Browse By Person: Tyson, Gene W

Aroney, Sam, Newell, Rhys, Tyson, Gene, & Woodcroft, Ben (2024) Recovering novel genomes from the rare biosphere using Bin Chicken. [Preprint] (Unpublished)

235

Wilson, Liam A., Melville, Jamie N., Pedroso, Marcelo M., Krco, Stefan, Hoelzle, Robert, Zaugg, Julian, Southam, Gordon, Virdis, Bernardino, Evans, Paul, Supper, Jenna, Harmer, Jeffrey R., Tyson, Gene, Clark, Alice, Schenk, Gerhard, & Bernhardt, Paul V. (2024) Kinetic, electrochemical and spectral characterization of bacterial and archaeal rusticyanins; unexpected stability issues and consequences for applications in biotechnology. Journal of Inorganic Biochemistry, 256, Article number: 112539.

McGivern, Bridget B., Cronin, Dylan R., Ellenbogen, Jared B, Borton, Mikayla A, Knutson, Eleanor L, Freire-Zapata, Viviana, Bouranis, John A, Bernhardt, Lukas, Hernandez, Alma I, Flynn, Rory M, Woyda, Reed, Cory, Alexandra B, Wilson, Rachel M., Chanton, Jeffrey P., Woodcroft, Ben J., Ernakovich, Jessica G, Tfaily, Malak M, Sullivan, Matthew B., Tyson, Gene W, Rich, Virginia I., Hagerman, Ann E, & Wrighton, Kelly C. (2024) Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nature Microbiology, 9(6), pp. 1454-1466.

8

8

Messer, Lauren, Bourne, David G., Robbins, Steven J., Clay, Megan, Bell, Sara, McIlroy, Simon, & Tyson, Gene (2024) A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience. Nature Communications, 15(1), Article number: 2902.

3

Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J., & Tyson, Gene W. (2024) Correction to: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning (Nature Methods, (2023), 20, 8, (1203-1212), 10.1038/s41592-023-01940-w). Nature Methods, 21(4), p. 735.

2

Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Wood, David L.A., Krause, Lutz, Tyson, Gene W., Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T., de Zubicaray, Greig I., Thompson, Paul M., McMahon, Katie L., Wright, Margaret J., Visscher, Peter M., Dawson, Paul A., Dissanayake, Cheryl, Eapen, Valsamma, Heussler, Helen S., McRae, Allan F., Whitehouse, Andrew J.O., Wray, Naomi R., & Gratten, Jacob (2024) Erratum: Autism-related dietary preferences mediate autism-gut microbiome associations (Cell (2021) 184(24) (5916–5931.e17), (S0092867421012319), (10.1016/j.cell.2021.10.015)). Cell, 187(2), pp. 495-510.

2

1

Wu, Mengxiong, Li, Jie, Lai, Chun-Yu, Leu, Andy, Sun, Shengjie, Gu, Rui, Erler, Dirk V., Liu, Lian, Li, Lin, Tyson, Gene, Yuan, Zhiguo, McIlroy, Simon, & Guo, Jianhua (2024) Nitrate-driven anaerobic oxidation of ethane and butane by bacteria. The ISME Journal, 18(1), Article number: wrad011.

7

Echeveste Medrano, Maider J., Leu, Andy O., Pabst, Martin, Lin, Yuemei, McIlroy, Simon J., Tyson, Gene W., van Ede, Jitske, Sanchez-Andrea, Irene, Jetten, Mike S.M., Jansen, Robert, & Welte, Cornelia U. (2024) Osmoregulation in freshwater anaerobic methane-oxidizing archaea under salt stress. The ISME Journal, 18(1), Article number: wrae137.

2

Ellenbogen, Jared B, Borton, Mikayla A., McGivern, Bridget B, Cronin, Dylan R., Hoyt, David W, Freire-Zapata, Viviana, McCalley, Carmody K., Varner, Ruth K., Crill, Patrick M., Wehr, Richard A., Chanton, Jeffrey P., Woodcroft, Ben J, Tfaily, Malak M, Tyson, Gene W, Rich, Virginia I, & Wrighton, Kelly C. (2024) Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems, 9(1), Article number: e0069823.

8

Wu, Mengxiong, Liu, Xiawei, Engelberts, Pam, Tyson, Gene, McIlroy, Simon, & Guo, Jianhua (2024) Anaerobic oxidation of ammonium and short-chain gaseous alkanes coupled to nitrate reduction by a bacterial consortium. The ISME Journal, 18(1), Article number: wrae063.

3

Cronin, Dylan, Li, Yueh Fen, Evans, Paul, Tyson, Gene W., Woodcroft, Ben J., Rich, Virginia I., Varner, Ruth K., Hough, Moira, Perry, Apryl, Irwin-Raab, Nicole, Jansen, Joachim, Bennett, Kathryn A., & other, and (2024) Impact of storage and extraction methods on peat soil microbiomes. PeerJ, 12(12), Article number: e18745.

Kobel, Carl M., Leu, Andy, Vera Ponce de León, Arturo, Oyas, Ove, Lai, Wanxin, Altshuler, Ianina, Hagen, Live Heldal, Wollenberg, Rasmus Dam, Bakshani, Cassie R., Willats, William G.T., Nicoll, Laura, McIlroy, Simon, Hvidsten, Torgeir R., Schmidt, Oliver, Greening, Chris, Tyson, Gene, Roehe, Rainer, Aho, Velma T.E., & Pope, Phil (2024) Protozoal populations drive system-wide variation in the rumen microbiome. bioRxiv. [Preprint]

Sternes, Peter R., Shah, Ayesha, Ayala Pintos, Camila, Fairlie, Thomas, Koloski, Natasha, Kang, Seungha, Tousignant, Kaylyn D., McIlroy, Simon J., Morrison, Mark, Tyson, Gene W., & Holtmann, Gerald J. (2024) The biogeography of the mucosa-associated microbiome in health and disease. Frontiers in Microbiology, 15, Article number: 1454910.

Zhang, Xueqin, Xie, Mengying, Cai, Chen, Rabiee, Hesamoddin, Wang, Zhiyao, Virdis, Bernadino, Tyson, Gene, McIlroy, Simon, Yuan, Zhiguo, & Hu, Shihu (2023) Pyrogenic carbon promotes anaerobic oxidation of methane coupled with iron reduction via the redox-cycling mechanism. Environmental Science and Technology, 57(48), pp. 19793-19804.

41

8

Zhang, Xueqin, Joyce, Georgina H., Leu, Andy O., Zhao, Jing, Rabiee, Hesamoddin, Virdis, Bernardino, Tyson, Gene W., Yuan, Zhiguo, McIlroy, Simon J., & Hu, Shihu (2023) Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens'. Nature Communications, 14, Article number: 6118.

23

20

Zhou, Joyce, Boyd, Joel A, Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L A, Hugenholtz, Philip, Tyson, Gene W, Krause, Lutz, & Ó Cuív, Páraic (2023) Draft genome sequence of two "Candidatus Intestinicoccus colisanans" strains isolated from faeces of healthy humans. BMC Research Notes, 16(1), Article number: 174.

1

Zhou, Joyce, Boyd, Joel A, Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L A, Hugenholtz, Philip, Tyson, Gene W, Krause, Lutz, & Ó Cuív, Páraic (2023) Draft genome sequence of two 'Candidatus Intestinicoccus colisanans' strains isolated from faeces of healthy humans. BMC Research Notes, 16(1), Article number: 174.

1

Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J, & Tyson, Gene W (2023) CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), pp. 1203-1212.

232

234

Li, Jie, Liu, Tao, McIlroy, Simon, Tyson, Gene, & Guo, Jianhua (2023) Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings. ISME Communications, 3, Article number: 39.

30

Volmer, James G, Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L, Woodcroft, Benjamin J, Tyson, Gene W, Hugenholtz, Philip, & Morrison, Mark (2023) Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21(1), Article number: 59.

8

7

McIlroy, Simon J., Leu, Andy O., Zhang, Xueqin, Newell, Rhys, Woodcroft, Ben J., Yuan, Zhiguo, Hu, Shihu, & Tyson, Gene W. (2023) Anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens' has a pleomorphic life cycle. Nature Microbiology, 8(2), pp. 321-331.

57

23

Wu, Mengxiong, Li, Jie, Leu, Andy, Erler, Dirk, Stark, Terra, Tyson, Gene, Yuan, Zhiguo, McIlroy, Simon, & Guo, Jianhua (2022) Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia. Nature Communications, 13(1), Article number: 6115.

61

24

25

Zhang, Xueqin, McIlroy, Simon J., Vassilev, Igor, Rabiee, Hesamoddin, Plan, Manuel R., Cai, Chen, Virdis, Bernadino, Tyson, Gene W., Yuan, Zhiguo, & Hu, Shihu (2022) Polyhydroxyalkanoate-driven current generation via acetate by an anaerobic methanotrophic consortium. Water Research, 221, Article number: 118743.

34

11

Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J., & Tyson, Gene W. (2022) CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. bioRxiv. [Preprint]

Wilson, Rachel M., Hough, Moira A., Verbeke, Brittany A., Hodgkins, Suzanne B., Tyson, Gene, Sullivan, Matthew B., Brodie, Eoin, Riley, William J., Woodcroft, Ben, McCalley, Carmody, Dominguez, Sky C., Crill, Patrick M., Varner, Ruth K., Frolking, Steve, Cooper, William T., Chanton, Jeff P., Saleska, Scott D., Rich, Virginia I., Tfaily, Malak M., & other, and (2022) Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. Science of the Total Environment, 820, Article number: 152757.

26

24

Raina, Jean-Baptiste, Lambert, Bennett S, Parks, Donovan H, Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I, Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W, & Seymour, Justin R (2022) Chemotaxis shapes the microscale organization of the ocean's microbiome. Nature, 605(7908), pp. 132-138.

61

Chadwick, Grayson L., Skennerton, Connor T., Laso-Perez, Rafael, Leu, Andy O., Speth, Daan R., Yu, Hang, Morgan-Lang, Connor, Hatzenpichler, Roland, Goudeau, Danielle, Malmstrom, Rex, Brazelton, William J., Woyke, Tanja, Hallam, Steven J., Tyson, Gene W., Wegener, Gunter, Boetius, Antje, & Orphan, Victoria J. (2022) Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biology, 20(1), Article number: e3001508.

135

74

64

Yu, Hang, Skennerton, Connor T, Chadwick, Grayson L, Leu, Andy O, Aoki, Masataka, Tyson, Gene W, & Orphan, Victoria J (2022) Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. The ISME Journal, 16(1), pp. 168-177.

25

24

Hallstrom, Soren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R., & Riemann, Lasse (2022) Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16(11), pp. 2525-2534.

15

Ou, Ya-Fei, Dong, Hong-Po, McIlroy, Simon, Crowe, Sean, Hallam, Steven J., Han, Ping, Kallmeyer, Jens, Simister, Rachel, Vuillemin, Aurele, Leu, Andy, Liu, Zhanfei, Zheng, Yan-Ling, Sun, Qian-Li, Liu, Min, Tyson, Gene, & Hou, Li-Jun (2022) Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. The ISME Journal, 16(10), pp. 2373-2387.

59

25

24

Bramucci, Anna, Focardi, Amaranta, Rinke, Christian, HugenHoltz, Philip, Tyson, Gene, Seymour, Justin, & Raina, Jean-Baptiste (2021) Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1, Article number: 79.

24

14

Emerson, Joanne B., Varner, Ruth K, Wik, Martin, Parks, Donovan H, Neumann, Rebecca B, Johnson, Joel E, Singleton, Caitlin M, Woodcroft, Ben J, Tollerson, Rodney, Owusu-Dommey, Akosua, Binder, Morgan, Freitas, Nancy L, Crill, Patrick M, Saleska, Scott R, Tyson, Gene W, & Rich, Virginia I (2021) Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications, 12(1), Article number: 5815.

56

22

21

Shi, Ling-Dong, Lv, Pan-Long, McIlroy, Simon J, Wang, Zhen, Dong, Xiao-Li, Kouris, Angela, Lai, Chun-Yu, Tyson, Gene W, Strous, Marc, & Zhao, He-Ping (2021) Methane-dependent selenate reduction by a bacterial consortium. The ISME Journal, 15(12), pp. 3683-3692.

13

30

Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A, Deng, Yu, Parks, Donovan H, Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J, Tyson, Gene W, Hugenholtz, Philip, Polz, Martin F, & Zhang, Tong (2021) Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9(1), Article number: 199.

87

52

49

Yap, Chloe X, Henders, Anjali K, Alvares, Gail A, Wood, David L A, Krause, Lutz, Tyson, Gene W, Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K, Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P, Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E, Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L, Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T, de Zubicaray, Greig I, Thompson, Paul M, McMahon, Katie L, Wright, Margaret J, Visscher, Peter M, Dawson, Paul A, Dissanayake, Cheryl, Eapen, Valsamma, Heussler, Helen S, McRae, Allan F, Whitehouse, Andrew J O, Wray, Naomi R, & Gratten, Jacob (2021) Autism-related dietary preferences mediate autism-gut microbiome associations. Cell, 184(24), 5916-5931.e17.

200

191

Pribyl, 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., & Hugenholtz, Philip (2021) Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1(1), Article number: 14.

55

17

Parks, Donovan H, Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W, & 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, Article number: 643682.

85

24

27

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Tyson, Gene, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Woodcroft, Ben, Ye, Jun, & other, and (2021) Author Correction: A genomic catalog of Earth's microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39(4), p. 521.

8

6

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magaña, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O’Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjöling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Tyson, Gene, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Walsh, David A., Weimer, Bart C., Whitman, Thea, van der Wielen, Paul, Williams, Timothy J., Woodcroft, Ben, Ye, Jun, & other, and (2021) Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39(4), p. 520.

4

Donner, 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, & Blackall, Linda (2021) Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42(1), pp. 18-22.

43

4

6

Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I. Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, Jose P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric, Allen, Michelle A., Alteio, Lauren V., Andersen, Gary, Anesio, Alexandre M., Attwood, Graeme, Avila-Magana, Viridiana, Badis, Yacine, Bailey, Jake, Baker, Brett, Baldrian, Petr, Barton, Hazel A., Beck, David A.C., Becraft, Eric D., Beller, Harry R., Beman, J. Michael, Bernier-Latmani, Rizlan, Berry, Timothy D., Bertagnolli, Anthony, Bertilsson, Stefan, Bhatnagar, Jennifer M., Bird, Jordan T., Blanchard, Jeffrey L., Blumer-Schuette, Sara E., Bohannan, Brendan, Borton, Mikayla A., Brady, Allyson, Brawley, Susan H., Brodie, Juliet, Brown, Steven, Brum, Jennifer R., Brune, Andreas, Bryant, Donald A., Buchan, Alison, Buckley, Daniel H., Buongiorno, Joy, Cadillo-Quiroz, Hinsby, Caffrey, Sean M., Campbell, Ashley N., Campbell, Barbara, Carr, Stephanie, Carroll, Jo Lynn, Cary, S. Craig, Cates, Anna M., Cattolico, Rose Ann, Cavicchioli, Ricardo, Chistoserdova, Ludmila, Coleman, Maureen L., Constant, Philippe, Conway, Jonathan M., Mac Cormack, Walter P., Crowe, Sean, Crump, Byron, Currie, Cameron, Daly, Rebecca, DeAngelis, Kristen M., Denef, Vincent, Denman, Stuart E., Desta, Adey, Dionisi, Hebe, Dodsworth, Jeremy, Dombrowski, Nina, Donohue, Timothy, Dopson, Mark, Driscoll, Timothy, Dunfield, Peter, Dupont, Christopher L., Dynarski, Katherine A., Edgcomb, Virginia, Edwards, Elizabeth A., Elshahed, Mostafa S., Figueroa, Israel, Flood, Beverly, Fortney, Nathaniel, Fortunato, Caroline S., Francis, Christopher, Gachon, Claire M.M., Garcia, Sarahi L., Gazitua, Maria C., Gentry, Terry, Gerwick, Lena, Gharechahi, Javad, Girguis, Peter, Gladden, John, Gradoville, Mary, Grasby, Stephen E., Gravuer, Kelly, Grettenberger, Christen L., Gruninger, Robert J., Guo, Jiarong, Habteselassie, Mussie Y., Hallam, Steven J., Hatzenpichler, Roland, Hausmann, Bela, Hazen, Terry C., Hedlund, Brian, Henny, Cynthia, Herfort, Lydie, Hernandez, Maria, Hershey, Olivia S., Hess, Matthias, Hollister, Emily B., Hug, Laura A., Hunt, Dana, Jansson, Janet, Jarett, Jessica, Kadnikov, Vitaly V., Kelly, Charlene, Kelly, Robert, Kelly, William, Kerfeld, Cheryl A., Kimbrel, Jeff, Klassen, Jonathan L., Konstantinidis, Konstantinos T., Lee, Laura L., Li, Wen Jun, Loder, Andrew J., Loy, Alexander, Lozada, Mariana, MacGregor, Barbara, Magnabosco, Cara, Maria da Silva, Aline, McKay, R. Michael, McMahon, Katherine, McSweeney, Chris S., Medina, Mónica, Meredith, Laura, Mizzi, Jessica, Mock, Thomas, Momper, Lily, Moran, Mary Ann, Morgan-Lang, Connor, Moser, Duane, Muyzer, Gerard, Myrold, David, Nash, Maisie, Nesbø, Camilla L., Neumann, Anthony P., Neumann, Rebecca B., Noguera, Daniel, Northen, Trent, Norton, Jeanette, Nowinski, Brent, Nüsslein, Klaus, O'Malley, Michelle A., Oliveira, Rafael S., Maia de Oliveira, Valeria, Onstott, Tullis, Osvatic, Jay, Ouyang, Yang, Pachiadaki, Maria, Parnell, Jacob, Partida-Martinez, Laila P., Peay, Kabir G., Pelletier, Dale, Peng, Xuefeng, Pester, Michael, Pett-Ridge, Jennifer, Peura, Sari, Pjevac, Petra, Plominsky, Alvaro M., Poehlein, Anja, Pope, Phillip B., Ravin, Nikolai, Redmond, Molly C., Reiss, Rebecca, Rich, Virginia, Rinke, Christian, Rodrigues, Jorge L.Mazza, Rodriguez-Reillo, William, Rossmassler, Karen, Sackett, Joshua, Salekdeh, Ghasem Hosseini, Saleska, Scott, Scarborough, Matthew, Schachtman, Daniel, Schadt, Christopher W., Schrenk, Matthew, Sczyrba, Alexander, Sengupta, Aditi, Setubal, Joao C., Shade, Ashley, Sharp, Christine, Sherman, David H., Shubenkova, Olga V., Sierra-Garcia, Isabel Natalia, Simister, Rachel, Simon, Holly, Sjoling, Sara, Slonczewski, Joan, Correa de Souza, Rafael Soares, Spear, John R., Stegen, James C., Stepanauskas, Ramunas, Stewart, Frank, Suen, Garret, Sullivan, Matthew, Sumner, Dawn, Swan, Brandon K., Swingley, Wesley, Tarn, Jonathan, Taylor, Gordon T., Teeling, Hanno, Tekere, Memory, Teske, Andreas, Thomas, Torsten, Thrash, Cameron, Tiedje, James, Ting, Claire S., Tully, Benjamin, Ulloa, Osvlado, Valentine, David L., Van Goethem, Marc W., VanderGheynst, Jean, Verbeke, Tobin J., Vollmers, John, Vuillemin, Aurèle, Waldo, Nicholas B., Williams, Timothy J., Tyson, Gene, Woodcroft, Ben, & other, and (2021) A genomic catalog of Earth's microbiomes. Nature Biotechnology, 39(4), pp. 499-509.

118

436

447

Altemani, Faisal, Barrett, Helen L., Gomez-Arango, Luisa, Josh, Peter, David McIntyre, H., Callaway, Leonie K., Morrison, Mark, Tyson, Gene W., & Dekker Nitert, Marloes (2021) Pregnant women who develop preeclampsia have lower abundance of the butyrate-producer Coprococcus in their gut microbiota. Pregnancy Hypertension, 23, pp. 211-219.

55

57

Wilson, R. M., Zayed, A. A., Crossen, K. B., Woodcroft, B., Tfaily, M. M., Emerson, J., Raab, N., Hodgkins, S. B., Verbeke, B., Tyson, G., Crill, P., Saleska, S., Chanton, J. P., Rich, V. I., & other, and (2021) Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PLoS ONE, 16(2), Article number: e0245857.

68

12

Zinke, Laura A., Evans, Paul N., Santos-Medellín, Christian, Schroeder, Alena L., Parks, Donovan H., Varner, Ruth K., Rich, Virginia I., Tyson, Gene W., & Emerson, Joanne B. (2021) Evidence for non‐methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environmental Microbiology, 23(1), pp. 340-357.

67

18

20

Gagen, Emma J., Levett, Alan, Paz, Anat, Bostelmann, Heike, Valadares, Rafael Borges da Silva, Bitencourt, José Augusto Pires, Gastauer, Markus, Nunes, Gisele Lopes, Oliveira, Guilherme, Vasconcelos, Paulo M., Tyson, Gene W., & Southam, Gordon (2020) Accelerating microbial iron cycling promotes re‐cementation of surface crusts in iron ore regions. Microbial Biotechnology, 13(6), pp. 1960-1971.

52

11

Leu, Andy O., McIlroy, Simon J., Ye, Jun, Parks, Donovan H., Orphan, Victoria J., & Tyson, Gene W. (2020) Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family Methanoperedenaceae. mBio, 11(3), Article number: e01325-20.

222

53

50

Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark, & Holtmann, Gerald J. (2020) Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Gastroenterology, 158(6 (Suppl. 1)), S-542.

Leu, Andy O., Cai, Chen, McIlroy, Simon J., Southam, Gordon, Orphan, Victoria J., Yuan, Zhiguo, Hu, Shihu, & Tyson, Gene W. (2020) Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. The ISME Journal, 14(4), pp. 1030-1041.

153

227

212

Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R., & Hugenholtz, Philip (2020) Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) (The ISME Journal, (2019), 13, 3, (663-675), 10.1038/s41396-018-0282-y). ISME Journal, 14(3), Article number: 878 878.

2

Cuiv, Paraic O., Krause, Lutz, Wood, David, Hugenholtz, Phil, & Tyson, Gene (2020) Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives. Neurogastroenterology and Motility, 32(S1), p. 155.

Woodcroft, Ben, Emerson, Joanne B., Varner, Ruth K., Wik, Martin, Parks, Donovan H., Neumann, Rebecca B., Johnson, Joel E., Singleton, Caitlin M., Tollerson, Rodney, Owusu-Dommey, Akosua, Binder, Morgan, Freitas, Nancy L., Crill, Patrick M., Saleska, Scott R., Tyson, Gene W, & Rich, Virginia I. (2020) Diverse Arctic lake sediment microbiota shape methane emission temperature sensitivity. [Preprint]

Leu, Andy O., McIlroy, Simon J., Ye, Jun, Parks, Donovan H., Orphan, Victoria J., & Tyson, Gene W. (2020) Lateral gene transfer drives metabolic flexibility in the anaerobic methane oxidising archaeal family Methanoperedenaceae.

Bolduc, Benjamin, Hodgkins, Suzanne B., Varner, Ruth K., Crill, Patrick M., McCalley, Carmody K., Chanton, Jeffrey P., Tyson, Gene W., Riley, William J., Palace, Michael, Duhaime, Melissa B., Hough, Moira A., Saleska, Scott R., Sullivan, Matthew B., Rich, Virginia I., other, and, & Woodcroft, Ben (2020) The IsoGenie database: An interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ, 8, Article number: e9467.

73

5

Hua, Zheng Shuang, Wang, Yu Lin, Evans, Paul N., Qu, Yan Ni, Goh, Kian Mau, Rao, Yang Zhi, Qi, Yan Ling, Li, Yu Xian, Huang, Min Jun, Jiao, Jian Yu, Chen, Ya Ting, Mao, Yan Ping, Shu, Wen Sheng, Hozzein, Wael, Hedlund, Brian P., Tyson, Gene W., Zhang, Tong, & Li, Wen Jun (2019) Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications, 10, Article number: 4574.

106

95

94

Luangthongkam, Pawarisa, Strong, Peter James, Syed Mahamud, Syarifah Nuraqmar, Evans, Paul, Jensen, Paul, Tyson, Gene, Laycock, Bronwyn, Lant, Paul Andrew, & Pratt, Steven (2019) The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture. Bioresources and Bioprocessing, 6(1), Article number: 50.

159

26

22

Robbins, S.J., Singleton, C.M., Chan, C.X., Messer, L.F., Geers, Aileen U., Ying, H., Baker, A., Bell, S.C., Morrow, K.M., Ragan, M.A., Miller, D.J., Forêt, S., Ball, E., Beeden, R., Berumen, M., Aranda, Manuel, Ravasi, T., Bongaerts, P., Hoegh-Guldberg, O., Cooke, I., Leggat, Bill, Sprungala, S., Fitzgerald, A., Shang, Catherine, Lundgren, P., Fyffe, Theresa, Rubino, F., van Oppen, M., Weynberg, K., Voolstra, C.R., Tyson, G.W., & Bourne, D.G. (2019) A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4, pp. 2090-2100.

164

153

Cai, Chen, Shi, Ying, Guo, Jianhua, Tyson, Gene W., Hu, Shihu, & Yuan, Zhiguo (2019) Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environmental Science and Technology, 53(13), pp. 7371-7379.

22

55

Zhang, Xueqin, Xia, Jun, Pu, Jiaoyang, Cai, Chen, Tyson, Gene W., Yuan, Zhiguo, & Hu, Shihu (2019) Biochar-Mediated Anaerobic Oxidation of Methane. Environmental Science and Technology, 53(12), pp. 6660-6668.

52

107

102

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., & Xenarios, Ioannis (2019) Consent insufficient for data release−Response. Science, 364(6439), p. 446.

Rinke, C., Rubino, F., Messer, L.F., Youssef, N., Parks, D.H., Chuvochina, M., Brown, Mark, Jeffries, T., Tyson, G.W., Seymour, J.R., & Hugenholtz, P. (2019) A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME Journal, 13, pp. 663-675.

71

118

119

Wilson, Rachel M., Neumann, Rebecca B., Crossen, Kelsey B., Raab, Nicole M., Hodgkins, Suzanne B., Saleska, Scott R., Bolduc, Ben, Woodcroft, Ben J., Tyson, Gene W., Chanton, Jeffrey P., & Rich, Virginia I. (2019) Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production. Frontiers in Earth Science, 7, Article number: 59 1-22.

179

12

14

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S.G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, De Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P.A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A.N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., & Xenarios, Ioannis (2019) Data access: Toward unrestricted use of public genomic data. Science, 363(6425), pp. 350-352.

46

Martinez, Miguel A., Woodcroft, Ben J., Espinoza, Julio C. Ignacio, Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh-Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W., & Rich, Virginia I. (2019) Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology, 42(1), pp. 54-66.

94

17

12

Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S., & Tyson, Gene W. (2019) Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13(5), pp. 1269-1279.

133

51

46

Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip, & Tyson, Gene W. (2019) An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17(4), pp. 219-232.

93

363

346

Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B., & Hugenholtz, Philip (2019) The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42(1), pp. 15-21.

93

71

70

Santini, T. C., Warren, K., Raudsepp, M., Carter, N., Hamley, D., McCosker, C., Couperthwaite, S., Southam, G., Tyson, G. W., & Warren, L. A. (2019) Accelerating bauxite residue remediation with microbial biotechnology. In Chesonis, Corleen (Ed.) Light Metals 2019. Springer, Cham, Switzerland, pp. 69-77.

8

6

Gagen, Emma J., Zaugg, Julian, Tyson, Gene W., & Southam, Gordon (2019) Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum. Frontiers in Microbiology, 10, Article number: 2938.

63

27

26

Singleton, Caitlin M, McCalley, Carmody K, Woodcroft, Ben J, Boyd, Joel A, Evans, Paul N, Hodgkins, Suzanne B, Chanton, Jeffrey P, Frolking, Steve, Crill, Patrick M, Saleska, Scott R, Rich, Virginia I, & Tyson, Gene W (2018) Methanotrophy across a natural permafrost thaw environment. The ISME Journal, 12, pp. 2544-2558.

104

95

89

Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B., & Rich, Virginia I. (2018) Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3(5), Article number: e00076-18 1-21.

170

188

177

Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., & Bowers, Robert M. (2018) Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36, Article number: 660.

14

12

Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I., & Tyson, Gene W. (2018) Genome-centric view of carbon processing in thawing permafrost. Nature, 560(7716), pp. 49-54.

271

268

Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I., & Sullivan, Matthew B. (2018) Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3, pp. 870-880.

154

344

320

Boyd, Joel A., Woodcroft, Ben J, & Tyson, Gene W. (2018) GraftM: A tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research, 46(10), Article number: e59 1-9.

148

91

99

Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip, & Tyson, Gene W. (2018) Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3, Article number: 253.

26

27

Raudsepp, Maija J., Fluggen, Markus, Shypanski, Adam H., Tyson, Gene W., Golding, Suzanne D., & Southam, Gordon (2018) Biogenic Methane Cycling in a Laboratory Model of an Abandoned Bituminous Coal Mine. Geomicrobiology Journal, 35(6), pp. 491-502.

2

1

Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. Murat, Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, & Woyke, Tanja (2018) Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017). Nature Biotechnology, 36(2), Article number: 196.

3

1

Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuiv, Paraic O., Hugenholtz, Philip, Tyson, Gene W., & Morrison, Mark (2018) Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12, pp. 2942-2953.

22

23

Cai, Chen, Leu, Andy O., Xie, Guo-Jun, Guo, Jianhua, Feng, Yuexing, Zhao, Jian-Xin, Tyson, Gene W., Yuan, Zhiguo, & Hu, Shihu (2018) A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME Journal, 12, pp. 1929-1939.

4

284

269

Orphan, Victoria, Tyson, Gene, Meile, Christof, McGlynn, Shawn, Yu, Hang, Chadwick, Grayson, Marlow, Jeffrey, Trembath-Reichert, Elizabeth, Dekas, Anne, Hettich, Robert, Pan, Chongle, Ellisman, Mark, Hatzenpichler, Roland, Skennerton, Connor, & Scheller, Silvan (2017) Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions. U.S. Department of Energy, United States of America.

Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W., & Orphan, Victoria J. (2017) Erratum for Skennerton et al., "Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea". mBio, 8(5), Article number: e01561-17.

29

2

Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip, & Tyson, Gene W. (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2, pp. 1533-1542.

201

1,106

1,092

Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R., & Li, Changsheng (2017) Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. Journal of Advances in Modeling Earth Systems, 9(2), pp. 1412-1430.

62

19

18

Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A., & Schenk, Gerhard (2017) Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9(8), pp. 1157-1168.

15

13

Cayford, Barry I, Jiang, Guangming, Keller, Jurg, Tyson, Gene, & Bond, Philip L (2017) Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. Biofouling, 33(9), pp. 780-792.

26

Shiffman, Miriam E., Soo, Rochelle M., Dennis, Paul G., Morrison, Mark, Tyson, Gene W., & Hugenholtz, Philip (2017) Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, Article number: e4075.

65

36

38

Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W., & Orphan, Victoria J. (2017) Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea. mBio, 8(4), Article number: e00530-17.

78

72

71

Tout, Jessica, Astudillo-Garcia, Carmen, Taylor, Michael W., Tyson, Gene W, Stocker, Roman, Ralph, Peter J, Seymour, Justin R, & Webster, Nicole S (2017) Redefining the sponge‐symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host‐derived compounds. Environmental Microbiology Reports, 9(6), pp. 750-755.

17

Raudsepp, Maija J., Gagen, Emma J., Golding, Suzanne D., Tyson, Gene W., & Southam, Gordon (2017) The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina. Fuel, 205, pp. 60-70.

9

7

Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R., & Stocker, Roman (2017) A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2, pp. 1344-1349.

48

47

Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip, & Tyson, Gene W. (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1, Article number: 16170 1-9.

154

383

364

Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptiste, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W., & Hugenholtz, Philip (2016) Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4, Article number: e2486 1-28.

87

54

52

Woodcroft, Ben J., Boyd, Joel A., & Tyson, Gene W. (2016) OrfM: A fast open reading frame predictor for metagenomic data. Bioinformatics, 32(17), pp. 2702-2703.

107

29

27

Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W., & Rabaey, Korneel (2016) Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6, Article number: 39114.

56

60

54

Angly, Florent E., Pantos, Olga, Morgan, Thomas C., Rich, Virginia, Tonin, Hemerson, Bourne, David G., Mercurio, Philip, Negri, Andrew P., & Tyson, Gene W. (2016) Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ, 4, Article number: e1758.

76

6

5

Robbins, Steven J., Evans, Paul N., Parks, Donovan H., Golding, Suzanne D., & Tyson, Gene W. (2016) Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. Frontiers in Microbiology, 7, Article number: 731.

91

50

47

Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel, & Tyson, Gene W. (2016) Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environmental Microbiology, 18(9), pp. 3144-3158.

108

102

Angly, Florent E., Heath, Candice, Morgan, Thomas C., Tonin, Hemerson, Rich, Virginia, Schaffelke, Britta, Bourne, David G., & Tyson, Gene W. (2016) Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ, 4, Article number: e1511.

79

52

45

Barr, Jeremy J., Dutilh, Bas E., Skennerton, C.T., Fukushima, Toshikazu, Hastie, Marcus L., Gorman, J.J., Tyson, G.W., & Bond, Philip L. (2016) Metagenomic and metaproteomic analyses of Accumulibacter phosphatis‐enriched floccular and granular biofilm. Environmental Microbiology, 18(1), pp. 273-287.

36

34

Strong, Peter James, Laycock, Bronwyn, Mahamud, Syarifah, Jensen, Paul, Lant, Paul, Tyson, Gene, & Pratt, Steven (2016) The Opportunity for High-Performance Biomaterials from Methane. Microorganisms, 4(1), Article number: 11.

70

99

89

Rahman, Nurdyana Abdul, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W., & Hugenholtz, Philip (2016) A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres. Frontiers in Microbiology, 6, Article number: 1469.

76

82

74

Skennerton, Connor T., Haroon, Mohamed F., Briegel, Ariane, Shi, Jian, Jensen, Grant J., Tyson, Gene W., & Orphan, Victoria J. (2016) Phylogenomic analysis of Candidatus ‘Izimaplasma’ species: free-living representatives from a Tenericutes clade found in methane seeps. ISME Journal, 10, pp. 2679-2692.

65

62

Robbins, Steven J., Evans, Paul N., Esterle, Joan S., Golding, Suzanne D., & Tyson, Gene W. (2016) The effect of coal rank on biogenic methane potential and microbial composition. International Journal of Coal Geology, 154-155, pp. 205-212.

75

64

Raudsepp, M. J., Gagen, E. J., Evans, P., Tyson, G. W., Golding, S. D., & Southam, G. (2016) The influence of hydrogeological disturbance and mining on coal seam microbial communities. Geobiology, 14(2), pp. 163-175.

30

22

Santini, Talitha C., Malcolm, Laura I., Tyson, Gene W., & Warren, Lesley A. (2016) pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue. Environmental Science & Technology, 50(20), pp. 11164-11173.

54

53

Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim, J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M., & Mueller, C.W. (2015) Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5, Article number: 18165.

109

15

14

Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W., & Hugenholtz, Philip (2015) Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus. PeerJ, 3, Article number: e968.

136

84

75

Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip, & Tyson, Gene W. (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25(7), pp. 1043-1055.

167

6,719

6,707

Tout, Jessica, Jeffries, Thomas C., Petrou, Katherina, Tyson, Gene W., Webster, Nicole S., Garren, Melissa, Stocker, Roman, Ralph, Peter J., & Seymour, Justin R. (2015) Chemotaxis by natural populations of coral reef bacteria. ISME Journal, 9, pp. 1764-1777.

65

61

Wang, Jack T. H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W., & 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 & Biology Education, 16(1), pp. 50-60.

75

20

Liu, Yiwen, Sharma, K.R., Ni, Bing-Jie, Fan, Lu, Murthy, S., Tyson, Gene, & Yuan, Zhiguo (2015) Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment. Water Research, 74, pp. 155-165.

66

59

Skennerton, Connor T., Barr, Jeremy J., Slater, Frances R., Bond, Philip L., & Tyson, Gene W. (2015) Expanding our view of genomic diversity in Candidatus Accumulibacter clades. Environmental Microbiology, 17(5), pp. 1574-1585.

98

90

Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W., & Hugenholtz, Philip (2015) First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3, Article number: e740.

56

66

64

Pantos, Olga, Bongaerts, Pim, Dennis, Paul G., Tyson, Gene W., & Hoegh-Guldberg, Ove (2015) Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. ISME Journal, 9, pp. 1916-1927.

116

91

Evans, Paul N., Parks, Donovan H., Chadwick, Grayson L., Robbins, Steven J., Orphan, Victoria J., Golding, Suzanne D., & Tyson, Gene W. (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 350(6259), pp. 434-438.

561

538

Voolstra, C.R., Miller, D.J., Ragan, M.A., Hoffmann, A.A., Hoegh-Guldberg, O., Bourne, D.G., Ball, E.E., Ying, H., Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, N., Leggat, William, Sprungala, Susanne, Imelfort, M., Tyson, G.W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, T., Berumen, M.L., Abal, Eva, & Fyffe, Theresa (2015) The ReFuGe 2020 Consortium-using 'omics' approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2, Article number: 68.

85

70

66

Patil, Sunil A., Arends, Jan B. A., Vanwonterghem, Inka, van Meerbergen, Jarne, Guo, Kun, Tyson, Gene W., & Rabaey, Korneel (2015) Selective Enrichment Establishes a Stable Performing Community for Microbial Electrosynthesis of Acetate from CO2. Environmental Science & Technology, 49(14), pp. 8833-8843.

252

221

Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel, & Tyson, Gene W. (2015) Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters. Scientific Reports, 5, Article number: 8496.

72

116

101

Susilawati, Rita, Evans, Paul N., Esterle, Joan S., Robbins, Steven J., Tyson, Gene W., Golding, Suzanne D., & Mares, Tennille E. (2015) Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals. International Journal of Coal Geology, 137, pp. 66-76.

41

38

Waldor, Matthew K., Tyson, Gene, Borenstein, Elhanan, Ochman, Howard, Moeller, Andrew, Finlay, B. Brett, Kong, Heidi H., Gordon, Jeffrey I., Nelson, Karen E., Dabbagh, Karim, & Smith, Hamilton (2015) Where Next for Microbiome Research? PLoS Biology, 13(1), Article number: e1002050.

83

111

91

Hu, Shihu, Zeng, Raymond J., Haroon, Mohamed F., Keller, Jurg, Lant, Paul A., Tyson, Gene W., & Yuan, Zhiguo (2015) A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports, 5, Article number: 8706.

96

86

68

McCalley, Carmody K., Woodcroft, Ben J., Hodgkins, Suzanne B., Wehr, Richard A., Kim, Eun-Hae, Mondav, Rhiannon, Crill, Patrick M., Chanton, Jeffrey P., Rich, Virginia I., Tyson, Gene W., & Saleska, Scott R. (2014) Methane dynamics regulated by microbial community response to permafrost thaw. Nature, 514(7523), pp. 478-481.

308

290

Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip, & Tyson, Gene W. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2, Article number: e603 1-16.

137

210

191

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., & Tyson, Gene W. (2014) Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5, Article number: 3212 1-7.

143

138

Angly, Florent E., Fields, Christopher J., & Tyson, Gene W. (2014) The Bio-Community Perl toolkit for microbial ecology. Bioinformatics, 30(13), pp. 1926-1927.

77

14

10

De Vrieze, Jo, Gildemyn, Sylvia, Arends, Jan B. A., Vanwonterghem, Inka, Verbeken, Kim, Boon, Nico, Verstraete, Willy, Tyson, Gene W., Hennebel, Tom, & Rabaey, Korneel (2014) Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion. Water Research, 54, pp. 211-221.

135

130

Angly, F.E., Dennis, P.G., Skarshewski, A., Vanwonterghem, I., Hugenholtz, P., & Tyson, G.W. (2014) CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2, Article number: 11.

79

207

191

Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel, & Tyson, Gene W. (2014) Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, 8, pp. 2015-2028.

292

234

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., & Hugenholtz, Philip (2014) An Expanded Genomic Representation of the Phylum Cyanobacteria. Genome Biology and Evolution, 6(5), pp. 1031-1045.

75

218

202

Vanwonterghem, Inka, Jensen, Paul D., Ho, Dang P., Batstone, Damien J., & Tyson, Gene W. (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology, 27, pp. 55-64.

292

271

Bragg, Lauren & Tyson, Gene W (2014) Metagenomics Using Next-Generation Sequencing. In Paulsen, Ian T. & Holmes, Andrew J. (Eds.) Environmental Microbiology: Methods and Protocols. [2 ed.]. Humana Press, New York, NY, pp. 183-201.

78

Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, & Beiko, Robert G. (2014) STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics, 30(21), pp. 3123-3124.

3,055

2,990

Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W., & Webster, Nicole (2013) Erratum: Coral reef invertebrate microbiomes correlate with the presence of photosymbionts (ISME Journal (2013) 7 (1452-1458) DOI: 10.1038/ismej.2012.172). ISME Journal, 7(7), p. 1459.

9

10

Dennis, Paul G., Guo, Kun, Imelfort, Michael, Jensen, Paul, Tyson, Gene W., & Rabaey, Korneel (2013) Spatial uniformity of microbial diversity in a continuous bioelectrochemical system. Bioresource Technology, 129, pp. 599-605.

36

34

Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Tyson, Gene W., Vivanco, Jorge M., & Schenk, Peer M. (2013) Activation of the Jasmonic Acid Plant Defence Pathway Alters the Composition of Rhizosphere Bacterial Communities. PLoS ONE, 8(2), Article number: e56457.

80

161

136

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

1,019

951

Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W., & Webster, Nicole (2013) Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. ISME Journal, 7, 1452–1458.

126

121

Skennerton, Connor T., Imelfort, Michael, & Tyson, Gene W. (2013) Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Research, 41(10), Article number: e105.

82

115

108

Dennis, Paul G., Seymour, Justin, Kumbun, Kimber, & Tyson, Gene W. (2013) Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME Journal, 7, 1661–1664.

40

37

Pervin, H.M., Dennis, P.G., Lim, Hui J., Tyson, G.W., Batstone, D.J., & Bond, P.L. (2013) Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Research, 47(19), pp. 7098-7108.

109

99

Dennis, Paul G., Harnisch, Falk, Yeoh, Yun Kit, Tyson, Gene W., & Rabaey, Korneel (2013) Dynamics of Cathode-Associated Microbial Communities and Metabolite Profiles in a Glycerol-Fed Bioelectrochemical System. Applied and Environmental Microbiology, 79(13), 4008–4014.

65

52

Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo, & Tyson, Gene W. (2013) Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage (Nature (2013) 500 (567-570) doi:10.1038/nature12375). Nature, 501(7468), p. 578.

11

Dove, Sophie G., Kline, David I., Pantos, Olga, Angly, Florent E., Tyson, Gene W., & Hoegh-Guldberg, Ove (2013) Future reef decalcification under a business-as-usual CO2 emission scenario. Proceedings of the National Academy of Sciences of the United States of America, 110(38), pp. 15342-15347.

83

144

142

Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W., & Nielsen, Per H. (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31, 533–538.

948

905

Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip, & 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, pp. 3-19.

26

22

Carvalhais, L.C., Dennis, P.G., Tyson, G.W., & Schenk, P.M. (2013) Rhizosphere Metatranscriptomics: Challenges and Opportunities. In de Bruijn, Frans J. (Ed.) Molecular Microbial Ecology of the Rhizosphere. John Wiley & Sons, Hoboken, New Jersey, pp. 1137-1144.

18

Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, Alberti, Adriana, Cruaud, Corinne, Hallam, Steven, Konstantinidis, Kostas, Tyson, Gene, Wincker, Patrick, & Sullivan, Matthew B. (2013) Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics, 14, Article number: 320.

68

76

74

Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip, & Tyson, Gene W. (2013) Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data. PLoS Computational Biology, 9(4), Article number: e1003031.

87

242

222

Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W., & Schenk, Peer M. (2012) Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91(2), pp. 246-251.

137

108

Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip, & Tyson, Gene W. (2012) Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40(12), Article number: e94.

77

145

104

Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip, & Tyson, Gene W. (2012) Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9, 425–426.

282

274

Cayford, Barry I., Dennis, Paul G., Keller, Jurg, Tyson, Gene W., & Bond, Philip L. (2012) High-Throughput Amplicon Sequencing Reveals Distinct Communities within a Corroding Concrete Sewer System. Applied and Environmental Microbiology, 78(19), pp. 7160-7162.

3

67

59

Tyson, Gene & Angly, Florent (2011) Des communautés de phages divergentes contrôlent-elles la microflore intestinale ? (Are divergent viral communities controlling individual gut microbiota?). Medecine Sciences: M/S, 27(3), 229 - 231.

Shi, Yanmei, Tyson, Gene W., Eppley, John M., & DeLong, Edward F. (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME Journal, 5, 999–1013.

191

175

Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip, & Tyson, Gene W. (2011) Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System. PLoS ONE, 6(5), Article number: e20095.

59

47

42

Yilmaz, Suzan, Haroon, Mohamed F., Rabkin, Brian A., Tyson, Gene W., & Hugenholtz, Philip (2010) Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. ISME Journal, 4, 1352–1356.

63

57

Martinez, Asuncion, Tyson, Gene W., & DeLong, Edward F. (2010) Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology, 12(1), pp. 222-238.

155

141

Baker, Brett J., Tyson, Gene W., Goosherst, Lindsey, & Banfield, Jillian F. (2009) Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities. Applied and Environmental Microbiology, 75(7), 2192–2199.

97

83

Shi, Yanmei, Tyson, Gene W., & DeLong, Edward F. (2009) Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459, 266–269.

227

200

Frias-Lopez, Jorge, Shi, Yanmei, Tyson, Gene W., Coleman, Maureen L., Schuster, Stephan C., Chisholm, Sallie W., & DeLong, Edward F. (2008) Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105(10), pp. 3805-3810.

127

633

576

Hugenholtz, Philip & Tyson, Gene W. (2008) Microbiology - Metagenomics. Nature, 455, 481–483.

326

280

Tyson, Gene W. & Banfield, Jillian F. (2008) Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10(1), pp. 200-207.

270

248

Eppley, John M., Tyson, Gene W., Getz, Wayne M., & Banfield, Jillian F. (2007) Genetic exchange across a species boundary in the archaeal genus ferroplasma. Genetics, 177(1), 407–416.

57

54

Allen, Eric E., Tyson, Gene W., Whitaker, Rachel J., Detter, John C., Richardson, Paul M., & Banfield, Jillian F. (2007) Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104(6), pp. 1883-1888.

62

111

107

Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert L., & Banfield, Jillian F. (2007) Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446, 537–541.

185

181

Eppley, John M., Tyson, Gene W., Getz, Wayne M., & Banfield, Jillian F. (2007) Strainer: software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8, Article number: 398.

62

30

28

Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E., & Banfield, Jillian F. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314(5807), pp. 1933-1935.

176

163

Tyson, Gene W. & Hugenholtz, Philip (2005) Environmental shotgun sequencing. In Jorde, Lynn, Little, Peter, Dunn, Mike, & Subramaniam, Shankar (Eds.) Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley.

Ram, RJ, VerBerkmoes, N, Tyson, GW, Baker, BJ, Thelen, MP, Hettich, RL, & Banfield, JF (2005) Challenges of life in an extremely acidic environment. Abstracts of Papers of the American Chemical Society.

Tyson, GW & Banfield, JF (2005) Cultivating the uncultivated: a community genomics perspective. Trends in Microbiology, 13(9), pp. 411-415.

81

74

Tyson, GW, Lo, I, Baker, BJ, Allen, EE, Hugenholtz, P, & Banfield, JF (2005) Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Applied and Environmental Microbiology, 71(10), pp. 6319-6324.

214

186

Ram, R.J., VerBerkmoes, N.C., Thelen, M.P., Tyson, G.W., Baker, B.J., Blake II, R.C., Shah, M., Hettich, R.L., & Banfield, J.F. (2005) Microbiology: Community proteomics of a natural microbial biofilm. Science, 308(5730), 1915–1920.

688

Banfield, J, Tyson, G, Allen, E, & Whitaker, R (2005) Population dynamics in acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Geochimica et Cosmochimica Acta, 69(10 (suppl.)), A222.

1

Banfield, JR, Tyson, GW, Allen, EE, & Whitaker, RJ (2005) The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. In Reviews in Mineralogy & Geochemistry. Vol. 59. Mineralogical Society of America, pp. 1-7.

16

9

Tyson, GW, Chapman, J, Hugenholtz, P, Allen, EE, Ram, RJ, Richardson, PM, Solovyev, VV, Rubin, EM, Rokhsar, DS, & Banfield, JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428, 37–43.

1,808

1,616

Hugenholtz, P, Tyson, G W, & Blackall, L L (2002) Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. In Gene Probes. Methods in Molecular Biology. Humana Press, pp. 29-42.

124

Björnsson, L., Hugenholtz, P., Tyson, G.W., & Blackall, L.L. (2002) Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148(8).

288

Hugenholtz, P, Tyson, GW, Webb, RI, Wagner, AM, & Blackall, LL (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.

280

273

Export as	Atom RSS 1.0 RSS 2.0