Australian Centre for Ecogenomics

Parents: Faculty of Science  

Browse Results (46 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   3 Cited 4 times in Scopus4 4
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, 71 2: 494-504. doi:10.1007/s00248-015-0641-4 23   1 Cited 1 times in Scopus1 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   10 Cited 12 times in Scopus12 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   43 Cited 47 times in Scopus47 6
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 80   29 Cited 36 times in Scopus36 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     1 Cited 1 times in Scopus1 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   21 Cited 19 times in Scopus19 26
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   22 Cited 22 times in Scopus22 38
Ikeda-Ohtsubo, Wakako, Strassert, Juergen F. H., Kohler, Tim, Mikaelyan, Aram, Gregor, Ivan, Mchardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate and Brune, Andreas (2016) 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environmental Microbiology, 18 8: 2548-2564. doi:10.1111/1462-2920.13234     0 0 2
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   61 Cited 75 times in Scopus75 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   22 Cited 22 times in Scopus22 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   5 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
Gomez-Arango, Luisa F., Barrett, Helen L., McIntyre, H. David, Callaway, Leonie K., Morrison, Mark and Dekker Nitert, Marloes (2016) Connections between the gut microbiome and metabolic hormones in early pregnancy in overweight and obese women. Diabetes, 65 8: 2214-2223. doi:10.2337/db16-0278     0 Cited 2 times in Scopus2 28
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 65 1 Cited 3 times in Scopus3 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   30 Cited 34 times in Scopus34 91
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 78   2 0
Angly, Florent E., Pantos, Olga, Morgan, Thomas C., Rich, Virginia, Tonin, Hemerson, Bourne, David G., Mercurio, Philip, Negri, Andrew P. and Tyson, Gene W. (2016) Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ, 4 . doi:10.7717/peerj.1758     0 0 12
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 96   25 Cited 27 times in Scopus27 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   19 Cited 20 times in Scopus20 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   3 Cited 4 times in Scopus4 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   6 Cited 5 times in Scopus5 10
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 156   372 Cited 396 times in Scopus396 407
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/B978-0-12-407863-5.00001-0 129   3 Cited 3 times in Scopus3 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.2013.11.004 136   52 Cited 57 times in Scopus57 3
Angly, Florent E., Heath, Candice, Morgan, Thomas C., Tonin, Hemerson, Rich, Virginia, Schaffelke, Britta, Bourne, David G. and Tyson, Gene W. (2016) Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ, 4 1-24. doi:10.7717/peerj.1511     2 Cited 1 times in Scopus1 6
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 73   10 Cited 8 times in Scopus8 13
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   0 1
Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 16170: . doi:10.1038/nmicrobiol.2016.170     0 114
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 31   21 Cited 21 times in Scopus21 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 31 times in Scopus31 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 36   5 Cited 5 times in Scopus5 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   16 Cited 16 times in Scopus16 0
Nobu, Masaru K., Dodsworth, Jeremy A., Murugapiran, Senthil K., Rinke, Christian, Gies, Esther A., Webster, Gordon, Schwientek, Patrick, Kille, Peter, Parkes, R. John, Sass, Henrik, Jorgensen, Bo B., Weightman, Andrew J., Liu, Wen-Tso, Hallam, Steven J., Tsiamis, George, Woyke, Tanja and Hedlund, Brian P. (2016) Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. The ISME Journal, 10 2: 273-286. doi:10.1038/ismej.2015.97     5 Cited 2 times in Scopus2 1
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 3 Cited 4 times in Scopus4 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   17 Cited 18 times in Scopus18 60
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 77   Cited 3 times in Scopus3 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   9 Cited 15 times in Scopus15 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
McDougall, Carmel, Woodcroft, Ben J. and Degnan, Bernard M. (2016) The widespread prevalence and functional significance of silk-like structural proteins in metazoan biological materials. PLoS ONE, 11 7: . doi:10.1371/journal.pone.0159128     0 0 2
Goffredi, Shana K., Jang, Gene E. and Haroon, Mohamed F. (2015) Transcriptomics in the tropics: total RNA-based profiling of Costa Rican bromeliad-associated communities. Computational and Structural Biotechnology Journal, 13 18-23. doi:10.1016/j.csbj.2014.12.001     2 Cited 2 times in Scopus2 13
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 1-28. doi:10.7717/peerj.2486     0 42
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   15 Cited 17 times in Scopus17 17