a pathogen. Trends in Microbiol. 5: 343-349.
Lawrence, J. G. and H. Ochman (1997) Amelioration of bacterial genomes: rates of change and exchange. J. Molec. Evol. 44: 383-397.
Ochman, H. (1997) Miles of isles. Trends Microbiol. 5: 222.
Francino, M. P., L. Chao, M. A. Riley and H. Ochman (1996) Patterns of substitutions in enterobacterial genes are generated by transcription-coupled repair. Science 272: 107-109.
Groisman. E. A. and H. Ochman (1996) Pathogenicity islands: quantum leaps in bacterial evolution. Cell 87: 791-794.
Ochman, H. and J. G. Lawrence (1996) Phylogenetics and the amelioration of bacterial genomes. In F. C. Neidhardt et al. (eds.) Escherichia coli and Salmonella typhimurium: Molecular and Cellular Biology. 2nd edition. ASM Publications, Washington, Chapter 141.
Ochman, H., and E. A. Groisman (1996) Distribution of pathogenicity islands in Salmonella. Infect. Immun. 64: 5410-5412.
Ochman, H., Soncini, F. C., Solomon, F., and E. A. Groisman (1996) Identification of a pathogenicity island required for Salmonella survival in host cells. Proc. Natl. Acad. Sci. USA 93: 7800-7804.
Bergthorsson, U. and H. Ochman (1995) Heterogeneity of genome size among natural isolates of Escherichia coli. J. Bacteriol. 177: 5784-5789.
Li, J., H. Ochman, E. A. Groisman, E. F. Boyd, K. Nelson, and R. K. Selander (1995) Functional correlates of evolutionary rate variation among the invasion genes of Salmonella enterica. Proc. Natl. Acad. Sci. USA 92: 7252-7256.
Ochman, H. and L. A. Buckholtz (1995) Physical structure of human chromosome 21: an analysis of YACs spanning 21q. Mammalian Genome 6: 84-89.
Ochman, H. and U. Bergthorsson (1995) Genome evolution in enteric bacteria. Curr. Op. Gen. Devel. 5: 734-738.
Ochman, H. and E. A. Groisman (1995) The evolution of invasion in enteric bacteria. Can. J. Microbiol. 41: 555-561.
Groisman. E. A. and H. Ochman (1994) How to become a pathogen. Trends Microbiol. 2: 289-294.
Hartl, D. L. and H. Ochman (1994) Inverse polymerase chain reaction. In A. Harwood (ed.) Methods in Molecular Biology, Volume 31: Protocols for Gene Analysis. Humana Press Inc., Totowa, NJ, pp. 187-196.
Ochman, H. and E. A. Groisman (1994) The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. In B. Schierwater et al. (eds.) Molecular Ecology and Evolution: Approaches and Applications. Birkhauser Verlag, NY, pp. 479-493.
Bisercic, M. and H. Ochman (1993) Natural populations of Escherichia coli and Salmonella typhimurium harbor the same classes of insertion sequences. Genetics 133: 449-454.
Bisercic, M. and H. Ochman (1993) The ancestry of insertion sequences common to Escherichia coli and Salmonella typhimurium. J. Bacteriol. 175: 7863-7868.
Carulli, J. P., D. E. Krane, D. L. Hartl and H. Ochman (1993) Compositional heterogeneity and patterns of molecular evolution in the Drosophila genome. Genetics 134: 837-845.
Groisman, E. A. and H. Ochman (1993) Cognate genes govern invasion of host epithelial cells by Salmonella typhimurium and Shigella flexneri. EMBO J. 12: 3779-3787.
Groisman, E. A., M. Sturmoski, F. Soloman, R. Lin and H. Ochman (1993) Molecular, functional and evolutionary analysis of sequences specific to Salmonella. Proc. Natl. Acad. Sci. USA 90: 1033-1037.
Lawrence, J. G., D. L. Hartl and H. Ochman (1993) Sequencing products of the polymerase chain reaction. In R. Wu (ed.) Methods in Enzymology, Recombinant DNA, Part I. Academic Press, NY.
Ochman, H., F. J. Ayala and D. L. Hartl (1993) Use of the PCR to amplify segments outside the boundaries of known sequences. In R. Wu (ed.) Methods in Enzymology, Recombinant DNA, Part I. Academic Press, NY.
Groisman, E. A., M. H. Saier, Jr. and H. Ochman (1992) Horizontal transfer of a phosphatase gene as evidence for the mosaic structure of the Salmonella genome. EMBO J. 11: 1309-1316.
Lawrence, J. G., H. Ochman and D. L. Hartl (1992) The evolution of insertion sequences within enteric bacteria. Genetics 131: 9-20.
Hall, B.G., L. Xu and H. Ochman (1991) Physical map of the SAC operon of Escherichia coli K12. J. Bacteriol. 173: 5250.
Krane, D. E., D. L. Hartl and H. Ochman (1991) Rapid determination of nucleotide content and its application to the study of genome structure. Nucleic Acids Res. 19: 5181-5185.
Lawrence, J. G., D. L. Hartl and H. Ochman (1991) Molecular considerations in the evolution of bacterial genes. J. Molec. Evol. 33: 241-250.
Lawrence, J. G., H. Ochman and D. L. Hartl (1991) Molecular and evolutionary relationships among enteric bacteria. J. Gen. Microbiol.137: 1911-1921.
Ochman, H., J. W. Ajioka, D. Garza and D. L. Hartl (1990) Inverse polymerase chain reaction. In H. A. Erlich (ed.) PCR Technology: Principles and Applications for DNA Amplification. Stockton Press, NY (Reprinted in Biotechnology 8: 759-760.)
Higuchi, R. G. and H. Ochman (1989) Generation of single-stranded DNA templates by exonuclease digestion following the polymerase chain reaction. Nucleic Acids Res. 17: 5863.
Ochman, H., M. M. Medora, D. Garza and D. L. Hartl (1989) Amplification of flanking sequences: Inverse PCR for chromosome walking. In M. Innis et al. (eds.) PCR Protocols: Methods and Applications. Academic Press, NY.
Ochman, H., A. S. Gerber and D. L. Hartl (1988) Genetic applications of an inverse polymerase chain reaction. Genetics 120: 621-623.
Ochman, H., J. S. Jones and R. K. Selander (1987) Large scale patterns of genetic differentiation at enzyme loci in the landsnails Cepaea nemoralis and Cepaea hortensis. Heredity 58: 127-138.
Ochman, H. and A. C. Wilson (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Molec. Evol. 26: 74-86.
Ochman, H. and A. C. Wilson (1987) Evolutionary history of enteric bacteria. Pp. 1649-1454, in F. C. Neidhardt et al. (eds.) Escherichia coli and Salmonella typhimurium: Molecular and Cellular Aspects. ASM Publications, Washington.
Wilson, A. C., H. Ochman and E. M. Prager (1987) Molecular time scale for evolution. Trends in Genetics 3: 241-247.
Achtman, M., M. Heuzenroeder, B. Kusecek, H. Ochman, D. A. Caugant, R. K. Selander, V. Väisanen-Rhen, T. K. Korhonen, S. Stuart, F. Ørskov and I. Ørskov (1986) Clonal analysis of Escherichia coli O2:K1 isolated from diseased humans and animals. Infect. Immun. 51: 268-276.
Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. M. Gilmour and T. S. Whittam (1986) Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51: 873-884.
Foltz, D. W., H. Ochman, J. S. Jones and R. K. Selander (1985) Genetic heterogeneity within and among morphological types of the parthenogenetic snail Potamopyrgus jenkinsi. J. Moll. Studies 115: 242-245.
Levin, M. H., R. A. Weinstein, C. Nathan, R. K. Selander, H. Ochman and S. A. Kabins (1985) Association of infection caused by Pseudomonas aeruginosa serotype O11 with intravenous abuse of Pentazocine. J. Clin. Microbiol. 20: 758-762.
Foltz, D. W., H. Ochman and R. K. Selander (1984) Genetic diversity and breeding systems in terrestrial slugs of the families Arionidae and Limacidae. Malacologia 25: 593-605.
Ochman, H. and R. K. Selander (1984) Evidence for clonal population structure in Escherichia coli. Proc. Natl. Acad. Sci. USA 81: 198-201.
Ochman, H. and R. K. Selander (1984) Standard reference strains of Escherichia coli from natural populations. J. Bacteriol. 157: 690-693.
Ochman, H., R. A. Wilson, T. S. Whittam, and R. K. Selander (1984) Genetic diversity within serotypes of Escherichia coli, In Proceedings of the Fourth International Symposium on Neonatal Diarrhea. Veterinary Infectious Diseases Organization, University of Saskatchewan. VIDO Publications, Saskatoon, Canada, pp. 202-224.
Ochman, H., J. S. Jones and R. K. Selander (1983) Molecular area effects in Cepaea. Proc. Natl. Acad. Sci. USA 80: 4189-4193.
Ochman, H., T. S. Whittam, D. A. Caugant and R. K. Selander (1983) Enzyme polymorphism and genetic population structure in Escherichia coli and Shigella. J. Gen. Microbiol. 129: 2715-2726.
Selander, R. K. and H. Ochman (1983) The genetic structure of populations as illustrated by molluscs. In M. C. Rattazzi et al. (eds.) Isozymes: Current Topics in Biological and Medical Research. A. R. Liss, NY, pp. 93-123.
Whittam, T. S., H. Ochman and R. K. Selander (1983) Enzyme polymorphism and multilocus genetic structure in natural populations of Escherichia coli. Proc. Natl. Acad. Sci. USA 80: 1751-1755.
Whittam, T. S., H. Ochman and R. K. Selander (1983) Geographic components of linkage disequilibrium in natural populations of Escherichia coli. Mol. Biol. Evol. 1: 67-83.
Foltz, D. W., H. Ochman, J. S. Jones, S. M. Evangelisti and R. K. Selander (1982) Genetic population structure and breeding systems in arionid slugs. Biol. J. Linn. Soc. 17: 225-241.
Ochman, H., B. Stille, M. Niklasson, R. K. Selander and A. R. Templeton (1980) Evolution of parthenogenesis in the spear-winged fly Lonchoptera dubia. Evolution 34: 539-547.
Stille, B., H. Ochman and R. K. Selander (1980) Genetic structure of populations of Aporrectodea tuberculata. Oikos 34: 195-201.