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Quantifying the impact of workshops promoting microbiome data standards and data stewardship Kelliher, Julia M.; Rodriguez, Francisca E.; Johnson, Leah Y. D.; Roux, Simon; Smith, Montana; Clum, Alicia; Lynch, Wendi; Bias, Candace Hope; Finks, Sarai S.; Keenum, Ishi; Kiledal, E. Anders; Lin, Heng-An; Longley, Reid; Mcdonald, Ryan; Pitot, Thomas M.; Rodriguez-Ramos, Josue; Shen, Jiaxian; Sprockett, Daniel D.; Swift, Joel; Yadav, Archana; Eloe-Fadrosh, Emiley A. Share Save
Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution Tao, Gang; Ahrendt, Steven; Miyauchi, Shingo; Zhu, Xiaojie; Peng, Hao; Labutti, Kurt; Clum, Alicia; Hayes, Richard; Chain, Patrick S. G.; Grigoriev, Igor, V; Bonito, Gregory; Martin, Francis M. Share Save
Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti Nybo, J. L.; Vesth, T. C.; Theobald, S.; Frisvad, J. C.; Larsen, T. O.; Kjaerboelling, I.; Rothschild-Mancinelli, K.; Lyhne, E. K.; Barry, K.; Clum, A.; Yoshinaga, Y.; Ledsgaard, L.; Daum, C.; Lipzen, A.; Kuo, A.; Riley, R.; Mondo, S.; Labutti, K.; Haridas, S.; Pangalinan, J.; Salamov, A. A.; Simmons, B. A.; Magnuson, J. K.; Chen, J.; Drula, E.; Henrissat, B.; Wiebenga, A.; Lubbers, R. J. M.; Muller, A.; Gomes, A. C. dos Santos; Makela, M. R.; Stajich, J. E.; Grigorie, I., V; Mortensen, U. H.; Andersen, M. R. Share Save
Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses Steindorff, Andrei S.; Aguilar-Pontes, Maria Victoria; Robinson, Aaron J.; Andreopoulos, Bill; Labutti, Kurt; Kuo, Alan; Mondo, Stephen; Riley, Robert; Otillar, Robert; Haridas, Sajeet; Lipzen, Anna; Grimwood, Jane; Schmutz, Jeremy; Clum, Alicia; Reid, Ian D.; Moisan, Marie-Claude; Butler, Gregory; Nguyen, Thi Truc Minh; Dewar, Ken; Conant, Gavin; Drula, Elodie; Henrissat, Bernard; Hansel, Colleen; Singer, Steven; Hutchinson, Miriam I.; de Vries, Ronald P.; Natvig, Donald O.; Powell, Amy J.; Tsang, Adrian; Grigoriev, Igor V. Share Save
From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology Anthony, Winston E.; Allison, Steven D.; Broderick, Caitlin M.; Rodriguez, Luciana Chavez; Clum, Alicia; Cross, Hugh; Eloe-Fadrosh, Emiley; Evans, Sarah; Fairbanks, Dawson; Gallery, Rachel; Gontijo, Julia Brandao; Jones, Jennifer; McDermott, Jason; Pett-Ridge, Jennifer; Record, Sydne; Rodrigues, Jorge Luiz Mazza; Rodriguez-Reillo, William; Shek, Katherine L.; Takacs-Vesbach, Tina; Blanchard, Jeffrey L. Share Save
Genome-scale phylogeny and comparative genomics of the fungal order Sordariales Hensen, Noah; Bonometti, Lucas; Westerberg, Ivar; Brannstrom, Ioana Onut; Guillou, Sonia; Cros-Aarteil, Sandrine; Calhoun, Sara; Haridas, Sajeet; Kuo, Alan; Mondo, Stephen; Pangilinan, Jasmyn; Riley, Robert; Labutti, Kurt; Andreopoulos, Bill; Lipzen, Anna; Chen, Cindy; Yan, Mi; Daum, Chris; Ng, Vivian; Clum, Alicia; Steindorff, Andrei; Ohm, Robin A.; Martin, Francis; Silar, Philippe; Natvig, Donald O.; Lalanne, Christophe; Gautier, Valerie; Ament-Velasquezi, Sandra Lorena; Kruys, Asa; Hutchinson, Miriam I.; Powell, Amy Jo; Barry, Kerrie; Miller, Andrew N.; Grigoriev, Igor, V; Debuchy, Robert; Gladieux, Pierre; Thoren, Markus Hiltunen; Johannesson, Hanna Share Save
Terabase-Scale Coassembly of a Tropical Soil Microbiome Riley, Robert; Bowers, Robert M.; Camargo, Antonio Pedro; Campbell, Ashley; Egan, Rob; Eloe-Fadrosh, Emiley A.; Foster, Brian; Hofmeyr, Steven; Huntemann, Marcel; Kellom, Matthew; Kimbrel, Jeffrey A.; Oliker, Leonid; Yelick, Katherine; Pett-Ridge, Jennifer; Salamov, Asaf; Varghese, Neha J.; Clum, Alicia Share Save
A standardized quantitative analysis strategy for stable isotope probing metagenomics Vyshenska, Dariia; Sampara, Pranav; Singh, Kanwar; Tomatsu, Andy; Kauffman, W. Berkeley; Nuccio, Erin E.; Blazewicz, Steven J.; Pett-Ridge, Jennifer; Louie, Katherine B.; Varghese, Neha; Kellom, Matthew; Clum, Alicia; Riley, Robert; Roux, Simon; Eloe-Fadrosh, Emiley A.; Ziels, Ryan M.; Malmstrom, Rex R. Share Save
Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes Seshadri, Rekha; Roux, Simon; Huber, Katharina J.; Wu, Dongying; Yu, Sora; Udwary, Dan; Call, Lee; Nayfach, Stephen; Hahnke, Richard L.; Pukall, Rudiger; White, James R.; Varghese, Neha J.; Webb, Cody; Palaniappan, Krishnaveni; Reimer, Lorenz C.; Sarda, Joaquim; Bertsch, Jonathon; Mukherjee, Supratim; Reddy, T. B. K.; Hajek, Patrick P.; Huntemann, Marcel; Chen, I-Min A.; Spunde, Alex; Clum, Alicia; Shapiro, Nicole; Wu, Zong-Yen; Zhao, Zhiying; Zhou, Yuguang; Evtushenko, Lyudmila; Thijs, Sofie; Stevens, Vincent; Eloe-Fadrosh, Emiley A.; Mouncey, Nigel J.; Yoshikuni, Yasuo; Whitman, William B.; Klenk, Hans-Peter; Woyke, Tanja; Goeker, Markus; Kyrpides, Nikos C.; Ivanova, Natalia N. Share Save
Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium Chaput, Gina; Ford, Jacob; DeDiego, Lani; Narayanan, Achala; Tam, Wing Yin; Whalen, Meghan; Huntemann, Marcel; Clum, Alicia; Spunde, Alex; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Chen, I-Min; Stamatis, Dimitrios; Reddy, T. B. K.; O'Malley, Ronan; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Kyrpides, Nikos C.; Woyke, Tanja; Glavina del Rio, Tijana; DeAngelis, Kristen M. Share Save
Genetic determinants of endophytism in the Arabidopsis root mycobiome Mesny, Fantin; Miyauchi, Shingo; Thiergart, Thorsten; Pickel, Brigitte; Atanasova, Lea; Karlsson, Magnus; Huettel, Bruno; Barry, Kerrie W.; Haridas, Sajeet; Chen, Cindy; Bauer, Diane; Andreopoulos, William; Pangilinan, Jasmyn; LaButti, Kurt; Riley, Robert; Lipzen, Anna; Clum, Alicia; Drula, Elodie; Henrissat, Bernard; Kohler, Annegret; Grigoriev, Igor, V; Martin, Francis M.; Hacquard, Stephane Share Save
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Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion Martinez-Hidalgo, Pilar; Humm, Ethan A.; Still, David W.; Shi, Baochen; Pellegrini, Matteo; de la Roca, Gabriela; Veliz, Esteban; Maymon, Maskit; Bru, Pierrick; Huntemann, Marcel; Clum, Alicia; Palaniappan, Krishnaveni; Varghese, Neha; Mukherjee, Supratim; Reddy, T. B. K.; Daum, Chris; Ivanova, Natalia N.; Kyrpides, Nikos C.; Shapiro, Nicole; Eloe-Fadrosh, Emiley A.; Hirsch, Ann M. Share Save
Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics Van Goethem, Marc W.; Osborn, Andrew R.; Bowen, Benjamin P.; Andeer, Peter F.; Swenson, Tami L.; Clum, Alicia; Riley, Robert; He, Guifen; Koriabine, Maxim; Sandor, Laura; Yan, Mi; Daum, Chris G.; Yoshinaga, Yuko; Makhalanyane, Thulani P.; Garcia-Pichel, Ferran; Visel, Axel; Pennacchio, Len A.; O'Malley, Ronan C.; Northen, Trent R. Share Save
The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole Martin, Kara; Schmidt, Katrin; Toseland, Andrew; Boulton, Chris A.; Barry, Kerrie; Beszteri, Bank; Brussaard, Corina P. D.; Clum, Alicia; Daum, Chris G.; Eloe-Fadrosh, Emiley; Fong, Allison; Foster, Brian; Foster, Bryce; Ginzburg, Michael; Huntemann, Marcel; Ivanova, Natalia N.; Kyrpides, Nikos C.; Lindquist, Erika; Mukherjee, Supratim; Palaniappan, Krishnaveni; Reddy, T. B. K.; Rizkallah, Mariam R.; Roux, Simon; Timmermans, Klaas; Tringe, Susannah G.; van de Poll, Willem H.; Varghese, Neha; Valentin, Klaus U.; Lenton, Timothy M.; Grigoriev, Igor V.; Leggett, Richard M.; Moulton, Vincent; Mock, Thomas Share Save
DOE JGI Metagenome Workflow Clum, Alicia; Huntemann, Marcel; Bushnell, Brian; Foster, Brian; Foster, Bryce; Roux, Simon; Hajek, Patrick P.; Varghese, Neha; Mukherjee, Supratim; Reddy, T. B. K.; Daum, Chris; Yoshinaga, Yuko; O'Malley, Ronan; Seshadri, Rekha; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.; Chen, I-Min A.; Copeland, Alex; Ivanova, Natalia N. Share Save
Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism of Thermoflexus hugenholtzii and Three Candidate Species From China and Japan Thomas, Scott C.; Payne, Devon; Tamadonfar, Kevin O.; Seymour, Cale O.; Jiao, Jian-Yu; Murugapiran, Senthil K.; Lai, Dengxun; Lau, Rebecca; Bowen, Benjamin P.; Silva, Leslie P.; Louie, Katherine B.; Huntemann, Marcel; Clum, Alicia; Spunde, Alex; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Chen, I-Min; Stamatis, Dimitrios; Reddy, T. B. K.; O'Malley, Ronan; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Kyrpides, Nikos C.; Woyke, Tanja; Eloe-Fadrosh, Emiley; Hamilton, Trinity L.; Dijkstra, Paul; Dodsworth, Jeremy A.; Northen, Trent R.; Li, Wen-Jun; Hedlund, Brian P. Share Save
Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism Lastovetsky, Olga A.; Krasnovsky, Lev D.; Qin, Xiaotian; Gaspar, Maria L.; Gryganskyi, Andrii P.; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T. B. K.; Daum, Chris; Shapiro, Nicole; Ivanova, Natalia; Kyrpides, Nikos; Woyke, Tanja; Pawlowska, Teresa E. Share Save
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