Last updated 24 July 2024
Uz-Zaman M. H., S. D'Alton, J. E. Barrick, and H. Ochman (2024) Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli. PLoS Biol. 22:e3002418. doi: 10.1371/journal.pbio.3002418. online
Ochman H., E. M. Quandt , N. Gottell, and J. A. Gilbert (2024) Examining the taxonomic distribution of tetracycline resistance in a wastewater plant. Sustain Microbiol. 1(1):qvad003. doi: 10.1093/sumbio/qvad003 online
Kirchberger P. C. and H. Ochman (2023) Microviruses: A World Beyond phi X174. Annu Rev Virol. 10(1):99-118. doi: 10.1146/annurev-virology-100120-011239. online
Cobo-Simón M., R. Hart, and H. Ochman (2023) Gene flow and species boundaries of the genus Salmonella. mSystems. 8(4):e0029223. doi: 10.1128/msystems.00292-23 online
Cobo-Simón M., R. Hart, and H. Ochman (2023) Escherichia coli: What is and Which are? Mol Biol Evol. 40(1):msac273. doi: 10.1093/molbev/msac273.online
Edwards O., G. Jander, H. Ochman, R. Schuurink, and K. B. Singh (2022) Insects co-opt host genes to overcome plant defences. Fac Rev. 11(10). doi: 10.12703/r-01-000007 online
Kirchberger P. C., Z. A. Martinez, and H. Ochman (2022) Organizing the Global Diversity of Microviruses. mBio 13(3):e0058822. doi: 10.1128/mbio.00588-22 online
Nishida A.H. and H. Ochman (2021) Captivity and the co-diversification of great ape microbiomes. Nat Commun. 12(1):5632. doi: 10.1038/s41467-021-25732-y. online
Kirchberger P.C. , Z. A. Martinez, L. J. Luker, and H. Ochman (2021) Defensive hypervariable regions confer superinfection exclusion in microviruses. Proc Natl Acad Sci U S A . 118(28) e2102786118. doi: 10.1073/pnas.2102786118 online
Li Y., A. C. O'Donnell, and H. Ochman (2021) Discriminating arboviral species. J Gen Virol. 102(4). doi: 10.1099/jgv.0.001572 online
Bobay L. M., A. C. O'Donnell, and H. Ochman (2021) Recombination events are concentrated in the spike protein region of Betacoronaviruses. PLoS Genet. 16(12):e1009272. doi: 10.1371/journal.pgen.1009272. online
Kirchberger P. C., M. Schmidt, and H. Ochman (2020) The Ingenuity of Bacterial Genomes. Annu Rev Microbiol. 74:815-834. doi: 10.1146/annurev-micro-020518-115822 online
Kirchberger P. C. and H. Ochman (2020) Resurrection of a Global, Metagenomically Defined Gokushovirus. eLife 9:e51599 doi: 10.7554/eLife.51599 online
Moran N. A., H. Ochman, and T. J. Hammer (2019) Evolutionary and Ecological Consequences of Gut Microbial Communities. Annu Rev Ecol Syst. Vol. 50: 451-475. online
Nishida A. H. and H. Ochman (2019) A great-ape view of the gut microbiome. Nat Rev Genet. 20: 195-206. doi: 10.1038/s41576-018-0085-z online
Bobay L. M. and H. Ochman (2018) Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol. 18: 153. doi: 10.1186/s12862-018-1272-4. online
Bobay, L. M. and H. Ochman (2018). Biological species in the viral world. Proc Natl Acad Sci U S A. 115: 6040-6045. doi: 10.1073/pnas.1717593115 online
Bobay, L. M., B. S. Ellis, H. Ochman (2018). ConSpeciFix: Classifying prokaryotic species based on gene flow. Bioinformatics. 34: 3738-3740. doi: 10.1093/bioinformatics/bty400 online
Traverse, C. C. and H. Ochman (2018). A Genome-Wide Assay Specifies Only GreA as a Transcription Fidelity Factor in Escherichia coli. G3 (Bethesda). 8: 2257-2264. doi: 10.1534/g3.118.200209 online
Quandt, E. M., C. C. Traverse, and H. Ochman. (2018). Local genic base composition impacts protein production and cellular fitness. PeerJ. 6:e4286. doi: 10.7717/peerj.4286. online
Costea, P.I., F. Hildebrand, A. Manimozhiyan, F. Bäckhed, M. J. Blaser, F. D. Bushman, W. M. de Vos, S. D. Ehrlich, C. M. Fraser, M. Hattori, C. Huttenhower, I. B. Jeffery, D. Knights, J. D. Lewis, R. E. Ley, H. Ochman, P. W. O'Toole, C. Quince, D. A. Relman, F. Shanahan, S. Sunagawa, J. Wang, G. M.Weinstock, G. D. Wu, G. Zeller, L. Zhao, J. Raes, R. Knight , and P. Bork. (2018). Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 3: 8-16. doi: 10.1038/s41564-017-0072-8. online
Nishida, A. H. and H. Ochman (2017). Rates of Gut Microbiome Divergence in Mammals. Mol Ecol. 27: 1884-1897. doi: 10.1111/mec.14473. online
Traverse, C. C. and H. Ochman (2017). Genome-wide spectra of transcription insertions and deletions reveal that slippage depends on RNA:DNA hybrid complementarity. mBio 8:e01230-17. doi: 10.1128/mBio.01230-17 online
Bobay, L. M, and H. Ochman (2017). Impact of recombination on the base composition of Bacteria and Archaea. Mol Biol Evol. 34(10):2627-2636. doi: 10.1093/molbev/msx189. online
Bobay, L. M. and H. Ochman (2017). The evolution of bacterial genome architecture. Front Genet. 8:72. doi: 10.3389/fgene.2017.00072 online
Raymann, K., A. H. Moeller, A. L. Goodman, and H. Ochman (2017). Unexplored Archaeal diversity in the great ape gut microbiome. mSphere. 2(1). pii: e00026-17. doi: 10.1128/mSphere.00026-17. online
Bobay, L. M., and H. Ochman (2017). Biological species are universal across Life's domains. Genome Biol Evol. 3: 491–501. doi: 10.1093/gbe/evx026 online
Moeller, A. H., A. Caro-Quintero, D. Mjungu, A. V. Georgiev, E. V. Lonsdorf, M. N. Muller, A. E. Pusey, M. Peeters, B. H. Hahn, and H. Ochman (2016). Cospeciation of gut microbiota with hominids. Science 353: 380-382. doi: 10.1126/science.aaf3951 online
Wexler, A. G., Y. Bao, J. C. Whitney, L. M. Bobay, J. B. Xavier, W. B. Schofield, N. B. Barry, A. B. Russell, B. Q. Tran, Y. A. Goo, D. R. Goodlett, H. Ochman, J. D. Mougous , and A. L. Goodman (2016). Human symbionts inject and neutralize antibacterial toxins to persist in the gut. Proc Natl Acad Sci U S A. 113: 3639-3644. doi: 10.1073/pnas.1525637113 online
H. Ochman (2016). Realizing Microbial Evolution. Cold Spring Harb Perspect Biol. 2016 Mar 1. 8(5). pii: a018101. doi: 10.1101/cshperspect.a018101 online
Traverse, C. C. and H. Ochman (2016). Conserved rates and patterns of transcription errors across bacterial growth states and lifestyles. Proc Natl Acad Sci U S A.113: 3311-3316. doi: 10.1073/pnas.1525329113 online
Moeller, A. H., S. Foerster, M. L. Wilson, A. E. Pusey, B. H. Hahn, and H. Ochman (2016). Social behavior shapes the chimpanzee pan-microbiome. Sci Adv. 2: e1500997. online
Caro-Quintero, A. and H. Ochman (2015). Assessing the Unseen Bacterial Diversity in Microbial Communities. Genome Biol Evol. 2015 Nov 27. pii: evv234. [Epub ahead of print] online
Bobay, L. M., C. C. Traverse, and H. Ochman (2015). Impermanence of bacterial clones. Proc Natl Acad Sci U S A. 112: 8893-8900. online
Kelkar, Y. D., D. S. Phillips, and H. Ochman (2015). Effects of Genic Base Composition on Growth Rate in G+C-Rich Genomes. G3 (Bethesda). 5: 1247-1252. online
Moeller, A. H., M. Peeters, A. Ayouba, E. M. Ngole, A. Esteban, B. H. Hahn, and H. Ochman (2015). Stability of the Gorilla Microbiome Despite SIV Infection. Mol Ecol. 4: 690-697. doi: 10.1111/mec.13057. online
Raghavan, R., F. R. Kacharia, J. A. Millar, C. D. Sislak, and H. Ochman (2015). Genome rearrangements can make and break small RNA genes. Genome Biol Evol. 7: 557-566.
Waldor, M. K., G. Tyson, E. Borenstein, H. Ochman, A. Moeller, B. B. Finlay, H. H. Kong, J. I. Gordon, K. E. Nelson, K. Dabbagh K, and H. Smith (2015). Where Next for Microbiome Research? PLoS Biol. 13(1):e1002050. online
Moeller, A. H., Y. Li, E. Mpoudi Ngole, S. Ahuka-Mundeke, E. V. Lonsdorf, A. E. Pusey, M. Peeters, B. H. Hahn, and H. Ochman (2014). Rapid changes in the gut microbiome during human evolution. Proc Natl Acad Sci U S A. 111: 16431-16435. doi: 10.1073/pnas.1419136111. online
Moeller A. H. and H. Ochman. (2014). Microbiomes are true to type. Proc Natl Acad Sci U S A. 111: 9372-9373. online
Sloan, D. B., G. M. Bennett, P. Engel, D. Williams, and H. Ochman (2013). Disentangling associated genomes. Methods in Enzymology 531: 445–464. online
Moeller, A. H., M. Shilts, Y. Li, R. S. Rudicell, E. V. Lonsdorf, A. E. Pusey, M. L. Wilson, B. H. Hahn, and H. Ochman (2013). SIV-Induced instability of the chimpanzee gut microbiome. Cell Host Microbe 14: 340-345. online
Moeller, A. H., and H. Ochman (2013). Factors that drive variation among gut microbial communities. Gut Microbes. 4:403-408. online
Williams, D., W. L. Trimble, M. Shilts, F. Meyer, and H. Ochman (2013). Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes. BMC Genomics 14:537. online
Moeller, A. H., M. Peeters, J. B. Ndjango, Y. Li, B. H. Hahn, and H. Ochman (2013). Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res. 23: 1715-20. online
Kelkar, Y. D. and H. Ochman (2013). Genome reduction promotes increase in protein functional complexity in bacteria. Genetics 193: 303-7. online
Moeller, A. H., P. H. Degnan, A. E. Pusey, M. L. Wilson, B. H. Hahn and H. Ochman (2012). Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat Comm. 3: 1179 doi:10.1038/ncomms2159. online
Raghavan, R., Y. D. Kelkar, and H. Ochman (2012). A selective force favoring increased G+C content in bacterial genes. Proc Natl Acad Sci U S A. 109: 14504-14507. online
Raghavan, R., D.B. Sloan, and H. Ochman (2012). Antisense transcription is pervasive but rarely conserved in enteric bacteria. MBio. 3:1-7. online
Degnan, P. H., A. E. Pusey, E. V. Lonsdorf , J. Goodall, E. E. Wroblewski, M. L. Wilson, R. S. Rudicell, B. H. Hahn, and H. Ochman (2012). Factors associated with the diversification of the gut microbial communities within chimpanzees from Gombe National Park. Proc Natl Acad Sci U S A. 109: 13034-13039. online
Kelkar, Y. D. and H. Ochman (2012). Causes and consequences of genome expansion in fungi. Genome Biol Evol. 4:13-23. online
Degnan, P. H. and H. Ochman (2012). Illumina-based analysis of microbial community diversity. ISEM J. 6:183-4. online
Degnan, P. H., H. Ochman, and N. A. Moran (2011). Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera. PLoS Genet. 7(9): e1002252. online
Raghavan, R., E. A. Groisman, and H. Ochman (2011). Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res. 21: 1487-97. online
Raghavan, R., A. Sage, and H. Ochman (2011). Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli. J. Bacteriol. 193:2871-74. online
Ochman, H., M. Worobey, C. H. Kuo, J. B. Ndjango, M. Peeters, B. H. Hahn, and P. Hugenholtz (2010). Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology. 8: e1000546. online
Kuo, C. H., and H. Ochman (2010) The extinction dynamics of bacterial pseudogenes. PLoS Genet. 6: e1001050. online
Vaishampayan, P. A., J. V. Kuehl, J. L. Froula, J. L. Morgan, H. Ochman, and M. P. Francino (2010). Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol. Evol. 2010:53-66. pdf, online
Engelbrektson, A., V. Kunin, K. C. Wrighton, N. Zvenigorodsky, F. Chen, H. Ochman, and P. Hugenholtz (2010). Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4:642-7. pdf
Jarvik, T., C. Smillie, E. A. Groisman, and H. Ochman (2010). Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome. J. Bacteriol. 192:560-7. pdf
Stavrinides, J., A. No, and H. Ochman (2010). A single genetic locus in the phytopathogen Pantoea stewartii enables gut colonization and pathogenicity in an insect host. Environ. Microbiol. 12:147-55. pdf
Ochman, H. and R. Raghavan. (2009). Systems Biology. Excavating the functional landscape of bacterial cells (Perspective). Science 326:1200-1. pdf
Kuo, C. H. and H. Ochman. (2009). Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria. Biol. Direct. 4:35. pdf
Ochman, H. (2009). Afterword: Genomics Update update. Environ. Microbiol. 11:2193. pdf
Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz (2009). Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environ. Microbiol. 12:118-23. pdf
Kuo, C. H., N .A. Moran, and H. Ochman (2009). The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-4. pdf
Ochman, H. (2009). Radical views of the Tree of Life. Environ. Microbiol. 11:731-2. pdf
Stavrinides, J., J. K. McCloskey, and H. Ochman (2009). The pea aphid as both host and vector for the phytopathogenic bacterium, Pseudomonas syringae. Appl. Environ. Microbiol. 75:2230-5. pdf
Kuo, C. H., and H. Ochman (2009). Deletional bias across the three domains of life. Genome Biol. Evol. 1:145-152. pdf
Kuo, C. H., and H. Ochman (2009). The fate of new bacterial genes. FEMS Microbiol. Rev. 33:38-43. pdf
Narra, H. P., M. H. Cordes, and H. Ochman (2008). Structural features and the persistence of acquired proteins. Proteomics. 8:4772-81. pdf
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. pdf
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. pdf
van Passel, M. W. and H. Ochman (2007). Selection on the genic location of disruptive elements. Trends Genet. 23:601-4. pdf
Liu, R. and H. Ochman (2007). Origins of flagellar gene operons and secondary flagellar systems. J. Bacteriol. 189:7098-104. pdf
Liu, R. and H. Ochman (2007). Stepwise formation of the bacterial flagellar system. Proc. Natl. Acad. Sci. U S A 104:7116-21. pdf Erratum 104:11507 pdf
H. Ochman (2007). Single-cell genomics. Environ. Microbiol. 9:7. pdf
van Passel, M. W., C. S. Smillie, and H. Ochman (2007). Gene decay in Archaea. Archaea. 2:137-143. pdf
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. pdf
Narra, H.P. and H. Ochman (2006). Of what use is sex to bacteria? Curr. Biol. 16:R705-R710. pdf
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. pdf
Ochman, H. and L.M. Davalos (2006). The nature and dynamics of bacterial genomes. Science 311:1730-1733. pdf
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. pdf
Ochman, H. (2005). Genomes on the shrink. Proc. Natl. Acad. Sci U S A 102:11959-11960. pdf
Lerat, E. and H. Ochman (2005). Recognizing pseudogenes in bacterial genomes. Nucleic Acids Research, 33(10):3125-32. pdf
Lerat, E., V. Daubin, H. Ochman, and N. A. Moran (2005). Evolutionary origins of genomic repertoires in bacteria. PloS Biology, 3(5):e130. pdf
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. pdf
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. pdf
Ochman, H. and S. R. Santos. (2005). Exploring microbial microevolution with microarrays. Infect. Genet. Evol. 5:103-108. pdf
Dale, C., H. Dunbar, N. A. Moran, 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.pdf
Daubin, V. and H. Ochman (2004). Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res. 14: 1036-1042. pdf
Daubin, V. and H. Ochman (2004). Start-up entities in the evolution of new genes. Curr. Opin. Genet. Devel. 14: 616-619. pdf
Lerat, E. and H. Ochman (2004). Ψ-Φ: Exploring the outer limits of bacterial pseudogenes. Genome Research 14: 2273-2278. pdf
Daubin, V. and H. Ochman (2004). Recognizing lateral gene transfer by quartet mapping. Molec. Biol. Evol. 21: 48-51. pdf
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. pdf
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. pdf
Daubin, V., N. A. Moran, and H. Ochman (2003). Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832. pdf
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. pdf
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. pdf
Ochman, H. (2003). Neutral mutations and neutral substitutions in bacterial genomes. Molec. Biol. Evol. 20: 2091-2096. pdf
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. pdf
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. pdf
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. pdf
Lawrence, J. G. and H. Ochman (2002). Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10: 1-4. pdf
Mira, A. and H. Ochman (2002). Gene location and bacterial sequence divergence. Molec. Biol. Evol. 19: 1350-1358. pdf
Ochman, H. (2002). Chromosome arithmetic and geometry. Curr. Biol. 12: R427-R428. pdf
Ochman, H. (2002). Distinguishing the ORFS from the ELFs: Short bacterial genes and the over-annotation of genomes. Trends Genet. 18: 335-337. pdf
Ochman, H. (2002). Side-stepping genetics. (Book review) Nature Cell Biol. 4: E158. pdf
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. pdf
Mira, A., H. Ochman, and N. A. Moran (2001). Deletional bias and the evolution of bacterial genomes. Trends Genet. 10: 589-596. pdf
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. pdf
Ochman, H. (2001). Lateral and oblique gene transfer. Curr. Opin. Genet. Devel. 11: 616-619. pdf
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. pdf
Francino, M. P. and H. Ochman (2000). Strand symmetry around the ß-globin origin of replication in primates. Molec. Biol. Evol. 17: 416-422. pdf
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. pdf
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. pdf
Ochman, H., J. G. Lawrence, and E. A. Groisman (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-305. pdf
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. pdf
Bergthorsson, U. and H. Ochman (1999). Chromosomal changes during experimental evolution in laboratory populations of Escherichia coli. J. Bacteriol. 181: 1360-1363. pdf
Francino, M. P. and H. Ochman (1999). A comparative genomics approach to DNA asymmetries. Ann. NY Acad. Sci. 870: 428-431. pdf
Francino, M. P. and H. Ochman (1999). Isochores result from mutation not selection. Nature 400: 30-31. pdf
Ochman, H. (1999). Bacterial evolution: Jittery genomes. Curr. Biol. 9: 485-486. pdf
Ochman, H. (1999). Editorial Overview. Curr. Opin. Microbiol. 2: 517-518. pdf
Ochman, H., S. Elwyn, and N. A. Moran (1999). Calibrating bacterial evolution. Proc. Natl. Acad. Sci. USA 96: 12638-12643. pdf
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. pdf
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. pdf
Ochman, H. and U. Bergthorsson (1998). Rates and patterns of chromosome evolution in enteric bacteria. Curr. Opin. Microbiol. 1: 580-583. pdf
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.pdf
Francino, M. P. and H. Ochman (1997). Strand asymmetries in DNA evolution. Trends in Genetics 13: 240-245. pdf
Groisman, E. A. and H. Ochman (1997). How Salmonella became a pathogen. Trends in Microbiol. 5: 343-349. pdf
Lawrence, J. G. and H. Ochman (1997). Amelioration of bacterial genomes: rates of change and exchange. J. Molec. Evol. 44: 383-397. pdf
Ochman, H. (1997) Miles of isles. Trends Microbiol. 5: 222. pdf
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. pdf
Groisman, E. A. and H. Ochman (1996). Pathogenicity islands: quantum leaps in bacterial evolution. Cell 87: 791-794. pdf
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. pdf
Ochman, H., F. C. Soncini, F. Solomon, 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. pdf
Bergthorsson, U. and H. Ochman (1995). Heterogeneity of genome size among natural isolates of Escherichia coli. J. Bacteriol. 177: 5784-5789. pdf
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. pdf
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. pdf
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. pdf
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. pdf
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. pdf
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. pdf
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. pdf
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.
