Australian Centre for Ecogenomics

Parents: Faculty of Science  

Browse Results (37 results found)

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Hu, Shihu, Zeng, Raymond J., Haroon, Mohamed F., Keller, Jurg, Lant, Paul A., Tyson, Gene W. and Yuan, Zhiguo (2015) A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports, 5 8706: 1-9. doi:10.1038/srep08706 40   2 Cited 3 times in Scopus3 3
Leong, Lex E. X., Denman, Stuart E., Hugenholtz, Philip and McSweeney, Christopher S. (2015) Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions. Microbial Ecology, . doi:10.1007/s00248-015-0641-4 23   0 1
Abdul Rahman, Nurdyana, Parks, Donovan H., Willner, Dana L., Engelbrektson, Anna L., Goffredi, Shana K., Warnecke, Falk, Scheffrahn, Rudolf H. and Hugenholtz, Philip (2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome, 3 5: 1-16. doi:10.1186/s40168-015-0067-8 18   3 Cited 3 times in Scopus3 4
Hobson-Peters, Jody, Yam, Alice Wei Yee, Lu, Jennifer Wei Fei, Setoh, Yin Xiang, May, Fiona J., Kurucz, Nina, Walsh, Susan, Prow, Natalie A., Davis, Steven S., Weir, Richard, Melville, Lorna, Hunt, Neville, Webb, Richard I., Blitvich, Bradley J., Whelan, Peter and Hall, Roy A. (2013) A new insect-specific flavivirus from Northern Australia suppresses replication of West Nile Virus and Murray Valley Encephalitis Virus in co-infected mosquito cells. PLoS One, 8 2: . doi:10.1371/journal.pone.0056534 105   31 Cited 32 times in Scopus32 4
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2012) Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91 2: 246-251. doi:10.1016/j.mimet.2012.08.011 81   24 Cited 30 times in Scopus30 3
Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M. and Mueller, C.W. (2015) Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5 . doi:10.1038/srep18165     0 0 3
Kelly, Linda Wegley, Barott, Katie L., Dinsdale, Elizabeth, Friedlander, Alan M., Nosrat, Bahador, Obura, David, Sala, Enric, Sandin, Stuart A., Smith, Jennifer E., Vermeij, Mark J. A., Williams, Gareth J., Willner, Dana and Rohwer, Forest (2012) Black reefs: Iron-induced phase shifts on coral reefs. ISME Journal, 6 3: 638-649. doi:10.1038/ismej.2011.114 79   15 Cited 15 times in Scopus15 23
Costello, Mary-Ellen, Ciccia, Francesco, Willner, Dana, Warrington, Nicole, Robinson, Philip C., Gardiner, Brooke, Marshall, Mhairi, Kenna, Tony J., Triolo. Giovanni and Brown, Matthew A. (2015) Brief report: intestinal dysbiosis in ankylosing spondylitis. Arthritis and Rheumatology, 67 3: 686-691. doi:10.1002/art.38967 36   6 Cited 6 times in Scopus6 31
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 7: 1043-1055. doi:10.1101/gr.186072.114 19   14 Cited 15 times in Scopus15 29
Flowers, Jason J., He, Shaomei, Malfatti, Stephanie, Glavina del Rio, Tijana, Tringe, Susannah G., Hugenholtz, Philip and McMahon, Katherine D. (2013) Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal, 7 12: 2301-2314. doi:10.1038/ismej.2013.117 39   14 Cited 14 times in Scopus14 3
Anderson, Iain, Goker, Markus, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Huber, Harald, Yasawong, Montri, Rohde, Manfred, Spring, Stefan, Abt, Birte, Sikorski, Johannes, Wirth, Reinhard, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2011) Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A(T)). Standards in Genomic Sciences, 4 3: 381-392. doi:10.4056/sigs.2014648 80   5 Cited 5 times in Scopus5 4
Goker, Markus, Daligault, Hajnalka, Mwirichia, Romano, Lapidus, Alla, Lucas, Susan, Deshpande, Shweta, Pagani, Ioanna, Tapia, Roxanne, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Han, Cliff, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Wirth, Reinhard, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. Standards in Genomic Sciences, 5 3: 407-415. doi:10.4056/sigs.2465574 68   4 Cited 5 times in Scopus5 4
Munk, A. Christine, Lapidus, Alla, Lucas, Susan, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Del Rio, Tijana Glavina, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Huntemann, Marcel, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Tapia, Roxanne, Han, Cliff, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Yasawong, Montri, Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Tsukamurella paurometabola type strain (no. 33(T)). Standards in Genomic Sciences, 4 3: 342-351. doi:10.4056/sigs.1894556 59   3 Cited 4 times in Scopus4 1
Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014) Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online 1-14. doi:10.1038/ismej.2014.50 66 1 0 12
Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 3212.1-3212.7. doi:10.1038/ncomms4212 68   15 Cited 19 times in Scopus19 90
Willner, D., Hugenholtz, P., Tan, M.E., Yerkovich, S.T., Hopkins, P.M. and Chambers, D.C. (2012). Distinct microbial signatures of healthy and failing lung allografts. In: Abstract Issue: International Society for Heart and Lung Transplantation 32nd Annual Meeting and Scientific Sessions. 32nd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation/Meeting of the ISHLT Academy Core Competencies in Mechanical Circulatory Support, Prague, Czech Republic, (S32-S32). 17-21 April 2012. doi:10.1016/j.healun.2012.01.072 79   2 0
Pervin, Hasina M., Dennis, Paul G., Lim, Hui J., Tyson, Gene W., Batstone, Damien J. and Bond, Philip L. (2013) Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Research, 47 19: 7098-7108. doi:10.1016/j.watres.2013.07.053 97   17 Cited 19 times in Scopus19 1
Dennis, Paul G., Harnisch, Falk, Yeoh, Yun Kit, Tyson, Gene W. and Rabaey, Korneel (2013) Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system. Applied and Environmental Microbiology, 79 13: 4008-4014. doi:10.1128/AEM.00569-13 123   17 Cited 17 times in Scopus17 1
Liu, Yiwen, Sharma, Keshab R., Ni, Bing-Jie, Fan, Lu, Murthy, Sudhir, Tyson, Gene Q. and Yuan, Zhiguo (2015) Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment. Water Research, 74 155-165. doi:10.1016/j.watres.2015.02.017 17   1 Cited 2 times in Scopus2 2
Clingenpeel, Scott, Schwientek, Patrick, Hugenholtz, Philip and Woyke, Tanja (2014) Effects of sample treatments on genome recovery via single-cell genomics. The ISME Journal, 8 12: 2546-2549. doi:10.1038/ismej.2014.92 24   3 Cited 3 times in Scopus3 11
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2013) Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences, 9 1: 83-92. doi:10.4056/sigs.4338002 59   0 0 1
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 7459: 431-437. doi:10.1038/nature12352 157   264 Cited 271 times in Scopus271 389
Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013) In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531 3-19. doi:10.1016/B978-0-12-407863-5.00001-0 85   2 Cited 2 times in Scopus2 0
Vanwonterghem, Inka, Jensen, Paul D., Ho, Dang P., Batstone Damien J. and Tyson, Gene W. (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology, 27 55-64. doi:10.1016/j.copbio.2013.11.004 141   30 Cited 30 times in Scopus30 3
Bragg,Lauren and Tyson, Gene W. (2014). Metagenomics using next-generation sequencing. In Ian T. Paulsen and Andrew J. Holmes (Ed.), Environmental Microbiology: Methods and Protocols (pp. 183-201) New York, NY United States: Humana Press Inc.. doi:10.1007/978-1-62703-712-9_15 74   7 Cited 7 times in Scopus7 14
Hoedt, Emily, Evans, Paul, Denman, Stuart E., McSweeney, Chris S., Ó Cuív, Paraic and Morrison, Mark (2015) Methane matters in animals and man: from beginning to end. Microbiology Australia, 36 1: 4-7. doi:10.1071/MA15003 19   1
McMullen, Allison R., Albayrak, Harun, May, Fiona J., Davis, C. Todd, Beasley, David W. C. and Barrett, Alan D. T. (2013) Molecular evolution of lineage 2 West Nile virus. Journal of General Virology, 94 Part 2: 318-325. doi:10.1099/vir.0.046888-0 32   16 Cited 15 times in Scopus15 0
Treangen, Todd J., Sommer, Dan D., Angly, Florent E., Koren, Sergey and Pop, Mihai (2011) Next generation sequence assembly with AMOS. Current Protocols in Bioinformatics, s33: 1-18. doi:10.1002/0471250953.bi1108s33 63   Cited 25 times in Scopus25 3
Paungfoo-Lonhienne, Chanyarat, Yeoh, Yun Kit, Kasinadhuni, Naga Rup Pinaki, Lonhienne, Thierry G. A., Robinson, Nicole, Hugenholtz, Philip, Ragan, Mark A. and Schmidt, Susanne (2015) Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.. Scientific Reports, 5 8678: 1-6. doi:10.1038/srep08678 30   1 Cited 1 times in Scopus1 14
Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip and Tyson, Gene W. (2011) Phage encoded H-NS: A potential Achilles heel in the bacterial defence system. Plos One, 6 5: e20095-1-e20095-7. doi:10.1371/journal.pone.0020095 85   15 Cited 14 times in Scopus14 0
Garrity, George M., Banfield, Jill, Eisen, Jonathan, van der Lelie, Niels, McMahon, Trina, Rusch, Doug, Delong, Edward, Moran, Mary Ann, Currie, Cameron, Furhman, Jed, Hallam, Steve, Hugenholtz, Phil, Moran, Nancy, Nelson, Karen, Roberts, Richard and Stepanauskas, Ramunas (2013) Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2012. Standards in Genomic Sciences, 8 3: 561-570. doi:10.4056/sigs.4638348 48 1 2 Cited 2 times in Scopus2 0
D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 7: e68465.1-e68465.11. doi:10.1371/journal.pone.0068465 42   13 Cited 13 times in Scopus13 59
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. In Frans J. de Bruijn (Ed.), Molecular Microbial Ecology of the Rhizosphere (pp. 1137-1144) Hoboken, NJ United States: Wiley-Blackwell. doi:10.1002/9781118297674.ch109 78   Cited 1 times in Scopus1 0
Webster, N. S., Luter, H. M., Soo, R. M., Botté, E. S., Simister, R. L., Abdo, D. and Whalan, S. (2012) Same, same but different: symbiotic bacterial associations in GBR sponges. Frontiers in Microbiology, 3 444: 1-11. doi:10.3389/fmicb.2012.00444 24   8 Cited 13 times in Scopus13 1
Ragonesi, Leanne, Huygens, Flavia, Turner, Ross, Hugenholtz, Philip, Lourie, Rohan, Beagley, Ken and Pelzer, Elise (2015). The microbial community of eutherian origin: Effects of maternal microbiota on the placental microbiome. In: unknown, unknown, (A41-A41). unknown. doi:10.1016/j.placenta.2015.07.308     0 0
Pelzer, Elise, Hugens, Flavia, Hugenholtz, Philip, Lourie, Rohan, Beagley, Kenneth and Turner, Ross (2015). The placental microbiome; microbial presence in nature’s transplant. In: unknown, unknown, (A23-A23). unknown. doi:10.1016/j.placenta.2015.07.252     0 0
Waldor, Matthew K., Tyson, Gene, Borenstein, Elhanan, Ochman, Howard, Moeller, Andrew, Finlay, Brett B., Kong, Hedi H., Gordon, Jeffrey I., Nelson, Karen E., Dabbagh, Karim and Smith, Hamilton (2015) Where next for microbiome research?. PLoS Biology, 13 1: 1-9. doi:10.1371/journal.pbio.1002050 28   5 Cited 4 times in Scopus4 17