The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis

by Matthew R. Olm, Cristina N. Butterfield, Alex Copeland, T. Christian Boles, Brian C. Thomas, Jillian F. Banfield, C. Titus Brown, Dianne K. Newman
Published 2017-02-01

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

by Konstantinos Mavromatis, Miriam L Land, Thomas S Brettin, Daniel J Quest, Alex Copeland, Alicia Clum, Lynne Goodwin, Tanja Woyke, Alla Lapidus, Hans Peter Klenk, Robert W Cottingham, Nikos C Kyrpides
Published 2012-01-01

One bacterial cell, one complete genome.

by Tanja Woyke, Damon Tighe, Konstantinos Mavromatis, Alicia Clum, Alex Copeland, Wendy Schackwitz, Alla Lapidus, Dongying Wu, John P McCutcheon, Bradon R McDonald, Nancy A Moran, James Bristow, Jan-Fang Cheng
Published 2010-04-01

Assembling the marine metagenome, one cell at a time.

by Tanja Woyke, Gary Xie, Alex Copeland, José M González, Cliff Han, Hajnalka Kiss, Jimmy H Saw, Pavel Senin, Chi Yang, Sourav Chatterji, Jan-Fang Cheng, Jonathan A Eisen, Michael E Sieracki, Ramunas Stepanauskas
Published 2009-01-01

Draft genome sequence of Marinobacterium rhizophilum CL-YJ9T (DSM 18822T), isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica

by Dong Han Choi, Gwang II Jang, Alla Lapidus, Alex Copeland, T. B. K. Reddy, Supratim Mukherjee, Marcel Huntemann, Neha Varghese, Natalia Ivanova, Manoj Pillay, Brian J. Tindall, Markus Göker, Tanja Woyke, Hans-Peter Klenk, Nikos C. Kyrpides, Byung Cheol Cho
Published 2017-10-01

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States

by Rachel Mackelprang, Alyssa M. Grube, Regina Lamendella, Ederson da C. Jesus, Ederson da C. Jesus, Alex Copeland, Chao Liang, Chao Liang, Randall D. Jackson, Randall D. Jackson, Charles W. Rice, Stefanie Kapucija, Bayan Parsa, Susannah G. Tringe, James M. Tiedje, James M. Tiedje, Janet K. Jansson
Published 2018-08-01

DOE JGI Metagenome Workflow

by Alicia Clum, Marcel Huntemann, Brian Bushnell, Brian Foster, Bryce Foster, Simon Roux, Patrick P. Hajek, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Yuko Yoshinaga, Ronan O’Malley, Rekha Seshadri, Nikos C. Kyrpides, Emiley A. Eloe-Fadrosh, I-Min A. Chen, Alex Copeland, Natalia N. Ivanova
Published 2021-06-01

A single-cell genomics pipeline for environmental microbial eukaryotes

by Doina Ciobanu, Alicia Clum, Steven Ahrendt, William B. Andreopoulos, Asaf Salamov, Sandy Chan, C. Alisha Quandt, Brian Foster, Jan P. Meier-Kolthoff, Yung Tsu Tang, Patrick Schwientek, Gerald L. Benny, Matthew E. Smith, Diane Bauer, Shweta Deshpande, Kerrie Barry, Alex Copeland, Steven W. Singer, Tanja Woyke, Igor V. Grigoriev, Timothy Y. James, Jan-Fang Cheng
Published 2021-04-01

Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.

by Kira S Makarova, Marina V Omelchenko, Elena K Gaidamakova, Vera Y Matrosova, Alexander Vasilenko, Min Zhai, Alla Lapidus, Alex Copeland, Edwin Kim, Miriam Land, Konstantinos Mavrommatis, Samuel Pitluck, Paul M Richardson, Chris Detter, Thomas Brettin, Elizabeth Saunders, Barry Lai, Bruce Ravel, Kenneth M Kemner, Yuri I Wolf, Alexander Sorokin, Anna V Gerasimova, Mikhail S Gelfand, James K Fredrickson, Eugene V Koonin, Michael J Daly
Published 2007-09-01

Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress

by Salma Mukhtar, Ann M. Hirsch, Noor Khan, Kauser A. Malik, Ethan A. Humm, Matteo Pellegrini, Baochen Shi, Leah Briscoe, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishnaveni Palaniappan, Neha Varghese, Supratim Mukherjee, T.B.K. Reddy, Chris Daum, Alex Copeland, Natalia N. Ivanova, Nikos C. Kyrpides, Nicole Shapiro, Emiley A. Eloe-Fadrosh, Maskit Maymon, Muhammad S. Mirza, Samina Mehnaz
Published 2020-08-01

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades

by Briana S. Abraham, Deniz Caglayan, Natalie V. Carrillo, Matthew C. Chapman, Claire T. Hagan, Skye T. Hansen, Ralph O. Jeanty, Alexander A. Klimczak, Marcos J. Klingler, Thomas P. Kutcher, Sydney H. Levy, Angel A. Millard-Bruzos, Thomas B. Moore, David J. Prentice, Matthew E. Prescott, Richard Roehm, Jordan A. Rose, Mulan Yin, Ayumi Hyodo, Kathleen Lail, Christopher Daum, Alicia Clum, Alex Copeland, Rekha Seshadri, Tijana Glavina del Rio, Emiley A. Eloe-Fadrosh, Jonathan B. Benskin
Published 2020-01-01

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens.

by Bradford J Condon, Yueqiang Leng, Dongliang Wu, Kathryn E Bushley, Robin A Ohm, Robert Otillar, Joel Martin, Wendy Schackwitz, Jane Grimwood, NurAinizzati MohdZainudin, Chunsheng Xue, Rui Wang, Viola A Manning, Braham Dhillon, Zheng Jin Tu, Brian J Steffenson, Asaf Salamov, Hui Sun, Steve Lowry, Kurt LaButti, James Han, Alex Copeland, Erika Lindquist, Kerrie Barry, Jeremy Schmutz, Scott E Baker, Lynda M Ciuffetti, Igor V Grigoriev, Shaobin Zhong, B Gillian Turgeon
Published 2013-01-01

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

by Martina Peter, Annegret Kohler, Robin A. Ohm, Alan Kuo, Jennifer Krützmann, Emmanuelle Morin, Matthias Arend, Kerrie W. Barry, Manfred Binder, Cindy Choi, Alicia Clum, Alex Copeland, Nadine Grisel, Sajeet Haridas, Tabea Kipfer, Kurt LaButti, Erika Lindquist, Anna Lipzen, Renaud Maire, Barbara Meier, Sirma Mihaltcheva, Virginie Molinier, Claude Murat, Stefanie Pöggeler, C. Alisha Quandt, Christoph Sperisen, Andrew Tritt, Emilie Tisserant, Pedro W. Crous, Bernard Henrissat, Uwe Nehls, Simon Egli, Joseph W. Spatafora, Igor V. Grigoriev, Francis M. Martin
Published 2016-09-01

The Genome Sequence of Methanohalophilus mahii SLPT Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environmen...

by Stefan Spring, Carmen Scheuner, Alla Lapidus, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, Matt Nolan, Elizabeth Saunders, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Athanasios Lykidis, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Lynne Goodwin, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Tanja Woyke, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk
Published 2010-01-01