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2021 Journal Article Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineagesSun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0 |
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2021 Journal Article A standardized archaeal taxonomy for the Genome Taxonomy DatabaseRinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8 |
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2021 Journal Article Metagenomic compendium of 189,680 DNA viruses from the human gut microbiomeNayfach, Stephen, Páez-Espino, David, Call, Lee, Low, Soo Jen, Sberro, Hila, Ivanova, Natalia N., Proal, Amy D., Fischbach, Michael A., Bhatt, Ami S., Hugenholtz, Philip and Kyrpides, Nikos C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology, 6 (7), 960-970. doi: 10.1038/s41564-021-00928-6 |
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2021 Journal Article Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradientBay, Sean K., Waite, David W., Dong, Xiyang, Gillor, Osnat, Chown, Steven L., Hugenholtz, Philip and Greening, Chris (2021). Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME Journal, 15 (11), 3339-3356. doi: 10.1038/s41396-021-01001-0 |
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2021 Journal Article Wound healing and antioxidant evaluations of alginate from Sargassum ilicifolium and mangosteen rind combination extracts on diabetic mice modelWulandari, Pugar Arga Cristina, Ilmi, Zulfa Nailul, Husen, Saikhu Akhmad, Winarni, Dwi, Alamsjah, Mochammad Amin, Awang, Khalijah, Vastano, Marco, Pellis, Alessandro, MacQuarrie, Duncan and Pudjiastuti, Pratiwi (2021). Wound healing and antioxidant evaluations of alginate from Sargassum ilicifolium and mangosteen rind combination extracts on diabetic mice model. Applied Sciences, 11 (10) 4651, 1-18. doi: 10.3390/app11104651 |
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2021 Journal Article A rooted phylogeny resolves early bacterial evolutionColeman, Gareth A., Davín, Adrián A., Mahendrarajah, Tara A., Szánthó, Lénárd L., Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J. and Williams, Tom A. (2021). A rooted phylogeny resolves early bacterial evolution. Science, 372 (6542) eabe0511, eabe0511-+. doi: 10.1126/science.abe0511 |
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2021 Journal Article IFN-λ therapy prevents severe gastrointestinal graft-versus-host diseaseHenden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375 |
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2021 Journal Article Critical evaluation of faecal microbiome preservation using metagenomic analysisPribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2 |
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2021 Journal Article Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystemChen, Ya-Jou, Leung, Pok Man, Wood, Jennifer L., Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Franks, Ashley E., Cook, Perran L. M. and Greening, Chris (2021). Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal, 15 (10), 2986-3004. doi: 10.1038/s41396-021-00988-w |
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2021 Journal Article Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiomeParks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682 |
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2021 Journal Article Prokaryotic taxonomy and nomenclature in the age of big sequence dataHugenholtz, Philip, Chuvochina, Maria, Oren, Aharon, Parks, Donovan H. and Soo, Rochelle M. (2021). Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME Journal, 15 (7), 1879-1892. doi: 10.1038/s41396-021-00941-x |
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2021 Journal Article Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptationsJi, Mukan, Williams, Timothy J., Montgomery, Kate, Wong, Hon Lun, Zaugg, Julian, Berengut, Jonathan F., Bissett, Andrew, Chuvochina, Maria, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. The ISME Journal, 15 (9), 2692-2707. doi: 10.1038/s41396-021-00944-8 |
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2021 Conference Publication Interferon Lambda Protects Gastrointestinal Stem Cells from Acute GvhdHenden, Andrea S., Robb, Renee, Forero, Adriana, Kuns, Rachel D., Ensbey, Kathleen S., Chang, Karshing, Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nic, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey (2021). Interferon Lambda Protects Gastrointestinal Stem Cells from Acute Gvhd. 2021 TCT Meetings of ASTCT and CIBMTR, Online, 8-12 February 2021. Amsterdam, Netherlands: Elsevier. doi: 10.1016/s2666-6367(21)00107-x |
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2021 Journal Article Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in miceMoentadj, Rabia, Wang, Yiwen, Bowerman, Kate, Rehaume, Linda, Nel, Hendrik, O Cuiv, Paraic, Stephens, Juliette, Baharom, Amalina, Maradana, Muralidhara, Lakis, Vanessa, Morrison, Mark, Wells, Timothy, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2021). Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice. Annals of the Rheumatic Diseases, 80 (5) annrheumdis-2020-219009, annrheumdis-2020. doi: 10.1136/annrheumdis-2020-219009 |
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2021 Journal Article Wastewater monitoring for SARS-CoV-2Donner, Erica, Zamyadi, Arash, Jex, Aaron, Short, Michael, Drigo, Barbara, McCarthy, David, Crosbie, Nicholas, Ahmed, Warish, Mueller, Jochen, Thomas, Kevin, Monis, Paul, Keegan, Alex, Ginige, Maneesha, Hugenholtz, Philip, Tyson, Gene, Hill, Kelly and Blackall, Linda (2021). Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42 (1), 18-22. doi: 10.1071/ma21006 |
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2020 Journal Article Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiomeCampbell, B. C., Al Kouba, J., Timbrell, V., Noor, M. J., Massel, K., Gilding, E. K., Angel, N., Kemish, B., Hugenholtz, P., Godwin, I. D. and Davies, J. M. (2020). Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiome. Science of the Total Environment, 747 141189, 141189. doi: 10.1016/j.scitotenv.2020.141189 |
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2020 Journal Article COVID-19 pandemic reveals the peril of ignoring metadata standardsSchriml, Lynn M., Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A., Finn, Robert D., Hugenholtz, Philip, Hunter, Christopher I., Hurwitz, Bonnie L., Kyrpides, Nikos C., Meyer, Folker, Mizrachi, Ilene Karsch, Sansone, Susanna-Assunta, Sutton, Granger, Tighe, Scott and Walls, Ramona (2020). COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific Data, 7 (1) 188, 188. doi: 10.1038/s41597-020-0524-5 |
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2020 Journal Article Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensingBandara, H. M.H.N., Wood, D. L.A., Vanwonterghem, I., Hugenholtz, P., Cheung, B. P.K. and Samaranayake, L. P. (2020). Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing. Scientific Reports, 10 (1) 7769, 7769. doi: 10.1038/s41598-020-64761-3 |
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2020 Journal Article Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary diseaseBowerman, Kate L., Rehman, Saima Firdous, Vaughan, Annalicia, Lachner, Nancy, Budden, Kurtis F., Kim, Richard Y., Wood, David L. A., Gellatly, Shaan L., Shukla, Shakti D., Wood, Lisa G., Yang, Ian A., Wark, Peter A., Hugenholtz, Philip and Hansbro, Philip M. (2020). Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nature Communications, 11 (1) 5886, 1-15. doi: 10.1038/s41467-020-19701-0 |
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2020 Journal Article Author Correction: Roadmap for naming uncultivated Archaea and BacteriaMurray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 6 (1), 136-136. doi: 10.1038/s41564-020-00827-2 |
