Professor Philip Hugenholtz

ARC Australian Laureate Fellow

School of Chemistry and Molecular Biosciences
Faculty of Science

Affiliate Professor

The University of Queensland Diamantina Institute
Faculty of Medicine

Affiliate Professorial Res Fellow

Institute for Molecular Bioscience
p.hugenholtz@uq.edu.au
+61 7 336 53822

Overview

From a PhD in 1994 at the University of Queensland, Phil Hugenholtz developed a career in microbiology and genomics in the USA and in Australia. Phil’s last position in the USA was as Staff Scientist (2004-2010) at the DOE Joint Genome Institute. In late 2010 Phil returned home to establish the Australian Centre for Ecogenomics. The Centre was founded around himself as Director, and ARC QEII Fellow and Deputy Director, Dr Gene Tyson. Phil has published over one hundred papers in molecular microbial ecology including several Science & Nature papers.

Currently, Phil’s research interests include the microbial ecology and evolution of host-associated ecosystems such as the termite hindgut and human microbiome, and genomic mapping of the microbial tree of life. In 2006, Phil received the Young Investigators Award from the International Society of Microbial Ecology (ISME) and was elected in 2012 as a Fellow of the American Academy of Microbiology (AAM).

Research Interests

  • Metagenomics
    culture-independent sequence-based characterisation of microbial communities
  • Microbial diversity and evolution

Research Impacts

Phil has been a key contributor to transformative changes in the study of microbial ecology and evolution by helping to pioneer the use of culture-independent molecular methods to characterise microbial communities including marker gene and shotgun (metagenomic) approaches.

Qualifications

  • PhD, The University of Queensland
  • Bachelor of Science (Honours), The University of Queensland

Publications

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Grants

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Supervision

View all Supervision

Publications

Book Chapter

  • Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplifications of uncultivated organisms. In Slava S. Epstein (Ed.), Uncultivated microorganisms (pp. 83-100) Heidelberg, Germany: Springer. doi:10.1007/7171_2008_10

  • Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. In Lynn B. Jorde (Ed.), Encyclopedia of genetics, genomics, proteomics, and bioinformatics (pp. 1386-1391) West Sussex, U.K.: John Wiley & Sons. doi:10.1002/047001153X.g205313

  • Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117. In D. J. Brenner, N. R. Krieg and J. T. Staley (Ed.), Bergey's manual of systematic bacteriology: The proteobacteria. Part C. The alpha-, beta-, delta-, and epsilonproteobacteria 2nd ed. (pp. 258-263) New York, U.S.A.: Springer.

  • Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. In D. J. Brenner, N. R. Krieg and J. T. Staley (Ed.), Bergey's manual of systematic bacteriology 2nd ed. (pp. 452-459) New York, U.S.A.: Springer.

  • Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, Philip, Pawlowski, J. and Simpson, A.G. (2004). The tree of life: An overview. In Assembling the tree of life (pp. 43-75) New York: Oxford University Press.

  • Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). In Aquino de Muro. M and Rapley. R (Ed.), Gene Probes - Principles and Protocols (pp. 1-17) London: Humana Press.

Journal Article

  • Waite, David W. , Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017) Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.).. Frontiers in Microbiology, 8 . doi:10.3389/fmicb.2017.00682.

  • Soo, Rochelle M., Hemp, James, Parks, Donovan H., Fischer, Woodward W. and Hugenholtz, Philip (2017) On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 6332: 1436-1440. doi:10.1126/science.aal3794

  • Chotirmall, Sanjay H., Gellatly, Shaan L., Budden, Kurtis F., Mac Aogain, Micheál, Shukla, Shakti D., Wood, David L. A., Hugenholtz, Philip, Pethe, Kevin and Hansbro, Philip M. (2017) Microbiomes in respiratory health and disease: an Asia-Pacific perspective. Respirology, 22 2: 240-250. doi:10.1111/resp.12971

  • Varelias, Antiopi , Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko , Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A ., Hugenholtz, Philip and Hill, Geoffrey R. (2017) Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Blood, 129 15: 2172-2185. doi:10.1182/blood-2016-08-732628

  • Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016) Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 . doi:10.1038/srep39114

  • Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016) Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 . doi:10.1038/srep37389

  • Budden, Kurtis F. , Gellatly, Shaan L. , Wood, David L., Cooper, Matthew A. , Morrison, Mark, Hugenholtz, Philip and Hansbro, Philip M. (2016) Emerging pathogenic links between microbiota and the gut-lung axis.. Nature Reviews Microbiology, 15 1: 55-63. doi:10.1038/nrmicro.2016.142

  • 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

  • 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

  • Schofield, Benjamin J., Skarshewski, Adam, Lachner, Nancy, Ouwerkerk, Diane, Klieve, Athol V., Dart, Peter and Hugenholtz, Philip (2016) Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 11 1: . doi:10.1186/s40793-016-0189-z

  • Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016) Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 36.1-36.17. doi:10.1186/s40168-016-0181-2

  • Haroon, Mohamed F., Thompson, Luke R., Parks, Donovan H., Hugenholtz, Philip and Stingl, Ulrich (2016) A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data, 3 160050.1-160050.6. doi:10.1038/sdata.2016.50

  • Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat, Pendall, Elise, Phillips, Lori, Pirzl, Rebecca, Powell, Jeff R., Ragan, Mark A., Schmidt, Susanne, Seymour, Nicole, Snape, Ian, Stephen, John R., Stevens, Matthew, Tinning, Matt, Williams, Kristen, Yeoh, Yun Kit, Zammit, Carla M. and Young, Andrew (2016) Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 1: 21.1-21.11. doi:10.1186/s13742-016-0126-5

  • 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

  • Hugenholtz, Philip, Skarshewski, Adam and Parks, Donovan H. (2016) Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspectives in Biology, 8 6: . doi:10.1101/cshperspect.a018085

  • Simpson, Jodie L., Daly, Joshua, Baines, Katherine J., Yang, Ian A., Upham, John W., Reynolds, Paul N., Hodge, Sandra, James, Alan L., Hugenholtz, Philip, Willner, Dana and Gibson, Peter G. (2016) Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. European Respiratory Journal, 47 3: 792-800. doi:10.1183/13993003.00405-2015

  • Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip and Muyzer, Gerard (2016) Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology, 7 FEB: 211.1-211.18. doi:10.3389/fmicb.2016.00211

  • Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016) High-resolution phylogenetic microbial community profiling. ISME Journal, 10 8: 2020-2032. doi:10.1038/ismej.2015.249

  • Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016) A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 JAN: 1469.1-1469.15. doi:10.3389/fmicb.2015.01469

  • Yeoh, Yun Kit, Sekiguchi, Yuji, Parks, Donovan H. and Hugenholtz, Philip (2015) Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Molecular Biology and Evolution, 33 4: 915-927. doi:10.1093/molbev/msv281

  • Lu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015) Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 11: e0142720.1-e0142720.10. doi:10.1371/journal.pone.0142720

  • Matsuura, Norihisa, Tourlousse, Dieter M., Ohashi, Akiko, Hugenholtz, Philip and Sekiguchia, Yuji (2015) Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi. Genome Announcements, 3 5: . doi:10.1128/genomeA.00975-15

  • Ormerod, Kate L., George, Narelle M., Fraser, James A., Wainwright, Claire and Hugenholtz, Philip (2015) Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ, 3 e1223.1-e1223.27. doi:10.7717/peerj.1223

  • 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

  • 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

  • Yeoh, Yun Kit, Paungfoo-Lonhienne, Chanyarat, Dennis, Paul G., Robinson, Nicole, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2015) The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.. Environmental Microbiology, 18 5: 1338-1351. doi:10.1111/1462-2920.12925

  • Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguamg, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip and Kyrpides, Nikos C. (2015) Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences, 10 26: . doi:10.1186/s40793-015-0017-x

  • Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015) Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 1: 50-60. doi:10.1128/jmbe.v16i1.816

  • Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015) Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 5: Art. No.: e968-Art. No.: e968. doi:10.7717/peerj.968

  • 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

  • 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

  • Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015) First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 e740: 1-24. doi:10.7717/peerj.740

  • Chambers, Daniel C., Gellatly, Shaan L., Hugenholtz, Philip and Hansbro, Philip M. (2014) JTD special edition 'Hot Topics in COPD'- the microbiome in COPD. Journal of Thoracic Disease, 6 11: 1525-1531. doi:10.3978/j.issn.2072-1439.2014.11.08

  • Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 1: 1-16. doi:10.7717/peerj.603

  • Kyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Goker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chun, Jongsik, Colwell, Rita R., Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F., Detter, John C., De Vos, Paul, Donohue, Timothy J., Dong, Xiu-Zhu, Ehrlich, Dusko S., Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Jansson, Janet K., Keasling, Jay D., Knight, Rob, Labeda, David, Lapidus, Alla, Lee, Jung-Sook, Li, Wen-Jun, MA, Juncai, Markowitz, Victor, Moore, Edward R. B., Morrison, Mark, Meyer, Folker, Nelson, Karen E., Ohkuma, Moriya, Ouzounis, Christos A., Pace, Norman, Parkhill,Julian, Qin, Nan, Rossello-Mora, Ramon, Sikorski, Johannes, Smith, David, Sogin, Mitch, Stevens, Rick, Stingl, Uli, Suzuki, Ken-ichiro, Taylor, Dorothea, Tiedje, Jim M., Tindall, Brian, Wagner, Michael, Weinstock, George, Weissenbach, Jean, White, Owen, Wang, Jun, Zhang, Lixin, Zhou, Yu-Guang, Field, Dawn, Whitman, William B., Garrity, George M. and Klenk, Hans-Peter (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12 8: e1001920.1-e1001920.7. doi:10.1371/journal.pbio.1001920

  • Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014) STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 21: 3123-3124. doi:10.1093/bioinformatics/btu494

  • 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

  • Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014) An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access 1-42. doi:10.1093/gbe/evu073

  • Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014) A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 2: 142-154. doi:10.1111/1751-7915.12105

  • Willner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014) Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 2: e01064-13.1-e01064-13.10. doi:10.1128/mBio.01064-13

  • 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

  • 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

  • Göker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, 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, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2014) Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. Standards in Genomic Sciences, 9 3: 1105-1117. doi:10.4056/sigs.3016383

  • Goeker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Feng, 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, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2014) Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences, 9 3: 1076-1088. doi:10.4056/sigs.5138968

  • Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip and Sullivan, Matthe B. (2014) Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.. Nature, 513 242-245 + 13. doi:10.1038/nature13459

  • Lonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014) Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 2: 785-790. doi:10.2135/cropsci2013.07.0488

  • Braff, William A., Willner, Dana, Hugenholtz, Philip, Rabaey, Korneel and Buie, Cullen R. (2013) Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE, 8 1: e76751.1-e76751.7. doi:10.1371/journal.pone.0076751

  • 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

  • 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

  • Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 6: 533-538+. doi:10.1038/nbt.2579

  • Willner, Dana and Hugenholtz, Philip (2013) From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays, 35 5: 436-442. doi:10.1002/bies.201200174

  • He, Shaomei, Ivanova, Natalia, Kirton, Edward, Allgaier, Martin, Bergin, Claudia, Scheffrahn, Rudolf H., Kyrpides, Nikos C., Warnecke, Falk, Tringe, Susannah G. and Hugenholtz, Philip (2013) Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One, 8 4: . doi:10.1371/journal.pone.0061126

  • Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013) Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 4: e1003031.1-e1003031.18. doi:10.1371/journal.pcbi.1003031

  • Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 7464: 567-570. doi:10.1038/nature12375

  • 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

  • Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2013) Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences, 8 1: 15-25. doi:10.4056/sigs.3507020

  • Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2013) Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences, 8 1: 26-36. doi:10.4056/sigs.3527032

  • Liolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2013) Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences, 8 2: 165-176. doi:10.4056/sigs.3607108

  • Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2013) Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Standards in Genomic Sciences, 8 1: 47-57. doi:10.4056/sigs.3547050

  • 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

  • Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Woyke, Tanja, Kyrpides, Nikos C. and Klenk, Hans-Peter (2013) Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva. Standards in Genomic Sciences, 8 2: 228-238. doi:10.4056/sigs.3617113

  • Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, 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, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2013) Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences, 9 1: 57-70. doi:10.4056/sigs.4237901

  • Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2013) Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences, 8 2: 177-187. doi:10.4056/sigs.3637201

  • Abt, Birte, Goeker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Woyke, Tanja and Klenk, Hans-Peter (2013) Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Trep. Standards in Genomic Sciences, 8 1: 88-105. doi:10.4056/sigs.3096473

  • Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013) Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 3: 628-634. doi:10.4056/sigs.5068949

  • Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Bruce, David, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2013) High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Standards in Genomic Sciences, 8 1: 37-46. doi:10.4056/sigs.3537045

  • 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

  • Willner, Dana and Hugenholtz, Phil (2013) Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter, 35 1: 1-9. doi:10.1016/j.clinmicnews.2012.12.001

  • Harris, J. Kirk, Caporaso, J. Gregory, Walker, Jeffrey J., Spear, John R., Gold, Nicholas J., Robertson, Charles E., Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob and Pace, Norman R. (2013) Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME Journal, 7 1: 50-60. doi:10.1038/ismej.2012.79

  • 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

  • Willner, Dana L., Hugenholtz, Philip, Yerkovich, Stephanie T., Tan, Maxine E., Daly, Joshua N., Lachner, Nancy, Hopkins, Peter M. and Chambers, Daniel C. (2013) Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 187 6: 640-647. doi:10.1164/rccm.201209-1680OC

  • Chappell, K.J., Brealey, J.C., Mackay, I.M., Bletchly, C., Hugenholtz, P., Sloots, T.P., Sly, P.D. and Young, P.R. (2013) Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children. Journal of Medical Microbiology & Diagnosis, S 1: 1-9. doi:10.4172/2161-0703.S1-005

  • Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Ivanova, Natalia (2012) Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences, 7 2: 210-220. doi:10.4056/sigs.3117229

  • Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2012) Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging. Mbio, 3 6: . doi:10.1128/mBio.00373-12

  • Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sut Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2012) Defining the core Arabidopsis thaliana root microbiome. Nature, 488 7409: 86-90. doi:10.1038/nature11237

  • Anderson, Iain, Chertkov, Olga, Chen, Amy, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Mavromatis, Konstantinos (2012) Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences, 6 3: 293-303. doi:10.4056/sigs.2736042

  • Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 12: e94.1-e94.8. doi:10.1093/nar/gks251

  • Knight, Rob, Jansson, Janet, Field, Dawn, Fierer, Noah, Desai, Narayan, Fuhrman, Jed A., Hugenholtz, Phil, van der Lelie, Daniel, Meyer, Folker, Stevens, Rick, Bailey, Mark J., Gordon, Jeffrey I., Kowalchuk, George A. and Gilbert, Jack A. (2012) Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology, 30 6: 513-520. doi:10.1038/nbt.2235

  • Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 5: 245-246. doi:10.1038/nmeth.1990

  • Willner, Dana, Daly, Joshua, Whiley, David, Grimwood, Keith, Wainwright, Claire E. and Hugenholtz, Philip (2012) Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS One, 7 4: e34605.1-e34605.12. doi:10.1371/journal.pone.0034605

  • McDonald, Daniel, Price, Morgan N., Goodrich, Julia, Nawrocki, Eric P., DeSantis, Todd Z, Probst, Alexander, Andersen, Gary L, Knight, Rob and Hugenholtz, Philip (2012) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME Journal, 6 3: 610-618. doi:10.1038/ismej.2011.139

  • Godoy-Vitorino, Filipa, Goldfarb, Katherine C., Karaoz, Ulas, Leal, Sara, Garcia-Amado, Maria A., Hugenholtz, Philip, Tringe, Susannah G., Brodie, Eoin L. and Dominguez-Bello, Maria Gloria (2012) Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME Journal, 6 3: 531-541. doi:10.1038/ismej.2011.131

  • Copeland, Alex, Gu, Wei, Yasawong, Montri, 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, Land, Miriam, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Goker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2012) Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. Standards in Genomic Sciences, 6 1: 21-30. doi:10.4056/sigs.2435521

  • Copeland, Alex, Zhang, Xiaojing, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Djao, Olivier D. Ngatchou, Goeker, Markus, Sikorski, Johannes, Tindall, Brian J., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Mavromatis, Konstantinos (2012) Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). Standards in Genomic Sciences, 6 2: 145-154. doi:10.4056/sigs.2475579

  • Huntemann, Marcel, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Pan, Chongle, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2012) Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). Standards in Genomic Sciences, 6 2: 185-193. doi:10.4056/sigs.2786069

  • Copeland, Alex, Zeytun, Ahmet, Yassawong, Montri, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Mavromatis, Konstantinos, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Sikorski, Johannes, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2012) Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT). Standards in Genomic Sciences, 6 2: 240-250. doi:10.4056/sigs.2756060

  • Han, Cliff, Kotsyurbenko, Oleg, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Detter, John C. (2012) Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). Standards in Genomic Sciences, 6 1: 94-103. doi:10.4056/sigs.2456004

  • Abt, Birte, Han, Cliff, Scheuner, Carmen, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Gronow, Sabine, Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Detter, John C. (2012) Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov and emendations of the family Spirochaetaceae and the genus Sphaerochae. Standards in Genomic Sciences, 6 2: 194-209. doi:10.4056/sigs.2796069

  • Anderson, Iain, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, 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, Hauser, Loren, Jeffries, Cynthia D., Chang, Yun-juan, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2012) Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). Standards in Genomic Sciences, 6 2: 155-164. doi:10.4056/sigs.2665915

  • Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, 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, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2012) Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). Standards in Genomic Sciences, 7 1: 107-119. doi:10.4056/sigs.3216895

  • Anderson, Iain, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, 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, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2012) Genome sequence of the homoacetogenic bacterium holophaga foetida type strain (TMBS4(T)). Standards in Genomic Sciences, 6 2: 174-184. doi:10.4056/sigs.2746047

  • Goeker, Markus, Saunders, Elisabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, 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, Chang, Yun-juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2012) Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). Standards in Genomic Sciences, 6 2: 230-239. doi:10.4056/sigs.2726028

  • Riedel, Thomas, Held, Brittany, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Tice, Hope, Del Rio, Tijana Glavina, 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, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2012) Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). Standards in Genomic Sciences, 7 1: 120-130. doi:10.4056/sigs.3296896

  • Werner, Jeffrey J., Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z., Walters, William A., Caporaso, J. Gregory, Angenent, Largus T., Knight, Rob and Ley, Ruth E (2012) Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME Journal, 6 1: 94-103. doi:10.1038/ismej.2011.82

  • Mavromatis, Konstantinos, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Bruce, David, Goodwin, Lynne A., Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2012) Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (=HR1). Standards in Genomic Sciences, 6 2: 210-219. doi:10.4056/sigs.2816096

  • Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Brambilla, Evelyne-Marie, Rohde, Manfred, Abt, Birte, Verbarg, Susanne, Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2011) Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). Standards in Genomic Sciences, 5 3: 398-406. doi:10.4056/sigs.2344929

  • Reddy, Amitha P., Allgaier, Martin, Singer, Steven W., Hazen, Terry C., Simmons, Blake A., Hugenholtz, Philip and VanderGheynst, Jean S. (2011) Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction. Biotechnology and Bioengineering, 108 9: 2088-2098. doi:10.1002/bit.23176

  • Gladden, John M., Allgaier, Martin, Miller, Christopher S., Hazen, Terry C., VanderGheynst, Jean S., Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2011) Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Applied and Environmental Microbiology, 77 16: 5804-5812. doi:10.1128/AEM.00032-11

  • Pope, P. B., Smith, W., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C. and Morrison, M. (2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science, 333 6042: 646-648. doi:10.1126/science.1205760

  • Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James R., Amaral-Zettler, Linda, Gilbert, Jack A., Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Philippe, Sterk, Peter, Arumugam, Manimozhiyan, Bailey, Mark, Baumgartner, Laura, Birren, Bruce W., Blaser, Martin J., Bonazzi, Vivien, Booth, Tim, Bork, Peer, Bushman, Frederic D., Buttigieg, Pier Luigi., Chain, Patrick S. G., Charlson, Emily, Costello, Elizabeth K., Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, JA, Gallery, Rachel E., Gevers, Dirk, Gibbs, Richard A., Gil, Inigo San, Gonzalez, Antonio, Gordon, Jeffrey I., Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, J, Kau, Andrew L., Kelley, Scott T., Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian L., Legg, Teresa, Ley, Ruth E., Lozupone, Catherine A., Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methe, Barbara A., Meyer, Folker, Muegge, Brian, Nakielny, Sara, Nelson, Karen E., Nemergut, Diana, Neufeld, Josh D,, Newbold, Lindsay K., Oliver, Anna E., Pace, Norman R., Palanisamy, Giriprakash, Peplies, Jörg, Petrosino, Joseph, Proctor, Lita, Pruesse, Elmar, Quast, Christian, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David A., Assunta-Sansone, Susanna, Schloss, Patrick D., Schriml, Lynn, Sinha, Rohini, Smith, Michelle I., Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James M, Ward, Doyle V., Weinstock, George M., Wendel, Doug, White, Owen, Whiteley, Andrew, Wilke, Andreas, Wortman, Jennifer R., Yatsunenko, Tany and Glockner, Frank Oliver (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology, 29 5: 415-420. doi:10.1038/nbt.1823

  • 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

  • Gronow, Sabine, Held, Brittany, Lucas, Susan, Lapidus, Alla, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Eisen, Jonathan A. (2011) Complete genome sequence of Bacteroides salanitronis type strain (BL78(T)). Standards in Genomic Sciences, 4 2: 191-199. doi:10.4056/sigs.1704212

  • Pati, Amrita, Abt, Birte, Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Spring, Stefan, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Ivanova, Natalia (2011) Complete genome sequence of Cellulophaga lytica type strain (LIM-21(T)). Standards in Genomic Sciences, 4 2: 221-232. doi:10.4056/sigs.1774329

  • Pukall, Rüdiger, Zeytun, Ahmet, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, J. Chris, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Deinococcus maricopensis type strain (LB-34(T)). Standards in Genomic Sciences, 4 2: 163-172. doi:10.4056/sigs.1633949

  • Wirth, Reinhard, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ioanna, Pagani, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Bilek, Yvonne, Hader, Thomas, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Göker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Desulfurococcus mucosus type strain (O7/1(T)). Standards in Genomic Sciences, 4 2: 173-182. doi:10.4056/sigs.1644004

  • Zeytun, Ahmet, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Han, James, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Ngatchou-Djao, Olivier D., Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Han, Cliff, Detter, John C., Übler, Susanne, Rohde, Manfred, Tindall, Brian J., Göker, Markus, Wirth, Reinhard, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6(T)). Standards in Genomic Sciences, 4 2: 131-143. doi:10.4056/sigs.1463589

  • Pagani, Ioanna, Chertkov, Olga, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Held, Brittany, Goodwin, Lynne, Liolios, Konstantinos, Ovchinikova, Galina, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Han, Cliff, Tapia, Roxanne, Ngatchou-Djao, Olivier D., Rohde, Manfred, Göker, Markus, Spring, Stefan, Sikorski, Johannes, Woyke, Tanja, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Marivirga tractuosa type strain (H-43(T)). Standards in Genomic Sciences, 4 2: 154-162. doi:10.4056/sigs.1623941

  • Pati, Amrita, Zhang, Xiaojing, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Röhl, Alina, Mwirichia, Romano, Rohde, Manfred, Tindall, Brian J., Sikorski, Johannes, Wirth, Reinhard, Göker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Land, Miriam (2011) Complete genome sequence of Oceanithermus profundus type strain (506(T)). Standards in Genomic Sciences, 4 2: 210-220. doi:10.4056/sigs.1734292

  • Göker, Markus, Gronow, Sabine, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Rohde, Manfred, Detter, John C., Woyke, Tanja, Bristow, James, Markowitz, Victor, Hugenholtz, Philip, Eisen, Jonathan A., Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Odoribacter splanchnicus type strain (1651/6(T)). Standards in Genomic Sciences, 4 2: 200-209. doi:10.4056/sigs.1714269

  • Mavromatis, Konstantinos, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Gronow, Sabine, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845(T)). Standards in Genomic Sciences, 4 2: 144-153. doi:10.4056/sigs.1553865

  • Land, Miriam, Held, Brittany, Gronow, Sabine, Abt, Birte, Lucas, Susan, Del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Göker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2011) Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139(T)). Standards in Genomic Sciences, 4 2: 233-243. doi:10.4056/sigs.1784330

  • Deangelis, Kristen M., Allgaier, Martin, Chavarria, Yaucin, Fortney, Julian L., Hugenholtz, Philip, Simmons, Blake, Sublette, Kerry, Silver, Whendee L. and Hazen, Terry C. (2011) Characterization of trapped lignin-degrading microbes in tropical forest soil. Plos One, 6 4: e19306.1-e19306.9. doi:10.1371/journal.pone.0019306

  • Pitluck, Sam, Sikorski, Johannes, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Djao, Oliver D. Ngatchou, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Land, Miriam (2011) Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1 T). Standards in Genomic Sciences, 4 1: 54-62. doi:10.4056/sigs.1523807

  • Pagani, Ioanna, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Desh-Pande, Shweta, Cheng, Jan-Fang, Chertkov, Olga, Davenport, Karen, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelyne, Kannan, K. Palani, Djao, Olivier D. Ngatchou, Rohde, Manfred, Pukall, Rudiger, Spring, Stefan, Goker, Markus, Sikorski, Johannes, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz ,Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Desulfobulbus propionicus type strain (1pr3 T). Standards in Genomic Sciences, 4 1: 100-110. doi:10.4056/sigs.1613929

  • Daligault, Hajnalka, Lapidus, Alla, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Galvina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Verbarg, Susanne, Goker, Markus, Bristow, James, Eisen, JA, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2011) Complete genome sequence of Haliscomenobacter hydrossis type strain (O-T). Standards in Genomic Sciences, 4 3: 352-360. doi:10.4056/sigs.1964579

  • Goker, Markus, Cleland, David, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Detter, John C., Beck, Brian, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Phiip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Isosphaera pallida type strain (IS1BT). Standards in Genomic Sciences, 4 1: 63-71. doi:10.4056/sigs.1533840

  • Anderson, Iain, Sikorski, Johannes, Zeytun, Ahmet, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Ngatchou-Djao, Oliver D., Rohde, Manfred, Tindall, Brian J., Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1(T)). Standards in Genomic Sciences, 4 3: 322-330. doi:10.4056/sigs.1844518

  • Gronow, Sabine, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynn, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, Manfred, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, J.A., Markowitz, V., Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2011) Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T). Standards in Genomic Sciences, 4 1: 36-44. doi:10.4056/sigs.1503846

  • Han, Cliffe, Mwirichia, Romano, Chertkov, Olga, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, 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, Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Detter, John C. (2011) Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR(T)). Standards in Genomic Sciences, 4 3: 371-380. doi:10.4056/sigs.2004684

  • Chertkov, Olga, Sikorski, Johannes, Nolan, Matt, Lapidus, Alla, Lucas, Susan, del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Djao, Oliver D. N., Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brettin, Thomas, Han, Cliff, Detter, John C., Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Thermomonospora curvata type strain (B9 T). Standards in Genomic Sciences, 4 1: 13-22. doi:10.4056/sigs.1453580

  • Han, Cliff, Gronow, Sabine, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Zeytun, Ahmed, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Detter, John C. (2011) Complete genome sequence of Treponema succinifaciens type strain (6091(T)). Standards in Genomic Sciences, 4 3: 361-370. doi:10.4056/sigs.1984594

  • Ivanova, Natalia, Rohde, Christine, Munk, Christine, Nolan, Matt, Lucas, Susan, del Rio,Tijana Glavina, Tice, Hope, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Pitluck. Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Mikhailova,Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne, Rohde, , Manfred, Goker, Markus, Tindall, Brian J., 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 Truepera radiovictrix type strain (RQ-24 T). Standards in Genomic Sciences, 4 1: 91-96. doi:10.4056/sigs.1563919

  • 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

  • Lang, Elke, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, Hammon, Nancy, Deshpande, Shweta, Nolan, Matt, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Brambilla, Evelyne-Marie, Kopitz, Markus, Rohde, Manfred, Goker, Markus, Tindall, Brian J., Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of Weeksella virosa type strain (9751 T). Standards in Genomic Sciences, 4 1: 81-90. doi:10.4056/sigs.1603927

  • Abt, Birte, Teshima, Hazuki, Lucas, Susan, Lapidus, Alla, del Rio, Tijana Glavina, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Tindall, Brian J., Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of leadbetterella byssophila type strain (4M15 T). Standards in Genomic Sciences, 4 1: 2-12. doi:10.4056/sigs.1413518

  • Sikorski, Johannes, Teshima, Hazuki, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Tapia, Roxane, Han, Cliff, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Ngatchou-Djao, Oliver Duplex, Rohde, Manfred, Pukall, Rudiger, Spring, Stefan, Abt, Birte, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Markowitz, Victor, Hugenholtz, Philip, Eisen, Jonathan A., Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2011) Complete genome sequence of mahella australiensis type strain (50-1 BONT). Standards in Genomic Sciences, 4 3: 331-341. doi:10.4056/sigs.1864526

  • Goker, Markus, Teshima, Hazuki, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxane, 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, Rohde, Manfred, Spring, Stefan, 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 acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2(T)). Standards in Genomic Sciences, 4 3: 393-401. doi:10.4056/sigs.2064705

  • Ivanova, Natalia, Sikorski, Johannes, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kannan, K. Palani, Rohde, Manfred, Tindall, Brian J., Goker, Markus, 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 extremely halophilic Halanaerobium praevalens type strain (GSL(T)). Standards in Genomic Sciences, 4 3: 312-321. doi:10.4056/sigs.1824509

  • Woyke, Tanja, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Rohde, Manfred, Mwirichia, Romano, Sikorski, Johannes, Tindall, Brian J., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262(T)). Standards in Genomic Sciences, 5 1: 21-29. doi:10.4056/sigs.2124912

  • Liolios, Konstantinos, Sikorski, Johannes, Lu, Meagan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Ivanova, Natalia, Pagani, Ioanna, Mavromatis, Konstantinos, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne-Marie, Kotsyurbenko, Oleg, Rohde, Manfred, Tindall, Brian J., Abt, Birte, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2011) Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113(T)). Standards in Genomic Sciences, 5 1: 30-40. doi:10.4056/sigs.2154937

  • 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

  • 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

  • Huntemann, Marcel, Lu, Megan, Nolan, Matt, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Brambilla, Evelynne-Marie, Rohde, Manfred, Spring, Stefan, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Mavromatis, Konstantinos (2011) Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T). Standards in Genomic Sciences, 4 3: 303-311. doi:10.4056/sigs.1814460

  • Klenk, Hans-Peter, Lapidus, Alla, Chertkov, Olga, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Daum, Chris, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Detter, John C., Rohde, Manfred, Abt, Birte, Pukall, Rüdiger, Göker, Markus, Bristow, James, Markowitz, Victor, Hugenholtz, Philip and Eisen, Jonathan A. (2011) Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2(T)) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Ra. Standards in Genomic Sciences, 5 1: 121-134. doi:10.4056/sigs.2144922

  • Lapidus, Alla, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Huntemann, Marcel, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Brambilla, Evelyne, Rohde, Manfred, Abt, Birte, Spring, Stefan, Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Woyke, Tanja (2011) Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10(T)). Standards in Genomic Sciences, 5 1: 86-96. doi:10.4056/sigs.2235024

  • Zhang, Tao, Datta, Supratim, Eichler, Jerry, Ivanova, Natalia, Axen, Seth D., Kerfeld, Cheryl A., Chen, Feng, Kyrpides, Nikos, Hugenholtz, Philip, Cheng, Jan-Fang, Sale, Kenneth L., Simmons, Blake and Rubin, Eddy (2011) Identification of a haloalkaliphilic and thermostable cellulase with improved ionic liquid tolerance. Green Chemistry, 13 8: 2083-2090. doi:10.1039/c1gc15193b

  • Lykidis, Athanasios, Chen, Chia-Lung, Tringe, Susannah G., McHardy, Alice C., Copeland, Alex, Kyrpides, Nikos C., Hugenholtz, Philip, Macarie, Hervé, Olmos, Alejandro, Monroy, Oscar and Liu, Wen-Tso (2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME Journal, 5 1: 122-130. doi:10.1038/ismej.2010.125

  • Chang, Yun-Juan, Land, Miriam, Hauser, Loren, Chertkov, Olga, Del Rio, Tijana Galvina, Nolan, Matt, Copeland, Alex, Tice, Hope, Cheng, Jan-Feng, Lucas, Susan, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Ovchinikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Mavromatis, Konstantinos, Liolios, Konstantinos, Brettin, Thomas, Fiebig, Anne, Rohde, Manfred, Abt, Birte, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Lapidus, Alla (2011) Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21(T)). Standards in Genomic Sciences, 5 1: 97-111. doi:10.4056/sigs.2114901

  • Pati, Amrita, Gronow, Sabine, Lu, Megan, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Feng, Tapia, Roxanne, Han, Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Mikhailova, N, Huntemann, Marcel, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Detter, John C., Brambilla, Evelyne-Marie, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C., Klenk, Hans-Peter and Ivanova, Natalia (2011) Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20(T)). Standards in Genomic Sciences, 5 1: 41-49. doi:10.4056/sigs.2164949

  • Burnum, Kristin E., Callister, Stephen J., Nicora, Carrie D., Purvine, Samuel O., Hugenholtz, Philip, Warnecke, Falk, Scheffrahn. Rudolf H., Smith, Richard D. and Lipton, Mary S. (2011) Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome. ISME Journal, 5 1: 161-164. doi:10.1038/ismej.2010.97

  • Yilmaz, S, Allgaier, M and Hugenholtz, P (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nature Methods, 7 12: 943-944. doi:10.1038/nmeth1210-943

  • Anderson, Iain, Djao, Olivier Duplex, Misra, Monica, Chertkov, Olga, Nolan, Matt, Lucas, Susan, Lapidus, Alla, Giavina Del Rio, Tijana, Tice, Hope, Cheng, Jan-Fang, Tapia, Roxanne, Han. Cliff, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Brambilla, Evelyne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Sikorski, Johannes, Spring, Stefan, Rohde, Manfred, Elchinger, Konrad, Huber, Harald, Wirth, Reinhard, Goker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter and Kyrpides, Nikos C. (2010) Complete genome sequence of Methanothermus fervidus type strain (V24S). Standards in Genomic Sciences, 3 3: 315-324. doi:10.4056/sigs.1283367

  • Ochman, Howard, Worobey, Michael, Kuo, Chih-Horng, Ndjango, Jean-Bosco N., Peeters, Jean-Bosco N., Hahn, Beatrice H. and Hugenholtz, Philip (2010) Evolutionary relationships of wild hominids recapitulated by gut microbial communities. PLoS Biology, 8 11 Article number e1000546: . doi:10.1371/journal.pbio.1000546

  • Brambilla, Evelyne, Djao, Olivier Duplex, Daligault, Hajnalka, Lapidus, Alla, Lucas, Susan, Hammon, Nancy, Nolan , Matt, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan, Sikorski, Johannes, Goker, Markus, Woyke, Tanja, Bristow, James, Elsen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2010) Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). Standards in Genomic Sciences, 3 2: 203-211. doi:10.4056/sigs.1183143

  • Yilmaz, S, Haroon, MF, Rabkin, BA, Tyson, GW and Hugenholtz, P (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal, 4 10: 1352-1356. doi:10.1038/ismej.2010.73

  • He, Shaomei, Wurtzel, Omri, Singh, Kanwar, Froula, Jeff L., Yilmaz, Suzan, Tringe, Susannah G., Wang, Zhong, Chen, Feng, Lindquist, Erika A., Sorek, Rotem and Hugenholtz, Philip (2010) Validation of two ribosomal RNA removal methods for microbial metatranscriptomics. Nature Methods, 7 10: 807-812. doi:10.1038/NMETH.1507

  • Pope, P. B., Denman, S. E., Jones, M., Tringe, S. G., Barry, K., Malfatti, S. A., McHardy, A. C., Cheng, J. F., Hugenholtz, P., McSweeney, C. S. and Morrison, M. (2010) Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proceedings of the National Academy of Sciences of the United States of America, 107 33: 14793-1-14798-6. doi:10.1073/pnas.1005297107

  • Chang, Yun-Juan, Pukall, Rüdiger, Saunders, Elizabeth, Lapidus, Alla, Copeland, Alex, Nolan, Matt, Glavina Del Rio, Tijana, Lucas, Susan, Chen, Feng, Tice, Hope, Cheng, Jan-Fang, Han. Cliff, Detter, John C., Bruce, David, Goodwin, Lynne, Pitluck, Sam, Mikhailova, Natalia, Liolios, Konstantinos, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Brettin, Thomas, Rohde, Manfred, Goker, Markus, Bristow, James, Elsen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2010) Complete genome sequence of Acidaminococcus fermentans type strain (VR4). Standards in Genomic Sciences, 3 1: 1-14. doi:10.4056/sigs.1002553

  • Abt, Birte, Foster, Brian, Lapidus, Alla, Clum, Alicia, Sun, Hui, Pukall, Rüdiger, Lucas, Susan, Giavina Del Rio, Tijana, Nolan, Matt, Tice, Hope, Cheng, Jan-Fang, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Goodwin, Lynne, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, James, Elsen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2010) Complete genome sequence of Cellulomonas flavigena type strain (134). Standards in Genomic Sciences, 3 1: 15-25. doi:10.4056/sigs.1012662

  • Ivanova, Natalia, Tringe, Susannah G., Liolios, Konstantinos, Liu, Wen-Tso, Morrison, Norman, Hugenholtz, Philip and Kyrpides, Nikos C. (2010) A call for standardized classification of metagenome projects. Environmental Microbiology, 12 7: 1803-1805. doi:10.1111/j.1462-2920.2010.02270.x

  • Chertkov, Olga, Sikorski, Johannes, Brambilla, Evelyne, Lapidus, Alla, Copeland, Alex, Glavina Del Rio, Tijana, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Detter, John C., Bruce, David, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Ovchinnikova, Galina, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Spring, Stefan, Rohde, Manfred, Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2010) Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Standards in Genomic Sciences, 2 3: 280-289. doi:10.4056/sigs.902116

  • DeAngelis, Kristen M., Gladden, John M., Allgaier, Martin, D'haeseleer, Patrik, Fortney, Julian L., Reddy, Amitha, Hugenholtz, Philip, Singer, Steven W., Vander Gheynst, Jean S., Silver, Whendee L., Simmons, Blake A. and Hazen, Terry C. (2010) Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulolytic microbial communities. BioEnergy Research, 3 2: 146-158. doi:10.1007/s12155-010-9089-z

  • Engelbrektson, Anna, Kunin, Victor, Wrighton, Kelly C., Zvenigorodsky, Natasha, Chen, Feng, Ochman, Howard and Hugenholtz, Philip (2010) Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME Journal, 4 5: 642-647. doi:10.1038/ismej.2009.153

  • He, Shaomei, Kunin, Victor, Haynes, Matthew, Martin, Hector Garcia, Ivanova, Natalia, Rohwer, Forest, Hugenholtz, Philip and McMahon, Katherine D. (2010) Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environmental Microbiology, 12 5: 1205-1217. doi:10.1111/j.1462-2920.2010.02163.x

  • Allagier, Martin, Reddy, Amitha, Park, Joshua I., Ivanova, Natalia, D'haeseleer, Patrik, Lowry, Steve, Sapra, Rajat, Hazen, Terry C., Simmons, Blake A., VanderGheynst, Jean S. and Hugenholtz, Philip (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One, 5 1: e8812-1-e8812-9. doi:10.1371/journal.pone.0008812

  • Spring, Stefan, Scheuner, Carmen, Lapidus, Alla, Lucas, Susan, Del Rio, Tijana Glavina, Tice, Hope, Copeland, Alex, Cheng, Jan-Fang, Chen, Feng, Nolan, Matt, Saunders, Elizabeth, Pitluck, Sam, Liolios, Konstantinos, Ivanova, Natalia, Mavromatis, Konstantinos, Lykidis, Athanasios, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D., Goodwin, Lynne, Detter, John C., Brettin, Thomas, Rohde, Manfred, Goker, Markus, Woyke, Tanja, Bristow, Jim, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. and Klenk, Hans-Peter (2010) The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea- An International Microbiological Journal, . doi:10.1155/2010/690737

  • Wu, Dongying, Hugenholtz, Philip, Mavromatis, Konstantinos, Pukall, Ru¨diger, Dalin, Eileen, Ivanova, Natalia N., Kunin, Victor, Goodwin, Lynne, Wu, Martin, Tindall, Brian J., Hooper, Sean D., Pati, Amrita, Lykidis, Athanasios, Spring, Stefan, Anderson, Iain J., D'haeseleer, Patrik, Zemla, Adam, Singer, Mitchell, Lapidus, Alla, Nolan, Matt, Copeland, Alex, Han, Cliff, Chen, Feng, Cheng, Jan-Fang, Lucas, Susan, Kerfeld, Cheryl, Lang, Elke, Gronow, Sabine, Chain, Patrick, Bruce, David, Rubin, Edward M., Kyrpides, Nikos C., Klenk, Hans-Peter and Elsen, Jonathan A. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature, 462 7276: 1056-1060. doi:10.1038/nature08656

  • Liolios, Konstantinos, Chen, I-Min A., Mavromatis, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Markowitz, Victor M. and Kyrpides, Nikos C. (2009) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Research, 38 Supp. 1: D346-D354. doi:10.1093/nar/gkp848

  • Kristiansson, Erik, Hugenholtz, Philip and Dalevi, Daniel (2009) ShotgunFunctionalizeR: An R-package for functional comparison of metagenomes. Bioinformatics, 25 20: 2737-2738. doi:10.1093/bioinformatics/btp508

  • Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium and Detter, J. C. (2009) Genome project standards in a new era of sequencing. Science, 326 5950: 236-237. doi:10.1126/science.1180614

  • Kunin, Victor, Engelbrekston, Anna, Ochman, Howard and Hugenholtz, Philip (2009) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12 1: 118-123. doi:10.1111/j.1462-2920.2009.02051.x

  • Hugenholtz, P, Hooper, SD and Kyrpides, NC (2009) Focus: Synergistetes. Environmental Microbiology, 11 6: 1327-1329. doi:10.1111/j.1462-2920.2009.01949.x

  • Herlemann, D. P. R., Geissinger, O., Ikeda-Ohtsubo, W., Kunin, V., Sun, H., Lapidus, A., Hugenholtz, P. and Brune, A. (2009) Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Applied and Environmental Microbiology, 75 9: 2841-2849. doi:10.1128/AEM.02698-08

  • Tschop, MH, Hugenholtz, P and Karp, CL (2009) Getting to the core of the gut microbiome. Nature Biotechnology, 27 4: 344-346. doi:10.1038/nbt0409-344

  • Hugenholtz, P and Kyrpides, NC (2009) A changing of the guard: Genomics update. Environmental Microbiology, 11 3: 551-553. doi:10.1111/j.1462-2920.2009.01888.x

  • Mavromatis, Konstantinos, Ivanova, Natalia, Anderson, Iain, Lykidis, Athanasios, Hooper, Sean D., Sun, Hui, Kunin, Victor, Lapidus, Alla, Hugenholtz, Philip, Patel, Bharat and Kyrpides, Nikos C. (2009) Genome analysis of the anaerobic thermohalophilic bacterium Halothermothrix orenii. PLoS One, 4 1: e4192.1-e4192.8. doi:10.1371/journal.pone.0004192

  • Sims, David, Brettin, Thomas, Detter, John C., Han, Cliff, Lapidus, Alla, Copeland, Alex, Del Rio, Tijana Glavina, Nolan, Matt, Chen, Feng, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Bruce, David, Goodwin, Lynne, Pitluck, Sam, Ovchinnikova, Galina, Pati, Amrita, Ivanova, Natalia, Mavromatis, Konstantinos, Chen, Amy, Palaniappan, Krishna, D'haeseleer, Patrik, Chain, Patrick, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Schneider, Susanne, Goker, Markus, Pukall, Rudiger, Kyrpides, Nikos C. and Klenk, Hans-Peter (2009) Complete genome sequence of Kytococcus sedentarius type strain (541(T)). Standards in Genomic Sciences, 1 1: 12-20. doi:10.4056/sigs.761

  • Knierim, B., Webb, R., Wilmes, P., Hugenholtz, P., Liphardt, J., McDonald, K., Banfield, J. and Auer, M. (2009) Correlative tem and fish imaging of microbial communities. Microscopy and Microanalysis, 15 Suppl. 2: 834-835. doi:10.1017/S1431927609098250

  • Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. and Hugenholtz, P. (2008) A bioinformatician's guide to metagenomics. Microbiology and Molecular Biology Reviews, 72 4: 557-578. doi:10.1128/MMBR.00009-08

  • Wrighton, Kelly C., Agbo, Peter, Warnecke, Falk, Weber, Karrie A., Brodie, Eoin L., DeSantis, Todd Z., Hugenholtz, Philip, Andersen, Gary L. and Coates, John D. (2008) A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells. The ISME Journal, 2 11: 1146-1156. doi:10.1038/ismej.2008.48

  • Tringe, SG and Hugenholtz, P (2008) A renaissance for the pioneering 16S rRNA gene. Current Opinions in Microbiology, 11 5: 442-446. doi:10.1016/j.mib.2008.09.011

  • Peterson, S. Brook, Warnecke, Falk, Madejska, Julita, McMahon, Katherine D. and Hugenholtz, Philip (2008) Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal. Environmental Microbiology, 10 10: 2692-2703. doi:10.1111/j.1462-2920.2008.01690.x

  • Hugenhotz, Philip and Tyson, Gene W. (2008) Microbiology: Metagenomics. Nature, 455 7212: 481-483. doi:10.1038/455481a

  • Lars M. Blank, Philip Hugenholtz and Nielsen, Lars K. (2008) Evolution of Hyaluronic Acid Synthesis (has) Operon in Streptococcus zooepidemicus and other Pathogenic Streptococci. Journal of Molecular Evolution, 67 1: 13-22. doi:10.1007/s00239-008-9117-1

  • Elkins, James G., Podar, Mircea, Graham, David E., Makarova, Kira S., Wolf, Yuri, Randau, Lennart, Hedlund, Brian P., Brochier-Armanet, Celine, Kunin, Victor, Anderson, Iain, Lapidus, Alla, Goltsman, Eugene, Barry, Kerrie, Koonin, Eugene V., Hugenholtz, Philip, Kyrpides, Nikos, Wanner, Gerhard, Richardson, Paul, Keller, Martin and Stetter, Karl O. (2008) A korarchaeal genome reveals insights into the evolution of the Archaea. Proceedings of the National Academy of Sciences of the United States of America, 105 23: 8102-8107. doi:10.1073/pnas.0801980105

  • Field, Dawn, Garrity, George, Gray, Tanya, Morrison, Norman, Selengut, Jeremy, Sterk, Peter, Tatusova, Tatiana, Thomson, Nicholas, Allen, Michael J., Angiuoli, Samuel V., Ashburner, Michael, Axelrod, Nelson, Baldauf, Sandra, Ballard, Stuart, Boore, Jeffrey, Cochrane, Guy, Cole, James, Dawyndt, Peter, De Vos, Paul, dePamphilis, Claude, Edwards, Robert, Faruque, Nadeem, Feldman, Robert, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Goldstein, Philip, Guralnick, Robert, Haft, Dan, Hancock, David, Hermjakob, Henning, Hertz-Fowler, Christiane, Hugenholtz, Philip, Joint, Ian, Kagan, Leonid, Kane, Matthew, Kennedy, Jessie, Kowalchuk, George, Kottmann, Renzo, Kolker, Eugene, Kravitz, Saul, Kyrpides, Nikos, Leebens-Mack, Jim, Lewis, Suzanna E., Li, Kelvin, Lister, Allyson L., Lord, Phillip, Maltsev, Natalia, Markowitz, Victor, Martiny, Jennifer, Methe, Barbara, Mizrachi, Ilene, Moxon, Richard, Nelson, Karen, Parkhill, Julian, Proctor, Lita, White, Owen, Sansone, Susanna-Assunta, Spiers, Andrew, Stevens, Robert, Swift, Paul, Taylor, Chris, Tateno, Yoshio, Tett, Adrian, Turner, Sarah, Ussery, David, Vaughan, Bob, Ward, Naomi, Whetzel, Trish, Gil, Ingio San, Wilson, Gareth and Wipat, Anil (2008) The minimum information about a genome sequence (MIGS) specification. Nature Biotechnology, 26 5: 541-547. doi:10.1038/nbt1360

  • Sorek, R, Kunin, V and Hugenholtz, P (2008) CRISPR - A widespread system that provides acquired resistance against phages in bacteria and archaea. Nature Reviews Microbiology, 6 3: 181-186. doi:10.1038/nrmicro1793

  • Kunin, V., He, S., Warnecke, F., Peterson, S. B., Martin, H. G., Haynes, M., Ivanova, N., Blackall, L. L., Breitbart, M., Rohwer, F., McMahon, K. D. and Hugenholtz, P. (2008) A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Research, 18 2: 293-297. doi:10.1101/gr.6835308

  • Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, Chen, I-Min A., Grechkin, Yuri, Dubchak, Inna, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Hugenholtz, Philip and Kyrpides, Nikos C. (2008) IMG/M: A data management and analysis system for metagenomes. Nucleic Acids Research, 36 Supp. 1: D534-D538. doi:10.1093/nar/gkm869

  • Warnecke, Falk, Luginbuehl, Peter, Ivanova, Natalia, Ghassemian, Majid, Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Sorek, Rotem, Tringe, Susannah G., Podar, Mircea, Martin, Hector Garcia, Kunin, Victor, Dalevi, Daniel, Madejska, Julita, Kirton, Edward, Platt, Darren, Szeto, Ernest, Salamov, Asaf, Barry, Kerrie, Mikhailova, Natalia, Kyrpides, Nikos C., Matson, Eric G., Ottesen, Elizabeth A., Zhang, Xinning, Hernandez, Myriam, Murillo, Catalina, Acosta, Luis G., Rigoutsos, Isidore, Tamayo, Giselle, Green, Brian D., Chang, Cathy, Rubin, Edward M., Mathur, Eric J., Robertson, Dan E., Hugenholtz, Philip and Leadbetter, Jared R. (2007) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature, 450 7169: 560-565. doi:10.1038/nature06269

  • Dalevi, Daniel, DeSantis, Todd Z., Fredslund, Jakob, Andersen, Gary L., Markowitz, Victor M. and Hugenholtz, Philip (2007) Automated group assignment in large phylogenetic trees using GRUNT: GRouping, ungrouping, naming tool. BMC Bioinformatics, 8 . doi:10.1186/1471-2105-8-402

  • Yamada, Takeshi, Yamauchi, Toshihiro, Shiraishi, Koji, Hugenholtz, Philip, Ohashi, Akiyoshi, Harada, Hideki, Kamagata, Yoichi, Nakamura, Kazunori and Sekiguchi, Yuji (2007) Characterization of filamentous bacteria, belonging to candidate phylum KSB3, that are associated with bulking in methanogenic granular sludges. The ISME Journal, 1 3: 246-255. doi:10.1038/ismej.2007.28

  • Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Losekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, Szeto, Ernest, Platt, Darren, Hugenholtz, Philip, Relman, David A. and Quake, Stephen R. (2007) Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences of the United States of America, 104 29: 11889-11894. doi:10.1073/pnas.0704662104

  • Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Michael, Brown, Kyndall, Kyrpides, Nikos C. and Hugenholtz, Philip (2007) CRISPR Recognition Tool (CRT) : A tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics, 8 209-1-209-8. doi:10.1186/1471-2105-8-209

  • Hugenholtz, Philip and Ron, Eliora Z. (2007) Increasing focus on environmental biotechnology in the face of pressing environmental challenges. Current Opinion in Biotechnology, 18 3: 235-236. doi:10.1016/j.copbio.2007.05.004

  • McMahon, KD, Martin, HG and Hugenholtz, P (2007) Integrating ecology into biotechnology. Current Opinion in Biotechnology, 18 3: 287-292. doi:10.1016/j.copbio.2007.04.007

  • 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) Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. Journal of Clinical Microbiology, 45 6: 1954-1962. doi:10.1128/JCM.02187-06

  • Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerry, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam, Lapidus, Alla, Grigoriev, Igor, Richardson, Paul, Hugenholtz, Philip and Kyrpides, Nikos C. (2007) Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods, 4 6: 495-500. doi:10.1038/nmeth1043

  • von Mering, C., Hugenholtz, P., Raes, J., Tringe, S. G., Doerks, T., Jensen, L. J., Ward, N. and Bork, P. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315 5815: 1126-1130. doi:10.1126/science.1133420

  • McHardy, Alice Carolyn, Martin, Hector Garcia, Tsirigos, Aristotelis, Hugenholtz, Philip and Rigoutsos, Isidore (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nature Methods, 4 1: 63-72. doi:10.1038/NMETH976

  • Warnecke, F and Hugenholtz, P (2007) Building on basic metagenomics with complementary technologies. Genome Biology, 8 12: 231.1-231.5. doi:10.1186/gb-2007-8-12-231

  • Kunin, Victor, Sorek, Rotem and Hugenholtz, Philip (2007) Evolutionary conservation of sequence and secondary structures in CRISPR repeats. Genome Biology, 8 4 Article # R61: R61-1-R61-3. doi:10.1186/gb-2007-8-4-r61

  • Hugenholtz, Philip (2007) Riding giants. Environmental Microbiology, 9 1: 5-5. doi:10.1111/j.1462-2920.2006.01222_4.x

  • Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 5807: 1933-1935. doi:10.1126/science.1132690

  • Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006) An experimental metagenome data management and analysis system (vol 22, pg 359, 2006). Bioinformatics, 22 20: 2580-2580. doi:10.1093/bioinformatics/btl436

  • DeSantis, T. Z., 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 Research, 34 suppl 2: W394-W399. doi:10.1093/nar/gkl244

  • Watt, Michelle, Hugenholtz, Philip, White, Rosemary and Vinall, Kerry (2006) Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environmental Microbiology, 8 5: 871-884. doi:10.1111/j.1462-2920.2005.00973.x

  • Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, Kimura, Nobutada, Wagner, Michael, Ohashi, Akiyoshi and Harada, Hideki (2006) Non-sulfate-reducing, syntrophic bacteria affiliated with Desulfotomaculum cluster I are widely distributed in methanogenic environments. Applied and Environmental Microbiology, 72 3: 2080-2091. doi:10.1128/AEM.72.3.2080-2091.2006

  • DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., KELLER, K., Huber, T. L., Dalevi, D., Hu, P. and Andersen, G. L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72 7: 5069-5072. doi:10.1128/AEM.03006-05

  • Martín, Hector Garcia, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W., McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf A., Szeto, Ernest, Dalin, Eileen, Putnam, Nik H., Shapiro, Harris J., Pangilinan, Jasmyn L., Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nature Biotechnology, 24 10: 1263-1269. doi:10.1038/nbt1247

  • Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip and Kyrpides, Nikos C. (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Research, 34 Supp. 1: D332-D334. doi:10.1093/nar/gkj145

  • Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, Zhao, Xueling, Dubchak, Inna, Hugenholtz, Philip, Anderson, Iain, Lykidis, Athanasios, Mavromatis, Konstantinos, Ivanova, Natalia and Kyrpides, Nikos C. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Research, 34 Supp. 1: D344-D348. doi:10.1093/nar/gkj024

  • Shah, Nameeta, Teplitsky, Michael V., Minovitsky, Simon, Pennacchio, Len A., Hugenholtz, Philip, Hamann, Bernd and Dubchak, Inna L. (2005) SNP-VISTA: An interactive SNP visualization tool. BMC Bioinformatics, 6 . doi:10.1186/1471-2105-6-292

  • Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip and Banfield, Jillian F. (2005) Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Applied and Environmental Microbiology, 71 10: 6319-6324. doi:10.1128/AEM.71.10.6319-6324.2005

  • Tringe, Susannah Green, von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., Podar, Mircea, Short, Jay M., Mathur, Eric J., Detter, John C., Bork, Peer, Hugenholtz, Philip and Rubin, Edward M. (2005) Comparative metagenomics of microbial communities. Science, 308 5721: 554-557. doi:10.1126/science.1107851

  • Hugenholtz, Philip and Stackebrandt, Erko (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). International Journal of Systematic and Evolutionary Microbiology, 54 2049-2051. doi:10.1099/ijs.0.03028-0

  • Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip and Janssen, Peter H. (2004) Chthoniobacter flavus gen. nov., sp nov., the first pure-culture representative of subdivision two, Spartobacteria classis nov., of the phylum Verrucomicrobia. Applied and Environmental Microbiology, 70 10: 5875-5881. doi:10.1128/AEM.70.10.5875-5881.2004

  • Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip and Janssen, Peter H. (2004) Liquid serial dilution is inferior to solid media for isolation of cultures representative of the phylum-level diversity of soil bacteria. Applied and Environmental Microbiology, 70 7: 4363-4366. doi:10.1128/AEM.70.7.4363-4366.2004

  • Huber, T, Faulkner, G and Hugenholtz, P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, 20 14: 2317-2319. doi:10.1093/bioinformatics/bth226

  • Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 6978: 37-43. doi:10.1038/nature02340

  • Ginige, MP, Hugenholtz, P, Daims, H, Wagner, M, Keller, J and Blackall, LL (2004) Use of stable-isotope probing, full-cycle rRNA analysis, and fluorescence in situ hybridization-microautoradiography to study a methanol-fed denitrifying microbial community. Applied And Environmental Microbiology, 70 1: 588-596. doi:10.1128/AEM.70.1.588-596.2004

  • Joseph, SJ, Hugenholtz, P, Sangwan, P, Osborne, CA and Janssen, PH (2003) Laboratory cultivation of widespread and previously uncultured soil bacteria. Applied and Environmental Microbiology, 69 12: 7210-7215. doi:10.1128/AEM.69.12.7210-7215.2003

  • Baker, BJ, Hugenholtz, P, Dawson, SC and Banfield, JF (2003) Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Applied and Environmental Microbiology, 69 9: 5512-5518. doi:10.1128/AEM.69.9.5512-5518.2003

  • Zhang, H, Sekiguchi, Y, Hanada, S, Hugenholtz, P, Kim, H, Kamagata, Y and Nakamura, K (2003) Gemmatimonas aurantiaca gen. nov., sp nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.. International Journal of Systematic and Evolutionary Microbiology, 53 4: 1155-1163. doi:10.1099/ijs.0.02520-0

  • Janssen, PH and Hugenholtz, P (2003) Fermentation of glycolate by a pure culture of a strictly anaerobic gram-positive bacterium belonging to the family Lachnospiraceae. Archives of Microbiology, 179 5: 321-328. doi:10.1007/s00203-003-0528-5

  • Uzal, FA, Hugenholtz, P, Blackall, LL, Petray, S, Moss, S, Assis, RA, Miyakawa, MF and Carloni, G (2003) PCR detection of Clostridium chauvoei in pure cultures and in formalin-fixed, paraffin-embedded tissues. Veterinary Microbiology, 91 2-3: 239-248. doi:10.1016/S0378-1135(02)00291-2

  • Hugenholtz, P and Huber, T (2003) Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. International Journal of Systematic And Evolutionary Microbiology, 53 1: 289-293. doi:10.1099/ijs.0.02441-0

  • Rossetti, S, Blackall, LL, Majone, M, Hugenholtz, P, Plumb, JJ and Tandoi, V (2003) Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community. Microbiology-sgm, 149 459-469. doi:10.1099/mic.0.26018-0

  • Sait, M, Hugenholtz, P and Janssen, PH (2002) Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environmental Microbiology, 4 11: 654-666. doi:10.1046/j.1462-2920.2002.00352.x

  • Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 8: 2309-2318.

  • Thomsen, TR, Kjellerup, BV, Nielsen, JL, Hugenholtz, P and Nielsen, PH (2002) In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environmental Microbiology, 4 7: 383-391. doi:10.1046/j.1462-2920.2002.00316.x

  • McDevitt, Christopher A., Hugenholtz, Philip, Hanson, Graeme R. and McEwan, Alastair G. (2002) Molecular analysis of dimethyl sulphide dehydrogenase from Rhodovulum sulfidophilum: its place in the dimethyl sulphoxide reductase family of microbial molybdopterin-containing enzymes. Molecular Microbiology, 44 6: 1575-1587. doi:10.1046/j.1365-2958.2002.02978.x

  • Hugenholtz, P (2002) Exploring prokaryotic diversity in the genomic era. Genome Biology, 3 2: . doi:10.1186/gb-2002-3-2-reviews0003

  • McEwan, A. G., Ridge, J. P., McDevitt, C. A. and Hugenholtz, P. (2002) The DMSO reductase family of microbial molybdenum enzymes; Molecular properties and role in the dissimilatory reduction of toxic elements. Geomicrobiology Journal, 19 1: 3-21. doi:10.1080/014904502317246138

  • Hall, S. J., Hugenholtz, P., Siyambalapitiya, N., Keller, J. and Blackall, L. L. (2002) The development and use of real-time PCR for the quantification of nitrifiers in activated sludge. Water Science And Technology, 46 1-2: 267-272.

  • Klein, M., Friedrich, M., Roger, A. J., Hugenholtz, P., Fishbain, S., Abicht, H., Blackall, L. L., Stahl, D. A. and Wagner, M. (2001) Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. Journal of Bacteriology, 183 20: 6028-6035. doi:10.1128/JB.183.20.6028-6035.2001

  • Dalevi, D, Hugenholtz, P and Blackall, LL (2001) A multiple-outgroup approach to resolving division-level phylogenetic relationships using 16S rDNA data. International Journal of Systematic And Evolutionary Microbiology, 51 2: 385-391.

  • Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 1: 411-419. doi:10.1128/AEM.67.1.411-419.2001

  • Crocetti, GR, Hugenholtz, P, Bond, PL, Schuler, A, Keller, J, Jenkins, D and Blackall, LL (2000) Identification of polyphosphate-accumulating organisms and design of 16S rRNA-directed Probes for their detection and quantitation. Applied and Environmental Microbiology, 66 3: 1175-1182. doi:10.1128/AEM.66.3.1175-1182.2000

  • Fuerst, J. A. and Hugenholtz, P. (2000) Microorganisms should be high on DNA preservation list. Science, 290 5496: 1503-1503.

  • Sandler, S. J., Hugenholtz, P., Schleper, C., DeLong, E. F., Pace, N. R. and Clark, A. J. (1999) Diversity of radA genes from cultured and uncultured Archaea: Comparative analysis of putative RadA proteins and their use as a phylogenetic marker. Journal of Bacteriology, 181 3: 907-915.

  • Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998). Journal of Bacteriology, 180 24: 6793-6793.

  • Dojka, MA, Hugenholtz, P, Haack, SK and Pace, NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Applied and Environmental Microbiology, 64 10: 3869-3877.

  • Hugenholtz, P., Goebel, B. M. and Pace, N. R. (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180 18: 4765-4774.

  • Hugenholtz, P., Pitulle, C., Hershberger, K. L. and Pace, N. R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology, 180 2: 366-376.

  • Blackall, LL, Rossetti, S, Christensson, C, Cunningham, M, Hartman, P, Hugenholtz, P and Tandoi, V (1997) The characterization and description of representatives of 'G' bacteria from activated sludge plants. Letters in Applied Microbiology, 25 1: 63-69. doi:10.1046/j.1472-765X.1997.00176.x

  • Seviour, EM, Blackall, LL, Christensson, C, Hugenholtz, P, Cunningham, MA, Bradford, D, Stratton, HM and Seviour, RJ (1997) The filamentous morphotype Eikelboom Type 1863 is not a single genetic entity. Journal of Applied Microbiology, 82 4: 411-421. doi:10.1046/j.1365-2672.1997.00111.x

  • Fuerst, JA, Gwilliam, HG, Lindsay, M, Lichanska, A, Belcher, C, Vickers, JE and Hugenholtz, P (1997) Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon. Applied And Environmental Microbiology, 63 1: 254-262.

  • Bradford, D, Hugenholtz, P, Seviour, EM, Cunningham, MA, Stratton, H, Seviour, RJ and Blackall, LL (1996) 16S rRNA analysis of isolates obtained from gram-negative, filamentous bacteria micromanipulated from activated sludge. Systematic and Applied Microbiology, 19 3: 334-343.

  • Hugenholtz, P and Pace, NR (1996) Identifying microbial diversity in the natural environment: A molecular phylogenetic approach. Trends in Biotechnology, 14 6: 190-197. doi:10.1016/0167-7799(96)10025-1

  • Hugenholtz, P, Cunningham, MA, Hendrikz, JK and Fuerst, JA (1995) Desiccation Resistance of Bacteria Isolated From An Air-Handling System Biofilm Determined Using a Simple Quantitative Membrane-Filter Method. Letters in Applied Microbiology, 21 1: 41-46. doi:10.1111/j.1472-765X.1995.tb01003.x

  • Bond, P. L., Hugenholtz, P., Keller, J. and Blackall, L. L. (1995) Bacterial community structures of phosphate-removing and non-phosphate- removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology, 61 5: 1910-1916.

  • Blackall, LL, Seviour, EM, Cunningham, MA, Seviour, RJ and Hugenholtz, P (1995) Microthrix Parvicella Is a Novel, Deep Branching Member of the Actinomycetes Subphylum. Systematic and Applied Microbiology, 17 4: 513-518.

  • Blackall, LL, Barker, SC and Hugenholtz, P (1995) Phylogenetic Analysis and Taxonomic History of Nocardia-Pinensis and Nocardia-Amarae. Systematic and Applied Microbiology, 17 4: 519-525.

  • Yurkov, V, Stackebrandt, E, Holmes, A, Fuerst, JA, Hugenholtz, P, Golecki, J, Gadon, N, Gorlenko, VM, Kompantseva, EI and Drews, G (1994) Phylogenetic Positions of Novel Aerobic, Bacteriochlorophyll Alpha-Containing Bacteria and Description of Roseococcus-Thiosulfatophilus Gen-Nov, Sp-Nov, Erythromicrobium-Ramosum Gen-Nov, Sp-Nov, and Erythrobacter-Litoralis Sp-Nov. International Journal of Systematic Bacteriology, 44 3: 427-434.

  • Hugenholtz, P, Stackebrandt, E and Fuerst, JA (1994) A Phylogenetic Analysis of the Genus Blastobacter with a View to its Future Reclassification. Systematic and Applied Microbiology, 17 1: 51-57.

  • Hugenholtz, P and Fuerst, JA (1992) Heterotrophic Bacteria in An Air-Handling System. Applied and Environmental Microbiology, 58 12: 3914-3920.

  • Hugenholtz, P and Macrae, IC (1990) Stimulation of Aldrin and Dieldrin Loss From Soils Treated with Carbon Amendments and Saturated-Ring Analogs. Bulletin of Environmental Contamination and Toxicology, 45 2: 223-227.

Conference Publication

  • Robinson, N., Brackin, R., Paungfoo-Lonhienne, C., Lonhienne, T., Westermann, M., Salazar, M., Yeoh, Y. K ., Hugenholtz, P., Ragan, M. A., Redding, M., Pratt, C., Wang, W. J., Royle, A., DiBella, L., Lakshmanan, P. and Schmidt, S. (2016). Addressing the nitrogen problem in sugarcane production to reduce pollution of the Great Barrier Reef. In: 7th International Nitrogen Initiative Conference (INI 2016): Solutions to enhance nitrogen use efficiency for the world. International Nitrogen Initiative Conference, Melbourne, Australia, (). 4-8 December 2016.

  • Benham, Helen, Wood, John, Nagl, Lisa, Maradana, Muralidhara, Daly, Joshua, Lachner, Nancy, Hugenholtz, Philip and Thomas, Ranjeny (2016). An Australian prospective cohort of rheumatoid arthritis patients and their first-degree relatives characterising environmental, genetic, microbial and immune factors. In: Australian Rheumatology Association in conjunction with Rheumatology Health Professionals Association, 57th Annual Scientific Meeting, Darwin, NT, Australia, (7-7). 30 April–4 May 2016. doi:10.1111/imj.13052

  • Gellatly, S., Dennis, P., Jarnicki, A., Lachner, N., Wood, D., Fricker, M., Budden, K., Liu, G., Keely, S., Morrison, M., Willner, D., Cooper, M., Hugenholtz, P. and Hansbro, P. (2016). Healthy Gut Microbiota Ameliorates Experimental Chronic Obstructive Pulmonary Disease. In: Annual Scientific Meeting of the Thoracic Society of Australia and New Zealand and the Australian and New Zealand Society of Respiratory Science 2014, Perth Western Australia, (77-77). 1–6 April 2016. doi:10.1111/resp.12754_22

  • Rehaume, Linda, Kang, Alicia, Zbarskaya, Olga, Mullaney, Jane, Kim, Matthew, Cuiv, Paraic O., Angel, Nicola, Hugenholtz, Philip, Morrison, Mark and Thomas, Ranjeny (2015). Profiling Immunogenic Bacteria within the Microbiota of ZAP-70 Mutant SKG Mice Associated with Spondyloarthritis and Ileitis Using IgA-SEQ. In: *, *, (). *.

  • 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

  • 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

  • Fangrath, S, Mudge, S., Deng, Y, Robinson, N, Schmidt, S, Hugenholtz, P, Ragan, M and Paungfoo-Lonhienne, C (2014). Plant growth promoting rhizobacteria (PGPR) for use in horticulture.. In: The 29th International Horticultural Congress, Brisbane Convention Centre, Brisbane Qld, Australia, (). 17 - 22 August 2014.

  • Lu, Y., Slater, F., Bello Mendoza, R., Jensen, P., Hugenholtz, P. and Batstone, D. J. (2013). Granule shearing enables the high resolution microbial identity. In: Juan M. Lema, Fernando Fdez-Polanco, Marta Carballa, Jorge Rodríguez and Sonia Suárez, Proceedings of 13th World Congress on Anaerobic Digestion: Recovering (bio) Resources for the World. 13th World Congress on Anaerobic Digestion (AD 13), Santiago de Compostela, Spain, (1-4). 25-28 June, 2013.

  • Willner, D., Ab-Ghani, N. A., Yerkovich, S., Tan, M. E., Hopkins, P. M., Chambers, D. C. and Hugenholtz, P. (2013). Longitudinal holistic profiling of the lung transplant microbiome. In: ISHLT 33rd Annual Meeting and Scientific Sessions. 33rd Annual Meeting and Scientific Sessions of the International Society for Heart and Lung Transplantation, Montreal, Canada, (S10-S11). 24-27 April 2013. doi:10.1016/j.healun.2013.01.004

  • 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

  • Kristiansson, E., Hugenholtz, P. and Dalevi, D. (2010). ShotgunFunctionalizeR - an R-package for functional comparison of metagenomes. In: Febs Journal. 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg Sweden, (106-106). Jun 26-Jul 01, 2010.

  • Pope, P., Denman, S., Tringe, S., Hinds, L., Hugenholtz, P., McSweeney, C. and Morrison, M. (2009). Characterization and development of a systems-level understanding of microbial metabolism in the foregut microbiome of the Tammar wallaby (Macropus eugenii).. In: 2009 Conference on Gastrointestinal Function, Chicago, USA, (578-578). 20-22 April, 2009. doi:10.1007/s00248-009-9496-x

  • Yannarell, A. C., Hess, M., Hugenholtz, P. and Mackie, R. I. (2009). Diversity of fiber-adherent bacteria on three potential bioenergy feedstocks during digestion in the cow rumen. In: Conference on Gastrointestinal Function, Chicago, USA, (585-585). 20–22 April 2009. doi:10.1007/s00248-009-9496-x

  • Dalevi, Daneil, Ivanova, Natalia N., Mavromatis, Konstantinos, Hooper, Sean D., Szeto, Ernest, Hugenholtz, Philip, Kyrpides, Nikos C. and Markowitz, Victor M. (2008). Annotation of metagenome short reads using proxygenes. In: Anna Tramontano, ECCB 2008 Conference proceedings. Joint Meeting of the 7th European Conference on Computational Biology and the 5th Meeting of the Bioinformatics Italian Society (ECCB 2008), Cagliari, Italy, (I7-I13). 22-26 September 2008. doi:10.1093/bioinformatics/btn276

  • Markowitz, Victor M., Ivanova, Natalia, Palaniappan, Krishna, Szeto, Ernest, Korzeniewski, Frank, Lykidis, Athanasios, Anderson, Iain, Mavrommatis, Konstantinos, Kunin, Victor, Martin, Hector Garcia, Dubchak, Inna, Hugenholtz, Phil and Kyrpides, Nikos C. (2006). An experimental metagenome data management and analysis system. In: Philip E. Bourne and Soren Brunak, ISMB 2006 Conference proceedings. 14th Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Fortaleza, Brazil, (e359-e367). 6-10 August 2006. doi:10.1093/bioinformatics/btl217

  • Martín, Héctor García, Kunin, Victor, Ivanova, Natalia, Warnecke, Falk, Peterson, S. B., Barry, Kerrie, McHardy, Alice C., Yeates, Christine, He, Shaomei, Salamov, Asaf, Szeto, Ernest, Dalin, Eileen, Putnam, Nik, Rigoutsos, Isidore, Kyrpides, Nikos C., Blackall, Linda Louise, McMahon, Katherine D. and Hugenholtz, Philip (2006). Metagenomic analysis of phosphorus removing sludge communities. In: ISME Vienna 2006: 11th International Symposium on Microbial Ecology. The hidden powers: Microbial communities in action, Vienna, Austria, (A457-A457). 20-25 August 2006.

  • Baldauf, SL, Bhattacharya, D, Cockrill, J, Hugenholtz, P, Pawlowski, J and Simpson, AGB (2004). The tree of life - An overview. In: Assembling the Tree of Life. Conference on Assembling the Tree of Life, New York Ny, (43-75). May 30-Jun 01, 2002.

  • Hugenholtz, Phil (2000). Diverted Cultivation of Phylogenetically Novell Bacteria. In: Lindsay I. Sly, Proceedings of 9th International Congress for Culture Collections : Microbial, Cellular and Genetic Resources for the New Millenium. ICCC9 9th International Congress for Culture Collections, Brisbane, Australia, (41-41). 23-28 July, 2000.

  • Blackall, L. L., Hall, S. J., Hugenholtz, P., Keller, J. and Siyambalapitiya, N. (2000). Real-Time PCR: Can it accurately assess specific members in a mixed microbial community. In: Conference Proceedings of the 4th Annual Australian Environmental Engineering Research Event. 4th Annual Australian Environmental Engineering Research Event, Victor Harbor, South Australia, Australia, (CD ROM). 21-24 November, 2000.

  • Blackall, L. L., Bond, P. L., Crocetti, G., Hugenholtz, P., Jenkins, D., Keller, J. and Schuler, A. (1999). The determination of the bacteria involved in biological phosphorus removal from wastewater. In: IXth International Congress of Bacteriology and Applied Microbiology. IXth International Congress of Bacteriology and Applied Microbiology, Sydney, (20). August 2-6, 1999.

  • Blackall, L. L., Bond, P. L., Burrell, P. C., Crocetti, G. and Hugenholtz, P. (1999). The microbiology of biological nutrient removal - latest discoveries and developments. In: IBC Conference on Advanced Wastewater and Sludge Treatment. IBC Conference on Advanced Wastewater and Sludge Treatment, Sydney, Australia, (10-10). 27-28 Jan 1999.

  • Soddell, JA, Seviour, RJ, Blackall, LL and Hugenholtz, P (1998). New foam-forming nocardioforms found in activated sludge. In: Water Science and Technology. 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley California, (495-502). Jul 21-23, 1997. doi:10.1016/S0273-1223(98)00151-6

  • Blackall, L. L., Burrell, P. C., Gwilliam, H., Bradford, D., Bond, P. L. and Hugenholtz, P. (1998). The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge communities. In: Water Science and Technology. 2nd International Conference on Microorganisms in Activated Sludge and Biofilm Processes, Berkeley California, (451-454). Jul 21-23, 1997. doi:10.1016/S0273-1223(98)00144-9

  • Blackall, LL, Seviour, EM, Bradford, D, Stratton, HM, Cunningham, MA, Hugenholtz, P and Seviour, RJ (1996). Towards understanding the taxonomy of some of the filamentous bacteria causing bulking and foaming in activated sludge plants. In: Water Science and Technology. 18th Biennial Conference of the International-Association-on-Water-Quality, Singapore Singapore, (137-144). Jun 23-28, 1996. doi:10.1016/0273-1223(96)00639-7

Other Outputs

Grants (Administered at UQ)

PhD and MPhil Supervision

Current Supervision

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Principal Advisor

  • Doctor Philosophy — Associate Advisor

  • Doctor Philosophy — Associate Advisor

    Other advisors:

Completed Supervision