Advancing Genome-Resolved Metagenomics beyond the Shotgun

by Rex R. Malmstrom, Emiley A. Eloe-Fadrosh
Published 2019-05-01

Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity

by Simon Roux, Joanne B. Emerson, Emiley A. Eloe-Fadrosh, Matthew B. Sullivan
Published 2017-09-01

Ecotype diversity and conversion in Photobacterium profundum strains.

by Federico M Lauro, Emiley A Eloe-Fadrosh, Taylor K S Richter, Nicola Vitulo, Steven Ferriera, Justin H Johnson, Douglas H Bartlett
Published 2014-01-01

Towards a balanced view of the bacterial tree of life

by Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides, Tanja Woyke
Published 2017-10-01

Correction to: Towards a balanced view of the bacterial tree of life

by Frederik Schulz, Emiley A. Eloe-Fadrosh, Robert M. Bowers, Jessica Jarett, Torben Nielsen, Natalia N. Ivanova, Nikos C. Kyrpides, Tanja Woyke
Published 2017-11-01

Impact of oral typhoid vaccination on the human gut microbiota and correlations with s. Typhi-specific immunological responses.

by Emiley A Eloe-Fadrosh, Monica A McArthur, Anna M Seekatz, Elliott F Drabek, David A Rasko, Marcelo B Sztein, Claire M Fraser
Published 2013-01-01

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

by Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh-Fen Li, Benjamin Bolduc, Josué Rodríguez-Ramos, Emiley A. Eloe-Fadrosh, Virginia I. Rich, Matthew B. Sullivan
Published 2019-07-01

Genomic variation and biogeography of Antarctic haloarchaea

by Bernhard Tschitschko, Susanne Erdmann, Matthew Z. DeMaere, Simon Roux, Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Sarah Brazendale, Alyce M. Hancock, Emiley A. Eloe-Fadrosh, Ricardo Cavicchioli
Published 2018-06-01

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures

by Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe-Fadrosh, Paul Dijkstra, Brian P. Hedlund, Brian P. Hedlund
Published 2019-07-01

Differential response of the cynomolgus macaque gut microbiota to Shigella infection.

by Anna M Seekatz, Aruna Panda, David A Rasko, Franklin R Toapanta, Emiley A Eloe-Fadrosh, Abdul Q Khan, Zhenqiu Liu, Steven T Shipley, Louis J Detolla, Marcelo B Sztein, Claire M Fraser
Published 2013-01-01

Diversity, evolution, and classification of virophages uncovered through global metagenomics

by David Paez-Espino, Jinglie Zhou, Simon Roux, Stephen Nayfach, Georgios A. Pavlopoulos, Frederik Schulz, Katherine D. McMahon, David Walsh, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Susannah G. Tringe, Nikos C. Kyrpides
Published 2019-12-01

Optimizing de novo genome assembly from PCR-amplified metagenomes

by Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, Emiley A. Eloe-Fadrosh
Published 2019-05-01

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community

by Pratibha Panwar, Michelle A. Allen, Timothy J. Williams, Alyce M. Hancock, Sarah Brazendale, James Bevington, Simon Roux, David Páez-Espino, Stephen Nayfach, Maureen Berg, Frederik Schulz, I-Min A. Chen, Marcel Huntemann, Nicole Shapiro, Nikos C. Kyrpides, Tanja Woyke, Emiley A. Eloe-Fadrosh, Ricardo Cavicchioli
Published 2020-08-01

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-Reading Family-A DNA Polymerase

by Marike Palmer, Brian P. Hedlund, Brian P. Hedlund, Simon Roux, Philippos K. Tsourkas, Philippos K. Tsourkas, Ryan K. Doss, Casey Stamereilers, Astha Mehta, Jeremy A. Dodsworth, Michael Lodes, Scott Monsma, Tijana Glavina del Rio, Thomas W. Schoenfeld, Emiley A. Eloe-Fadrosh, David A. Mead
Published 2020-11-01

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

Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

by Emiley A. Eloe-Fadrosh, David Paez-Espino, Jessica Jarett, Peter F. Dunfield, Brian P. Hedlund, Anne E. Dekas, Stephen E. Grasby, Allyson L. Brady, Hailiang Dong, Brandon R. Briggs, Wen-Jun Li, Danielle Goudeau, Rex Malmstrom, Amrita Pati, Jennifer Pett-Ridge, Edward M. Rubin, Tanja Woyke, Nikos C. Kyrpides, Natalia N. Ivanova
Published 2016-01-01

Ecology and molecular targets of hypermutation in the global microbiome

by Simon Roux, Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven J. Hallam, Maria E. Hernandez, Matthias Hess, Wen-Tso Liu, Tim A. McAllister, Michelle A. O’Malley, Xuefeng Peng, Virginia I. Rich, Scott R. Saleska, Emiley A. Eloe-Fadrosh
Published 2021-05-01

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

Correction for Vangay et al., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities”

by Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V. Costes, Joan Damerow, William D. Duncan, Jose Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M. Galazka, Sean M. Gibbons, David Hays, Judson Hervey, Bin Hu, Bonnie L. Hurwitz, Pankaj Jaiswal, Marcin P. Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L. Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T. B. K. Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P. Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R. Thompson, Ruth E. Timme, Jie Zheng, Elisha M. Wood-Charlson, Emiley A. Eloe-Fadrosh
Published 2021-06-01