Gary Andersen's Publications

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Peer-Reviewed Publications

  1. Vaziri, N. D., Wong, J., Pahl, M., Piceno, Y. M., Yuan, J., DeSantis, T. Z., Ni, Z., Nguyen, T. H., and G. L. Andersen (2012) Chronic kidney disease alters intestinal microbial flora. Kidney Int. 2012 Sep 19 [Epub ahead of print] PMID: 22992469
  2. Korves, T. M., Piceno, Y. M., Tom, L. M., DeSantis, T. Z., Jones, B. W., Andersen, G. L., and G. L. Hwang (2012)  Bacterial communities in commercial aircraft high-efficiency particulate air (HEPA) filters assessed by PhyloChip analysis.  Indoor Air. 2012 May 7 [Epub ahead of print] PMID: 22941076
  3. Lam, V., Moulder, J. E., Salzman, N. H., Dubinsky, E. A., Andersen, G. L., and  J. E. Baker (2012) Intestinal microbiota as novel biomarkers of prior radiation exposure. Radiation Research 177: 573-583. PMID: 22439602
  4. Dubinsky, E.A., Esmaili, L., Hulls, J. R., Cao, Y., Griffith, J. F., and G. L. Andersen. (2012) Application of phylogenetic microarray analysis to discriminate sources of fecal pollution. Environmental Science & Technology 46: 4340-4347. PMID: 22360280 
  5. McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., DeSantis, T. Z., Probst, A., Andersen, G. L., Knight, R., and P. Hugenholtz. (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6:610-618.  PMID: 22134646
  6. Lee, P. K., Warnecke, F., Brodie, E. L., Macbeth, T. W., Conrad, M. E., Andersen, G. L., and L. Alvarez-Cohen. (2012) Phylogenetic Microarray Analysis of a Microbial Community Performing Reductive Dechlorination at a TCE-Contaminated Site. Environ Sci Technol. 46:1044-1054. PMID: 22091783
  7. Kellogg, C. A., Piceno, Y. M., Tom, L. M., DeSantis, T. Z., Zawada, D. G., and G. L. Andersen. (2011) PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology. J Microbiol Methods. 88:103-109. PMID: 22085912
  8. DeAngelis, K. M., Wu, C. H., Beller, H. R., Brodie, E. L., Chakraborty, R., DeSantis, T. Z., Fortney, J. L., Hazen, T. C., Osman, S. R., Singer, M. E., Tom, L. M., and G. L. Andersen. (2011) PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip. Appl. Environ. Microbiol. 77:6313-6322 PMID: 21764955
  9. Mendes, R., Kruijt, M., de Bruijn, I., Dekkers, E., van der Voort, M., Schneider, J. H., Piceno, Y. M., DeSantis, T. Z., Andersen, G. L., Bakker, P. A, and J. M. Raaijmakers. (2011) Deciphering the rhizosphere microbiome for disease-suppressive bacteria Science 332:1097-1100. PMID: 21551032
  10. DeSantis, T. Z., Keller, K., Karaoz, U., Alekseyenko, A. V., Singh, N. N., Brodie, E. L., Pei, Z., Andersen, G. L., and N. Larsen. (2011) Simrank: Rapid and sensitive general-purpose k-mer search tool. BMC Ecol. 11:11. PMID: 21524302
  11. Swarbreck, S. M., Lindquist, E. A., Ackerly, D. D., and G. L. Andersen. (2011) Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants. Plant Cell Physiol. 52:317-32. PMID: 21310848
  12. Hazen, T. C., Dubinsky, E. A., Desantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh. N. et. al. (2010) Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria. Science. 330:204-208 PMID: 20736401
  13. Wu, C. H., Sercu, B., Van de Werfhorst, L. C., Wong, J., DeSantis, T. Z., Brodie, E. L., Hazen, T. C., Holden, P. A., and G. L. Andersen. (2010) Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One. 5:e11285 PMID: 20585654
  14. Andersen, G. L., He. Z., DeSantis, T. Z., Brodie, E. L., and J. Zhou. (2010) The Use of Microarrays in Microbial Ecology, pp 87-110. In: Environmental Molecular Microbiology. Liu, W.T. and Jansson J. K. (Ed), Caister Academic Press, Norwich, UK.  ISBN 978-1-904455-52-3
  15. Rastogi, G., Osman, S., Kukkadapu, R., Engelhard, M., Vaishampayan, P. A., Andersen, G. L., and R. K. Sani. (2010) Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake Gold Mine, South Dakota. Microb Ecol. 59:94-108. PMID: 20386898
  16. La Duc, M. T., Osman, S., Vaishampayan, P., Piceno, Y., Andersen, G., Spry. J.A., and K. Venkateswaran. (2009) Comprehensive census of bacteria in clean rooms by using DNA microarray and cloning methods. Appl Environ Microbiol. 75:6559-6567. PMID: 19700540
  17. Andersen, G. L., Frisch, A.S., Kellogg, C.A., Levetin, E., Lighthart, B., Paterno, D. (2009) Aeromicrobiology/Air Quality, pages 11-26. In: The Encyclopedia of Microbiology, Third Edition. Moselio Schaechter (Ed),  Elsevier, Oxford, UK. ISBN 978-0-12-373939-1
  18. Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., and R. Knight.  (2009) PyNAST: A flexible tool for aligning sequences to a template alignment.  Bioinformatics  26:266-267. PMID: 19914921
  19. Fan, C., Lee, P. K, Ng, W. J., Alvarez-Cohen, L., Brodie, E. L., Andersen, G. L., and He, J. (2009) Influence of trace erythromycin and eryhthromycin-H2O on carbon and nutrients removal and on resistance selection in sequencing batch reactors (SBRs). Appl Microbiol Biotechnol. 85:185-95.
  20. Wu, C. H., Bernard, S. M., Andersen, G. L., Chen, W. (2009) Developing microbe-plant interactions as biotechnological tools. Microbial Biotechnology 2:428-440.
  21. Johnson, D. R., Nemir,  A., Andersen,  G. L., Zinder, S. H., Alvarez-Cohen L. (2009) Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiol. Lett. 294:198-206.
  22. Cruz-Martínez, K., Suttle, K. B., Brodie, E. L., Power, M. E., Andersen, G. L., and J. F. Banfield. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland.  ISME J. 3:738-744. PMID: 19279669
  23. Sagaram, U. S., DeAngelis, K. M., Trivedi, P., Andersen, G.L., Lu, S. E., Wang, N. (2009) Bacterial diversity analysis of Huanglongbing pathogen-infected citrus using PhyloChips and 16S rDNA clone library sequencing.  Appl. Env. Micro. 75:1566-1574.
  24. Sunagawa, S., DeSantis, T. Z., Piceno, Y. M., Brodie, E. L., DeSalvo, M. K., Voolstra, C. R., Weil, E., Andersen, G. L., Medina, M. (2009) Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J. 3:512-521.
  25. Yergeau, E., Schoondermark-Stolk, S. A., Brodie, E. L., Déjean, S., DeSantis, T. Z., Gonçalves, O., Piceno, Y. M., Andersen, G. L., and G. A. Kowalchuk. (2008) Environmental microarray analyses of Antarctic soil microbial communities. ISME J. 3:340-351. PMID: 19020556
  26. DeAngelis, K. M., Brodie, E. L., DeSantis, T. Z., Andersen, G. L., Lindow, S. E., Firestone, M. K. (2008) Selective progressive response of soil microbial community to wild oat roots. ISME J. 2008 Nov 13. [Epub ahead of print]
  27. Tsiamis, G., Katsaveli, K., Ntougias, S., Kyrpides, N., Andersen, G., Piceno, Y., Bourtzis, K. (2008) Prokaryotic community profiles at different operational stages of a Greek solar saltern. Research in Microbiology 159:609-627
  28. Chivian, D., Brodie, E. L., Alm, E. J., Culley, D. E., Dehal, P. S., DeSantis, T. Z., Gihring, T. M., Lapidus A, Lin, L. H., Lowry, S. R., Moser, D. P., Richardson, P. M., Southam, G., Wanger, G., Pratt, L. M, Andersen, G. L., Hazen, T. C., Brockman, F. J., Arkin, A. P., and T. C. Onstott. (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science 322:275-278. PMID: 18845759
  29. Wrighton, K. C., Agbo, P., Warnecke F., Weber, K. A., Brodie, E. L., Desantis, T. Z., Hugenholtz, P., Andersen, G. L., and Coates, J. D. (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. ISME J. 2008 2:1146-1156.
  30. Liu, Z., Desantis, T. Z., Andersen, G. L., and Knight R. (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 36:e120
  31. West, K. A., Johnson, D. R., Hu, P., DeSantis, T. Z., Brodie, E. L., Lee, P. K. H., Feil, H., Andersen, G. L., Zinder, S. H., and Alvarez-Cohen, L. (2008) Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains. Appl. Env. Micro. 74:3533-3540.
  32. Vogler A. J., Driebe E. M., Lee J., Auerbach R. K, Allender C. J., Stanley M., Kubota K., Andersen G. L., Radnedge L., Worsham P. L., Keim P, Wagner D. M. (2008) Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92. Biotechniques 44: 201-207.
  33. Johnson, D. R., Brodie, E. L., Hubbard, A. E., Andersen, G. L., Zinder, S. H., and Alvarez-Cohen, L. (2008) Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl. Env. Micro. 74:2864-2872.
  34. Dalevi D, Desantis T. Z., Fredslund J., Andersen G. L., Markowitz V. M., and Hugenholtz, P. (2008) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinformatics 8:402.
  35. Hillson, N. J., Hu, P., Andersen, G. L., and L. Shapiro. (2007) Caulobacter crescentus as a whole-cell uranium biosensor. Appl. Env. Micro. 73:7615-7621. PMID: 17905881
  36. DeSantis, T. Z., Brodie, E. L., Moberg, J. P., Zubieta, I. X., Piceno, Y. M. and G. L. Andersen. (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371-383. PMID: 17334858.
  37. Lynch, S. V., Dixon, L., Benoit, M. R., Brodie, E. L., Keyhan, M., Hu, P., Ackerley D. F., Andersen, G.L., and Matin, A. (2007) Role of the rapA Gene in Controlling Antibiotic Resistance of Escherichia coli Biofilms. Antimicrob. Agents Chemother. 51:3650-3658.
  38. Flanagan, J. L., Brodie, E. L., Weng, L., Lynch, S. V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T. Z., Andersen, G. L., Wiener-Kronish, J. P. and Bristow, J. (2007) Decline in bacterial diversity of intubated patients colonized with Pseudomonas aeruginosa. J. Clin. Microbiol. 45:1954-1962
  39. Brodie, E. L., DeSantis, T. Z., Parker, J. P., Zubietta, I. X., Piceno, Y. M., and G. L. Andersen. (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci. 104:299-304. PMID: 17182744
  40. Wilson, K. H., Brown, R. S., Andersen, G. L., Tsang, J., and Sartor, B., 2006 (2006) Comparison of fecal biota from specific pathogen free and feral mice. Anaerobe 12:249-253.
  41. Lin, L. H., Wang, P. L., Rumble, D., Lippmann-Pipke, J., Boice, E., Pratt, L. M., Sherwood Lollar, B., Brodie, E. L., Hazen, T. C., Andersen, G. L., DeSantis, T. Z., Moser, D. P., Kershaw, D., and T. C. Onstott. (2006) Long-term sustainability of a high-energy, low-diversity crustal biome. Science 314:479-482. PMID: 17053150
  42. Brodie, E. L., DeSantis, T. Z., Joyner, D. C., Baek, S. M., Larsen, J. T., Andersen, G. L., Hazen, T.C., Richardson, P. M., Herman, D. J., Tokunaga, T. K., Wan, J. M., and Firestone, M. K., (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl. Env. Micro. 72:6288-6298.
  43. DeSantis, T. Z. Jr., Hugenholtz, P., Keller, K., Brodie, E. L., Larsen, N., Piceno, Y.M., Phan, R., and Andersen, G. L., (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34 (Web Server issue): W394- W399.
  44. DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu P, and G. L. Andersen. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Env. Micro. 72:5069-5072. PMID: 16820507
  45. Chain, P. S. G., Hu, P., Malfatti, S. A., Radnedge, L., Larimer, F., Vergez, L. M., Worsham, P., Chu, M. C., and Andersen, G. L., (2006) Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J. Bacteriol. 188: 4453-4463.
  46. Clavijo, R. I., Loui, C., Andersen, G. L., Riley, L. W., and Lu, S., (2006)  Identification of genes associated with survival of Salmonella enterica serovar Enteritidis in chicken egg albumen. Appl. Env. Micro. 72:1055-1064.
  47. Hu, P., Brodie, E. L., Suzuki, Y., McAdams, H. H., and G. L. Andersen. (2005) Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J. Bacteriol. 187:8437-8449. PMID: 16321948
  48. DeSantis, T. Z., Stone, C. E., Murray, S. R., Moberg, J. P., and Andersen, G. L., (2005) Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Micro. Lett. 245: 271-278.
  49. DeSantis, T. Z., Dubosarskiy, I., and Andersen, G. L., (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. Bioinformatics 19: 1461-1468
  50. Radnedge, L., Agron, P. G., Hill, K. H., Jackson, P. J., Ticknor, L. O., Keim, P, and Andersen, G. L., (2003) Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl. Env. Micro. 69:2755-2764.
  51. Agron, P. G., Sobecky, P., and Andersen, G. L., (2002) Establishment of uncharacterized plasmids in Escherichia coli by in vitro transposition. FEMS Microbiology Letters 217: 249-254.
  52. Agron, P. G., Macht, M., Radnedge, L., Skowronski, E. W., Miller, W., and Andersen, G. L. (2002) Use of subtractive hybridization to survey comprehensively prokaryotic genomic differences. FEMS Microbiology Letters 211: 175-182.
  53. Radnedge, L., Agron, P. G., Worsham, P. L., and Andersen, G. L. (2002) Genome plasticity in Yersinia pestis. Microbiology 148: 1687-1698.
  54. Wilson, K. H., Wilson, W. J., Radosevich, J. L., DeSantis, T. Z., Viswanathan, V. S., Kuczmarski, T. A., and Andersen, G. L. (2002) High density microarray of small subunit ribosomal DNA probes. Appl. Env. Micro. 68: (5) 2535-2541.
  55. Wilson, W. J., Strout, C. L., DeSantis, T. Z., Stilwell, J. L., Carrano, A. V., and Andersen, G. L. (2002) Sequence specific identification of 18 pathogenic microorganisms using microarray technology. Molecular and Cellular Probes 16: (2) 119-127.
  56. Radosevich, J. L., Wilson, W. J., Shinn, J. H., DeSantis, T. Z., and Andersen, G. L. (2002) Development of a high-volume aerosol collection system for the identification of airborne microorganisms. Lett. Appl. Micro. 34:162-167.
  57. Radnedge, L., Gamez-Chin, S., McCready, P. M., Worsham, P. L. and Andersen, G. L. (2001) Identification of nucleotide sequences for the specific and rapid detection of Yersinia pestis.  Appl. Env. Micro. 67: (8) 3759-3762
  58. Agron, P. G., Walker, R. L., Kinde, H., Sawyer, S. J., Hayes, D. C., Wollard, J., and Andersen, G. L. (2001) Identification by subtractive hybridization of sequences specific for Salmonella enterica serovar Enteritidis. Appl. Env. Micro. 67: (11) 4984-4991
  59. Skowronski, E. W.; Armstrong, N, Andersen, G. L., Macht, M., and McCready, P. M. (2000) Magnetic, microplate-format plasmid isolation protocol for high-yield, sequencing-grade DNA. Biotechniques 29: 786-792.
  60. Bogush, M. L., Velikodvorskaya, T. V., Lebedev, Y. B., Nikolaev, L. G., Lukyanov, S. A., Fradkov, A. F., Pliyev, B. K., Boichenko, M. N., Usatova, G. N., Vorobiev, A. A., Andersen, G. L., and Sverdlov E. D. (1999) Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes with the use of suppressive subtractive hybridization. Molecular and General Genetics  262: 721-729
  61. Andersen, G. L., Beattie, G. A., and Lindow, S. E., (1998) Molecular characterization and sequence of a methionine biosynthetic locus from Pseudomonas syringae  J. Bacteriol. 180: 4497-4507.
  62. Andersen, G. L., Simchock, J., and Wilson, K. H. (1996).  Identification of a region of genetic variability among Bacillus anthracis strains and related species. J. Bacteriol. 178: 377-384.
  63. Lindow, S. E., and Andersen, G. L. (1996) Influence of immigration on epiphytic bacterial populations on navel orange leaves. Appl. Env. Micro. 62: 2978-2987.
  64. Andersen, G. L., Harrell, L., and Wilson, K. H. (1995)  Genetic variability of Bacillus anthracis and related species. J. Clin. Microbiol. 33: 1847-1850.
  65. Lindow, S., Andersen, G., and Beattie, G. (1993) Characteristics of insertional mutants of Pseudomonas syringae with reduced epiphytic fitness. Appl. Env. Micro. 59:1593-1601.
  66. Andersen G. L., Menkissoglou, O., and Lindow, S. E. (1991) Occurrence and properties of copper-tolerant strains of Pseudomonas syringae isolated from fruit-trees in California. Phytopathology 81:648-656.

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Book Chapters

  1. Andersen, G. L., He. Z., DeSantis, T. Z., Brodie, E. L., and Zhou, J. (2010) The Use of Microarrays in Microbial Ecology, pp 87-110. In Liu, W.T. and Jansson J. K. (ed), Environmental Molecular Microbiology. Horizon Scientific Press (In press).
  2. Andersen, G. L., Frisch, A.S., Kellogg, C.A., Levetin, E., Lighthart, B., Paterno, D. (2009) Aeromicrobiology/Air Quality. In Schaechter, M (editor-in-chief) Encyclopedia of Microbiology, Third Edition. Academic Press (May 15, 2009).
  3. Brodie, E. L., DeSantis, T.Z., Piceno, Y. M. and Andersen, G. L. (2009) High density DNA microarray analysis for monitoring microbial community composition and dynamics. In Kowalchuck, G.A. (ed), Molecular Microbial Ecology Manual. Kluwer Academic Publishers. (In press.)
  4. Andersen, G.L., Piceno, Y. M., DeSantis, T. Z. and Brodie, E. L. (2006) What DNA Microarrays Can Tell Us About Bacterial Diversity: A New Light on an Old Question. In Bailey, M.J. (ed), Microbial Ecology of Aerial Plant Surfaces Oxford University Press, pp. 251-267.

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Invited Talks

  1. A Phylogenetic Microarray Approach to Monitoring and Source Tracking Coastal-Zone Pollution. November 11, 2009, Santa Clara University.  Center for Science, Technology and Society, Innovation for Social Benefit Program.
  2. Uncovering Microbial Diversity with Phylogenetic Microarrays. November 6, 2009, Stanford University. Fall Seminar Series, Civil & Environmental Engineering Department
  3. Advances in High-Density PhyloChip Technology for Understanding the Dynamics of Microbial Communities Important to Human Health. May 2009, Philadelphia, PA.  Annual meeting of the American Society for Microbiology.
  4. Phylochip Analysis of Microbial Diversity, March 25-27, 2009 Walnut Creek, CA. JGI’s 4th Annual User Meeting
  5. Phylogenetic Microarrays for Analysis of Microbial Community Dynamics.  February 2009, UC Davis, CA.  Department of Plant Pathology 290 Seminar Speaker.
  6. A Systems Biology Approach to Environmental Biotechnology using Ecogenomics.  January 2009, Singapore.  National University of Singapore.
  7. Roundtable: Ecogenomics, Which Methods are Best?  August 2008, Cairns, Australia.  International Symposium of Microbial Ecology (ISME XII).
  8. Historical overview of broad-rang DNA target amplification and sequencing.  June 2008, Boston, MA. Annual meeting of the American Society for Microbiology.
  9. PhyloChip microarray analysis of bacterial diversity on the Phoenix Spacecraft and associated Astrobiology Science Conference (AbSciCon) April 14-17, 2008 Santa Clara, California.
  10. Application of 16S rRNA arrays in microbial ecology. February, 2008, Singapore.  National University of Singapore.
  11. Towards the development of a fungal microarray for microbial community characterization. September, 2007, Copenhagen, Denmark. FEISN/UNITE Mycology Meeting.
  12. Application of 16S rRNA arrays in microbial ecology. September 3-6, 2007, Edinburgh Scotland. 161st Meeting of the Society for General Microbiology.
  13. Characterization of microbial diversity with high-density microarrays. August, 2007, Baton Rouge, LA.  Mycological Society of America Annual Meeting.
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