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Naomi Ward

  1. Liesack, W., N. Ward, and E. Stackebrandt. 1991. Strategies for molecular microbial ecological studies. Actinomycetes 2:63-76.
  2. Rainey, F., N. Ward, H. Morgan, and E. Stackebrandt. 1993. The phylogenetic diversity of thermophilic anaerobes within the domain Bacteria, p. 573-577. In R. Guerrero and C. Pedros-Alio (ed.). Trends in Microbial Ecology, Spanish Society for Microbiology.
  3. Stackebrandt, E., W. Liesack, N. Ward, and B. M. Goebel. 1993. Genetic diversity of unculturable strains present in natural communities, p. 567-572. In R. Guerrero and C. Pedros-Alio (ed.). Trends in Microbial Ecology, Spanish Society for Microbiology.
  4. Rainey, F. A., N. L. Ward, H. W. Morgan, R. Toalster, and E. Stackebrandt.1993. Phylogenetic analysis of anaerobic thermophilic bacteria: aid for their reclassification. Journal of Bacteriology 175:4772-4779.
  5. Rainey, F. A., N. Ward, L. I. Sly, and E. Stackebrandt. 1994. Dependence on the taxon composition of clone libraries for PCR-amplified, naturally occurring 16S rDNA, on the primer pair and cloning system used. Experientia 50:796-797.
  6. Ward, N., F. A. Rainey, E. Stackebrandt, and H. Schlesner. 1995. Unraveling the extent of diversity within the order Planctomycetales. Applied and Environmental Microbiology 61:2270-2275.
  7. Stackebrandt, E., and N. Ward. 1995. Extraction of ribosomal RNA from microbial cultures, 1.6.2, p. 1-11. In A. D. L. Akkermans, J. D. van Elsas, and F. J. De Bruijn (ed.). Molecular Microbial Ecology Manual. Kluwer Academic Publishers, Dordrecht, The Netherlands.
  8. Ward, N., F. A. Rainey, B. Goebel, and E. Stackebrandt. 1995. Identifying and culturing the ‘unculturables’ - a challenge for microbiologists, p. 89-110. In D. Allsopp, D. L. Hawksworth and R. R. Colwell (ed.). Microbial diversity and ecosystem function. CAB International, Egham.
  9. Ward-Rainey, N., F. A. Rainey, H. Schlesner, and E. Stackebrandt. 1995. Assignment of hitherto unidentified 16S rDNA species to a main line of descent within the domain Bacteria. Microbiology (United Kingdom) 141:3247-3250.
  10. Ward-Rainey, N., F. A. Rainey, and E. Stackebrandt. 1996. Physical map of the genome of Planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage. Journal of  Bacteriology 178:1908-1913.
  11. Ward-Rainey, N., F. A. Rainey, and E. Stackebrandt. 1996. The phylogenetic structure of the genus Streptosporangium. Systematic and Applied Microbiology 19:50-55.
  12. Rainey, F. A., N. Ward-Rainey, P. H. Janssen, H. Hippe, and E. Stackebrandt. 1996. Clostridium paradoxum DSM 7308T contains multiple 16S rRNA operons with heterogeneous intervening sequences (IVSs). Microbiology (United Kingdom) 142:2087-2095.
  13. Ward-Rainey, N., F. A. Rainey, and E. Stackebrandt. 1996. A study of the bacterial flora associated with Holothuria atra. Journal of Experimental Marine Biology and Ecology 203:11-26.
  14. Rainey, F. A., N. Ward-Rainey, R. M. Kroppenstedt, and E. Stackebrandt. 1996. The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage; proposal of Nocardiopsaceae fam. nov. International Journal of Systematic Bacteriology 46:1088-1092.
  15. Stackebrandt, E., F. A. Rainey, and N. Ward-Rainey. 1996. Anoxygenic phototrophy across the phylogenetic spectrum: current understanding and future perspectives. Archives of Microbiology 166:211-223.
  16. Hain, T., N. Ward-Rainey, R. M. Kroppenstedt, E. Stackebrandt, and F. A. Rainey. 1997. Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S-23S rDNA intergenic spacers.International Journal of  Systematic Bacteriology 47:202-206.
  17. Stackebrandt, E., F. A. Rainey, and N. L. Ward-Rainey. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov.. International Journal of Systematic Bacteriology 47:479-491.
  18. Ward-Rainey, N., F. A. Rainey, and E. Stackebrandt. 1997. The presence of a dnaK (HSP70) multigene family in members of the orders Planctomycetales and Verrucomicrobiales. Journal of Bacteriology 179:6360-6366.
  19. Liesack, W., P. H. Janssen, F. A. Rainey, N. L. Ward-Rainey, and E. Stackebrandt. 1997. Microbial Diversity in Soil: The need for a combined approach using molecular and cultivation techniques. In D. van Elsas, J. T. Trevors, and E. M. H. Wellington (eds.), Modern Soil Microbiology, Marcel Dekker, New York.
  20. F. A. Rainey, N. Ward-Rainey, C. G. Gliesche, and E. Stackebrandt. 1998. Phylogenetic analysis and intrageneric structure of the genus Hyphomicrobium and the related genus Filomicrobium. International Journal of Systematic Bacteriology 48:635-639.
  21. Leary, B. A., N. Ward-Rainey, and T. R. Hoover. 1998. Cloning and characterization of Planctomyces limnophilus rpoN: complementation of a Salmonella typhimurium rpoN mutant strain. Gene 221:151-157.
  22. Clark, C. A., C. Chen, N. Ward-Rainey, and G. S. Pettis. 1998. Diversity within Streptomyces ipomoeae based on inhibitory interactions, rep-PCR, and plasmid profiles. Phytopathology 88:1179-1186.
  23. Griepenburg, U., N. Ward-Rainey, S. Mohamed, H. Schlesner, H. Marxsen, F. A. Rainey, E. Stackebrandt, and G. Auling. 1999. Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales. International Journal of Systematic Bacteriology 49:689-696.
  24. Rainey, F. A., K. E. Ray, and N. Ward-Rainey. 1999. Camels of the prokaryotic world. Revised Proceedings of the Eighth International Symposium on Microbial Ecology (ISME-8), Halifax, Canada, August, 1998.
  25. Rainey, F. A., and N. Ward-Rainey. 2000. Prokaryotic Diversity. In Seckbach, J. (ed.), Microbial Diversity (Cellular Origin and Life in Extreme Habitats series). Kluwer, The Netherlands.
  26. Borodina, E., D. P. Kelly, F. A. Rainey, N. L. Ward-Rainey, and A. P. Wood. 2000. Dimethylsulfone as a growth substrate for novel methylotrophic species of Hyphomicrobium and Arthrobacter. Archives of Microbiology 173:425-437.
  27. N.L. Ward, F. A. Rainey, B. P. Hedlund, J. T. Staley, W. Ludwig, and E. Stackebrandt. 2000. Comparative phylogenetic analysis of members of the orders Planctomycetales and Verrucomicrobiales: 23S rDNA sequence analysis supports the 16S rDNA-derived phylogeny. International Journal of Systematic and Evolutionary Microbiology 50:1965-1972.
  28. Pettis, G. S., N. Ward, and K. Schully. 2001. Expression characteristics of the transfer-related kilB gene product of Streptomyces plasmid pIJ101: implications for the plasmid spread function. Journal of Bacteriology 183:1339-1345.
  29. Ward, N., J. Eisen, C. Fraser, and E. Stackebrandt. 2001. Sequenced strains must be saved from extinction. Nature 414:148.
  30. Heidelberg,  J.F., I.T. Paulsen, K.E. Nelson, E.J. Gaidos, W.C. Nelson, T.D. Read, J.A. Eisen, R. Seshadri, N. Ward, B. Methe, R.A. Clayton, T. Meyer, A. Tsapin, J. Scott, M. Beanan, L. Brinkac, S. Daugherty, R.T. DeBoy, R.J. Dodson, A.S. Durkin, D.H. Haft, J.F. Kolonay, R. Madupu, J.D. Peterson, L.A. Umayam, O. White, A.M. Wolf, J. Vamathevan, J. Weidman, M. Impraim, K. Lee, K. Berry, C. Lee, J. Mueller, H. Khouri, J. Gill, T. R. Utterback, L.A. McDonald, T.V. Feldblyum, H.O. Smith, J.C. Venter, K.H. Nealson, and C.M. Fraser. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature Biotechnology 11:1118-23.
  31. Borodina, E. D.P. Kelly, P. Schumann, F.A. Rainey, N.L. Ward-Rainey, A.P. Wood. 2002. Enzymes of dimethylsulfone metabolism and the phylogenetic characterization of the facultative methylotrophs Arthrobacter sulfonivorans sp. nov., Arthrobacter methylotrophus sp. nov., and Hyphomicrobium sulfonivorans sp. nov. Archives of Microbiology 177:173 – 183.
  32. Seshadri, R., I.T. Paulsen, J.A. Eisen, T.D. Read, K.E. Nelson, W.C. Nelson, N. Ward, H. Tettelin, T. M. Davidsen, M. J. Beanan, R.T. Deboy, S.C. Daugherty, L.M. Brinkac, R. Madupu, R.J. Dodson, H.M. Khouri, K.H. Lee, H.A. Carty, D. Scanlan, R.A. Heinzen, H.A. Thompson, J.E. Samuel, C.M. Fraser, and J.F. Heidelberg. 2003.  Complete genome sequence of the Q-fever pathogen Coxiella burnetii. Proceedings of the National Academy of Sciences 100(9):5455-60.
  33. Shank, T., D. Fornari, D. Yoerger, S. Humphris, A. Bradley, S. Hammond, J. Lupton, D. Scheirer, R. Collier, A.-L. Reysenbach, K. Ding, W. Seyfried, D. Butterfield, E. Olson, M. Lilley, N. Ward, and J. Eisen. 2003. Deep submergence synergy: Alvin and ABE explore the Galápagos Rift at 86°W. Eos (Transactions, American Geophysical Union) 84:425-432.
  34. Methé, B.A., K.E. Nelson, J.A. Eisen, I.T. Paulsen, W. Nelson, J.F. Heidelberg, D. Wu, M. Wu, N. Ward, M.J. Beanan, R.J. Dodson, R. Madupu, L.M. Brinkac, S.C. Daugherty, R.T. DeBoy, A.S. Durkin, M. Gwinn, J.F. Kolonay, S.A. Sullivan, D.H. Haft, J. Selengut, T.M. Davidsen, N. Zafar, O. White, B. Tran, C. Romero, H.A Forberger, J. Weidman, H. Khouri, T.V. Feldblyum, T.R. Utterback, S.E. Van Aken, D.R. Lovley, and C.M. Fraser. 2003. Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments. Science. 302 (5652):1967-1969.
  35. Heidelberg, J. F., R. Seshadri, S.A. Haveman, C.L. Hemme, I.T. Paulsen, J.F. Kolonay, J.A. Eisen, N. Ward, B. Methe, L.M. Brinkac, S.C. Daugherty, R.T. Deboy, R.J. Dodson, A.S. Durkin, R. Madupu, W.C. Nelson, S.A. Sullivan, D. Fouts, D.H. Haft, J. Selengut, J.D. Peterson, T.M. Davidsen, N. Zafar, L. Zhou, D. Radune, G. Dimitrov, M. Hance, K. Tran, H. Khouri, J. Gill, T.R. Utterback, T.V. Feldblyum, J.D. Wall, G. Voordouw, and C.M. Fraser. 2004. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough: consequences for its energy metabolism and reductive metal bioremediation. Nature Biotechnology 22 (5) :554-9.
  36. Ward, N., Ø. Larsen, J.A. Eisen, H. Khouri, A.S. Durkin, G. Dimitrov, L. Jiang, D. Scanlan, K. Kang, M. Lewis, L. Bruseth, H. Tettelin, T. Read, B.  Methé, I. T. Paulsen, Q. Ren, D. Fouts, H.B. Jensen, S. Salzberg, R. Seshadri, K.E. Nelson, J.F. Heidelberg, R.T. DeBoy, R.J. Dodson, W. Nelson, T. Feldblyum, T. Utterback, S. Vanaken, N.K. Birkeland, I. Eidhammer, S. H. Grindhaug, I. Holt, I. Jonasen, J. Lillehaug, and C.M. Fraser. 2004. Genomic Insights into Methanotrophy: the Complete Genome Sequence of Methylococcus capsulatus (Bath).  Public Library of Science Biology. Vol. 2, No. 10, e303 DOI: 10.1371/journal.pbio.0020303.
  37. Ward, N., J.T. Staley, J.A. Fuerst, S. Giovannoni, H. Schlesner, and E. Stackebrandt. 2004. The Order Planctomycetales, including the Genera Planctomyces, Pirellula, Gemmata, and Isosphaera, and the Candidatus genera Brocadia, Kuenenia, and Scalindua, In: M. Dworkin et al., (eds). The Prokaryotes, An Evolving Electronic Resource for the Microbiology Community, 3rd edition. Springer-Verlag, New York. Release 3.18. http://141.150.157.117:8080/prokPUB/index.htm.
  38. Bauer, M., T. Lombardot, H. Teeling, N.L. Ward, R.I. Amann, and FO Glockner. 2004. Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum. Journal of Molecular Evolution 59:571-86.
  39. Moran, M. A., A. Buchan, J.M. González, J.F. Heidelberg, J. Henriksen, W.B. Whitman, R.P. Kiene, L. Brinkac, M. Lewis, S. Johri, B. Weaver, G. Pai, J.A. Eisen, G. King, M.R. Belas, C. Fuqua, E. Rahe, W. Sheldon, W. Ye, J.M. Carlton, D.A. Rasko, I.T. Paulsen, Q. Ren, S.C. Daugherty, R.T. Deboy, R.J. Dodson, A.S. Durkin, R. Madupu, W.C. Nelson, S.A. Sullivan, M. J. Rosovitz, D.H. Haft, J. Selengut,  and N. Ward. 2004. Genome Sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.
  40. Badger, J.H., J.A. Eisen, and N. Ward. 2005. Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA-based phylogenetic analysis; implications for the taxonomy of the orders Rhodobacterales and Caulobacterales. International Journal of Systematic and Evolutionary Microbiology 55:1021-6.
  41. Seshadri, R., L. Adrian, D.E. Fouts, J.A. Eisen, A.M. Phillippy, B.A. Methe, N.L. Ward, W.C. Nelson, R.T. Deboy, H.M. Khouri, J.F. Kolonay, R.J. Dodson, S.C. Daugherty, L.M. Brinkac, S.A. Sullivan, R.Madupu, K.E. Nelson, K.H. Kang, M. Impraim, K. Tran, J.M. Robinson, H.A. Forberger, C.M. Fraser, S.H. Zinder and J.F. Heidelberg. 2005. Genome sequence of the anaerobic PCE-bioremediating bacterium Dehalococcoides ethenogenes. Science 307(5706):105-8. Link
  42. Tettelin, H., V. Masignani, M.J. Cieslewicz, C. Donati, D. Medini, N.L. Ward, S.V. Angiuoli, J. Crabtree, A. Jones, A.S. Durkin, R.T. DeBoy, T.M. Davidsen, M. Mora, M. Scarselli, D. Maione, I.M. Ros, J.D. Peterson, C.R. Hauser, J.P. Sundaram, W.C.Nelson, R. Madupu, L.M. Brinkac, R.J. Dodson, M.J. Rosovitz, S.A. Sullivan, S.C. Daugherty, D.H. Haft, J. Selengut, M.L. Gwinn, L. Zhou, N. Zafar, H. Khouri, D. Radune, G. Dimitrov, K. Watkins, K.J.B. O’Connor, S. Smith, T.R. Utterback, O. White, C.E. Rubens, G. Grandi, L.C. Madoff, D.L. Kasper, J.L. Telford, M.R. Wessels, R. Rappuoli, and C.M. Fraser. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences 102 (39) :13950-5. Link
  43. Ward, N., and C.M. Fraser. 2005. How genomics has affected the concept of microbiology. Current Opinions in Microbiology. 8(5):564-71. Link
  44. Morales, S.E., P.J. Mouser, N. Ward, S.P. Hudman, N.J. Gotelli, D.S. Ross and T.. Lewis. 2006. Comparison of Bacterial Communities in New England Sphagnum Bogs Using Terminal Restriction Fragment Length Polymorphism (T-RFLP). Microbial Ecology 52:34-44. Link
  45. Ward, N. 2006. New directions and interactions in metagenomics research. FEMS Microbiology Ecology  55:331-8. Link
  46. Jenkins, C., F.A. Rainey, N.L. Ward, and J.T. Staley. 2006. Genus Prosthecomicrobium. In D. Brenner, N.R. Krieg, J.T. Staley, and G.M. Garrity (eds). Bergey’s Manual of Systematic Bacteriology, Second Edition. Volume 2 Part C. pp. 538-543. Springer, New York.
  47. Penn, K., D. Wu, and N. Ward. 2006. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72(2):1680-3. Link
  48. Haft, D.H., I.T. Paulsen, N.L. Ward, and J.D. Selengut. 2006.  Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biology  4:29. Link
  49. Badger, J.H., T.R. Hoover, Y.V. Brun, R.M. Weiner, M.T. Laub, G. Alexandre, Q. Ren, I.T. Paulsen, K.E. Nelson, H. Khouri, D. Radune, J. Sosa, R.J. Dodson, S.A. Sullivan, M.J. Rosovitz, R. Madupu, L.M. Brinkac, A.S. Durkin, S.C. Daugherty, S.P. Kothari, M. GwinnGiglio, L. Zhou, D.H. Haft, J.D. Selengut, T.M Davidsen, Q.Y., N. Zafar and N.L. Ward. 2006. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus. Journal of Bacteriology 188:6841-50. Link
  50. von Mering, C., P. Hugenholtz, J. Raes, S.G. Tringe, T. Doerks, L. J. Jensen, N. Ward, and P. Bork. 2007. Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments. Science 315(5815):1126-30. Link
  51. Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M.J., Ashburner, M., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., dePamphilis, C.,  Edwards, R., Faruque, N., Feldman, R., Glöckner, F.O., Haft, D., Hancock, D., Hermjakob,  H., Hertz-Fowler, C.,  Hugenholtz, P., Joint, I., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kyrpides, N., Leebens-Mack, J., Lewis, S.E., Liste, A., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Moxon, R., Nelson, K., Parkhill, J., Sansone, S.-A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T., Wilson, G. and A. Wipat. 2008. The Minimum Information about a Genome Sequence (MIGS) Specification. Nature Biotechnology 26 (5): 541-547. Link
  52. Wu D, Hartman A, Ward N, Eisen JA. 2008. An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP). PLoS ONE 3(7): e2566 doi:10.1371/journal.pone.0002566. Link
  53. Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE. 4(1):e4207. Epub 2009 Jan 16. Link
  54. Ward, N.L., J.F. Challacombe, P.H. Janssen, B. Henrissat, P.M. Coutinho, M. Wu, G. Xie, D.H. Haft, M. Sait, J. Badger, R.D. Barabote,, B. Bradley, T.S. Brettin, L.M. Brinkac, D. Bruce, T. Creasy, S.C. Daugherty, T.M Davidsen, R.T. DeBoy, J.C. Detter, R.J. Dodson, A.S. Durkin, A. Ganapathy, M. Gwinn-Giglio, C.S. Han, H. Khouri, H. Kiss, S.P. Kothari, R. Madupu, K. Nelson, W.C. Nelson, I. Paulsen, K. Penn, Q. Ren, M.J. Rosovitz, J.D. Selengut, S. Shrivastava, S.A. Sullivan, R. Tapia, L.S. Thompson,  K.L. Watkins, Q. Yang, C. Yu, N. Zafar, L. Zhou, and C.R. Kuske. 2009. Three genomes from the Phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Applied and Environmental Microbiology 75(7): 2046-56. Link
  55. Ward NL, Steven B, Penn K, Methé BA, Detrich WH 3rd. 2009. Characterization of the intestinal microbiota of two Antarctic notothenioid fish species. Extremophiles. May 27. [Epub ahead of print]. Link