Browse By Person: Woodcroft, Ben

Borton, Mikayla A., McGivern, Bridget B., Willi, Kathryn R., Woodcroft, Ben J., Mosier, Annika C., Singleton, Derick M., Bambakidis, Ted, Pelly, Aaron, Daly, Rebecca A., Liu, Filipe, Freiburger, Andrew, Edirisinghe, Janaka N., Faria, José P., Danczak, Robert, Leleiwi, Ikaia, Goldman, Amy E., Wilkins, Michael J., Hall, Ed K., Pennacchio, Christa, Roux, Simon, Eloe-Fadrosh, Emiley A., Good, Stephen P., Sullivan, Matthew B., Wood-Charlson, Elisha M., Miller, Christopher S., Ross, Matthew R.V., Henry, Christopher S., Crump, Byron C., Stegen, James C., & Wrighton, Kelly C. (2025) A functional microbiome catalogue crowdsourced from North American rivers. Nature, 637(8044), pp. 103-112.

Schoelmerich, Marie C., Ly, Lynn, West-Roberts, Jacob, Shi, Ling Dong, Shen, Cong, Malvankar, Nikhil S., Taib, Najwa, Gribaldo, Simonetta, Woodcroft, Ben J., Schadt, Christopher W., Al-Shayeb, Basem, Dai, Xiaoguang, Mozsary, Christopher, Hickey, Scott, He, Christine, Beaulaurier, John, Juul, Sissel, Sachdeva, Rohan, & Banfield, Jillian F. (2024) Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications, 15, Article number: 5414.

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Freire-Zapata, Viviana, Holland-Moritz, Hannah, Cronin, Dylan R., Aroney, Sam, Smith, Derek A., Wilson, Rachel M., Ernakovich, Jessica G., Woodcroft, Ben J., Bagby, Sarah C., Mondav, Rhiannon, Hodgkins, Suzanne B., Zayed, Ahmed A. F., Varner, Ruth K., Saleska, Scott R., Ibba, Michael, Ferriere, Regis, Fahnestock, Maria Florencia, E. Cross, Jennifer, Rich, Virginia I., Sullivan, Matthew B., Stegen, James C., Tfaily, Malak M., & other, and (2024) Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient. Nature Microbiology, 9(11), pp. 2892-2908.

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 [Preprint] (Unpublished)

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Kobel, Carl M., Aho, Velma T. E., Øyås, Ove, Nørskov-Lauritsen, Niels, Woodcroft, Ben J., & Pope, Phillip B. (2024) CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. bioRxiv. [Preprint]

Williams, Tom A., Davin, Adrian A., Szantho, Lenard l., Stamatakis, Alexandros, Wahl, Noah A., Woodcroft, Ben J., Soo, Rochelle M., Eme, Laura, Sheridan, Paul O., Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip, & Szollosi, Gergely J. (2024) Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18(1), Article number: wrae129.

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.

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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.

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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.

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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.

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.

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Hou, Jialin, Wang, Yinzhao, Zhu, Pengfei, Yang, Na, Liang, Lewen, Yu, Tiantian, Niu, Mingyang, Konhauser, Kurt, Woodcroft, Ben J., & Wang, Fengping (2023) Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment. Science Advances, 9(27), Article number: adf5069.

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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.

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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.

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Wang, Yu, Ni, Gaofeng, Tian, Wei, Yang, Lin, Hosegood, Ian, Newell, Rhys, Woodcroft, Ben J., Yang, Bicheng, Hu, Shihu, & Guo, Jianhua (2022) Detection of SARS-CoV-2 Variants of Concern with Tiling Amplicon Sequencing from Wastewater. ACS ES and T Water, 2(11), pp. 2185-2193.

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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.

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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.

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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.

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Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben, Hedlund, Brian P., Woyke, Tanja, HugenHoltz, Philip, & Rinke, Christian (2021) Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1, Article number: 30.

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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.

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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.

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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.

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Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip, & Rinke, Christian (2021) Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages. bioRxiv. [Preprint]

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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.

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Dombrowski, Nina, Williams, Tom A., Sun, Jiarui, Woodcroft, Benjamin J., Lee, Jun-Hoe, Minh, Bui Quang, Rinke, Christian, & Spang, Anja (2020) Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications, 11(1), Article number: 3939.

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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]

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.

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Priyam, Anurag, Woodcroft, Ben J., Rai, Vivek, Moghul, Ismail, Munagala, Alekhya, Ter, Filip, Chowdhary, Hiten, Pieniak, Iwo, Maynard, Lawrence J, Gibbins, Mark Anthony, Moon, HongKee, Davis-Richardson, Austin, Uludag, Mahmut, Watson-Haigh, Nathan S, Challis, Richard, Nakamura, Hiroyuki, Favreau, Emeline, Gómez, Esteban A, Pluskal, Tomás, Leonard, Guy, Rumpf, Wolfgang, & Wurm, Yannick (2019) Sequenceserver: A modern graphical user interface for custom BLAST databases. Molecular Biology and Evolution, 36(12), pp. 2922-2924.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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McDougall, Carmel, Woodcroft, Ben J., & Degnan, Bernard M. (2016) The widespread prevalence and functional significance of silk-like structural proteins in metazoan biological materials. PLoS ONE, 11(7), Article number: e0159128 1-18.

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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.

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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.

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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.

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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.

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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.

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Woodcroft, Ben J., McMillan, Paul J., Dekiwadia, Chaitali, Tilley, Leann, & Ralph, Stuart A. (2012) Determination of protein subcellular localization in apicomplexan parasites. Trends in Parasitology, 28(12), pp. 546-554.

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10

Ludin, Philipp, Woodcroft, Ben, Ralph, Stuart A., & Mäser, Pascal (2012) In silico prediction of antimalarial drug target candidates. International Journal for Parasitology: Drugs and Drug Resistance, 2, pp. 191-199.

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York, Patrick S, Cummins, Scott F, Degnan, Sandie M, Woodcroft, Ben J., & Degnan, Bernard M (2012) Marked changes in neuropeptide expression accompany broadcast spawnings in the gastropod Haliotis asinina. Frontiers in Zoology, 9, Article number: 9 1-16.

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Bonnal, Raoul J.P., Aerts, Jan, Githinji, George, Goto, Naohisa, MacLean, Dan, Miller, Chase A., Mishima, Hiroyuki, Pagani, Massimiliano, Ramirez-Gonzalez, Ricardo, Smant, Geert, Strozzi, Francesco, Syme, Rob, Vos, Rutger, Wennblom, Trevor J., Woodcroft, B. J., Katayama, Toshiaki, & Prins, Pjotr (2012) Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics, 28(7), pp. 1035-1037.

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Oehring, Sophie C, Woodcroft, Ben J, Moes, Suzette, Wetzel, Johanna, Dietz, Olivier, Pulfer, Andreas, Dekiwadia, Chaitali, Maeser, Pascal, Flueck, Christian, Witmer, Kathrin, Brancucci, Nicolas MB, Niederwieser, Igor, Jenoe, Paul, Ralph, Stuart A, & Voss, Till S (2012) Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum. Genome Biology, 13, Article number: R108 1-21.

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Erpenbeck, D., Voigt, O., Adamski, M., Woodcroft, B. J., Hooper, J. N. A., Worheide, G., & Degnan, B. M. (2011) NUMTs in the sponge genome reveal conserved transposition mechanisms in metazoans. Molecular Biology and Evolution, 28(1), pp. 1-5.

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York, Patrick S., Cummins, Scott F., Degnan, Sandie M., Woodcroft, Ben J., & Degnan, Bernard M. (2010) Identification of genes differentially expressed in the ganglia of growing haliotis asinina. Journal of Shellfish Research, 29(3), pp. 741-752.

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Koay, Ann, Woodcroft, Ben, Petrie, Emma J., Yue, Helen, Emanuelle, Shane, Bieri, Michael, Bailey, Michael F., Hargreaves, Mark, Park, Jong-Tae, Park, Kwan-Hwa, Ralph, Stuart, Neumann, Dietbert, Stapleton, David, & Gooley, Paul R. (2010) AMPK β subunits display isoform specific affinities for carbohydrates. FEBS Letters, 584(15), pp. 3499-3503.

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Srivastava, Mansi, Simakov, Oleg, Chapman, Jarrod, Fahey, Bryony, Gauthier, Marie E. A., Mitros, Therese, Richards, Gemma S., Conaco, Cecilia, Dacre, Michael, Hellsten, Uffe, Larroux, Claire, Putnam, Nicholas H., Stanke, Mario, Adamska, Maja, Darling, Aaron, Degnan, Sandie M., Oakley, Todd H., Plachetzki, David C., Zhai, Yufeng, Adamski, Marcin, Calcino, Andrew, Cummins, Scott F., Goodstein, David M., Harris, Christina, Jackson, Daniel J., Leys, Sally P., Shu, Shengqiang, Woodcroft, Ben J., Vervoort, Michel, Kosik, Kenneth S., Manning, Gerard, Degnan, Bernard M., & Rokhsar, Daniel S. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature, 466(7307), pp. 720-726.

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Doyle, Maria A, Gasser, Robin B, Woodcroft, Ben J, Hall, Ross S, & Ralph, Stuart A. (2010) Drug target prediction and prioritization: Using orthology to predict essentiality in parasite genomes. BMC Genomics, 11, Article number: 222 1-14.

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Woodcroft, Ben J., Hammond, Luke, Stow, Jennifer L., & Hamilton, Nicholas A. (2009) Automated organelle-based colocalization in whole-cell imaging. Cytometry Part A, 75A(11), pp. 941-950.

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Jackson, Daniel J., McDougall, Carmel, Woodcroft, Ben, Moase, Patrick, Rose, Robert A., Kube, Michael, Reinhardt, Richard, Rokhsar, Daniel S., Montagnani, Caroline, Joubert, Caroline, Piquemal, David, & Degnan, Bernard M. (2009) Parallel evolution of nacre Building gene sets in molluscs. Molecular Biology and Evolution, 27(3), pp. 591-608.

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Gardiner, Donald L., Woodcroft, Ben J., Dixon, Matthew W. A., Ralph, Stuart A., & Trenholme, Katharine R. (2009) REX1 and Pf62: Are they one and the same? Parasitology Research, 104, pp. 967-968.

Williams, Elizabeth A., Degnan, Bernard M., Gunter, Helen, Jackson, Daniel J., Woodcroft, Ben J., & Degnan, Sandie M. (2009) Widespread transcriptional changes pre-empt the critical pelagic-benthic transition in the vetigastropod Haliotis asinina. Molecular Ecology, 18(5), pp. 1006-1025.

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Grimson, Andrew, Srivastava, Mansi, Fahey, Bryony, Woodcroft, Ben J., Chiang, H. Rosaria, King, Nicole, Degnan, Bernard M., Rokhsar, Daniel S., & Bartel, David P. (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature, 455, pp. 1193-1197.

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Fahey, Bryony, Larroux, Claire, Woodcroft, Ben J., & Degnan, Bernard M. (2008) Does the high gene density in the sponge NK homeobox gene cluster reflect limited regulatory capacity? The Biological Bulletin, 214, pp. 205-217.

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