Luke R Thompson

ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 16

Top Venues

mSystems

Applied and environmental microbiology

Nature biotechnology

Microbiology spectrum

Atlantic Oceanographic and Meteorological Laboratory

Massachusetts Institute of Technology (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Atlantic Oceanographic and Meteorological Laboratory

United States

Assistant Research Professor

Education History

Massachusetts Institute of Technology

United States

PHD :: Biology

Stanford University

United States

BSC :: Biological Sciences

Publications

Helen Park, Shen Jean Lim, Jonathan Cosme, Kyle O'Connell, Jilla Sandeep, Felimon Gayanilo, George R Cutter, Enrique Montes, Chotinan Nitikitpaiboon, Sam Fisher, Hassan Moustahfid, Luke R Thompson
Investigation of machine learning algorithms for taxonomic classification of marine metagenomes. Microbiology spectrum (2023)
Luke R Thompson, Sean R Anderson, Paul A Den Uyl, Nastassia V Patin, Shen Jean Lim, Grant Sanderson, Kelly D Goodwin
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. GigaScience 11 (2022)
Shen Jean Lim, Luke R Thompson, Craig M Young, Terry Gaasterland, Kelly D Goodwin
Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola). Applied and environmental microbiology 88 (15) (2022)
Justin P Shaffer, Louis-Felix Nothias, Luke R Thompson, Jon G Sanders, Rodolfo A Salido, Sneha P Couvillion, Asker D Brejnrod, Franck Lejzerowicz, Niina Haiminen, Shi Huang, Holly L Lutz, Qiyun Zhu, Cameron Martino, James T Morton, Smruthi Karthikeyan, Mélissa Nothias-Esposito, Kai Dührkop, Sebastian Böcker, Hyun Woo Kim, Alexander A Aksenov, Wout Bittremieux, Jeremiah J Minich, Clarisse Marotz, MacKenzie M Bryant, Karenina Sanders, Tara Schwartz, Greg Humphrey, Yoshiki Vásquez-Baeza, Anupriya Tripathi, Laxmi Parida, Anna Paola Carrieri, Kristen L Beck, Promi Das, Antonio González, Daniel McDonald, Joshua Ladau, Søren M Karst, Mads Albertsen, Gail Ackermann, Jeff DeReus, Torsten Thomas, Daniel Petras, Ashley Shade, James Stegen, Se Jin Song, Thomas O Metz, Austin D Swafford, Pieter C Dorrestein, Janet K Jansson, Jack A Gilbert, Rob Knight, null null
Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity. Nature microbiology 7 (12) (2022)
Fátima Jorge, Jaelle C Brealey, Paul J Brindley, Marie Buysse, Cinzia Cantacessi, Olivier Duron, Raina Fichorova, Connor R Fitzpatrick, Megan Hahn, Christopher I Hunter, Vincent Hervé, Laura J Knoll, Kevin D Kohl, Marco Lalle, Julius Lukeš, Joaquín Martínez Martínez, Susan L Perkins, Robert Poulin, Karyna Rosario, Adam C Schneider, Lynn M Schriml, Luke R Thompson, Ramona L Walls, Nolwenn M Dheilly
MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms. ISME communications 2 (1) (2022)
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, José Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, William 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
Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities". mSystems 6 (3) (2021)
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, José Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, William 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
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. mSystems 6 (1) (2021)
Rob Knight, Alison Vrbanac, Bryn C Taylor, Alexander Aksenov, Chris Callewaert, Justine Debelius, Antonio Gonzalez, Tomasz Kosciolek, Laura-Isobel McCall, Daniel McDonald, Alexey V Melnik, James T Morton, Jose Navas, Robert A Quinn, Jon G Sanders, Austin D Swafford, Luke R Thompson, Anupriya Tripathi, Zhenjiang Z Xu, Jesse R Zaneveld, Qiyun Zhu, J Gregory Caporaso, Pieter C Dorrestein
Best practices for analysing microbiomes. Nature reviews. Microbiology 16 (7) (2019)
Cameron Martino, James T Morton, Clarisse A Marotz, Luke R Thompson, Anupriya Tripathi, Rob Knight, Karsten Zengler
A Novel Sparse Compositional Technique Reveals Microbial Perturbations. mSystems 4 (1) (2019)
Nolwenn M Dheilly, Joaquín Martínez Martínez, Karyna Rosario, Paul J Brindley, Raina Nakova Fichorova, Jonathan Z Kaye, Kevin D Kohl, Laura J Knoll, Julius Lukeš, Susan L Perkins, Robert Poulin, Lynn M Schriml, Luke R Thompson
Parasite microbiome project: Grand challenges. PLoS pathogens 15 (10) (2019)
Evan Bolyen, Jai Ram Rideout, Matthew R Dillon, Nicholas A Bokulich, Christian C Abnet, Gabriel A Al-Ghalith, Harriet Alexander, Eric John Alm, Manimozhiyan Arumugam, Francesco Asnicar, Yang Bai, Jordan E Bisanz, Kyle Bittinger, Asker Brejnrod, Colin J Brislawn, C Titus Brown, Benjamin J Callahan, Andrés Mauricio Caraballo-Rodriguez, John Chase, Emily K Cope, Ricardo Da Silva, Christian Diener, Pieter C Dorrestein, Gavin M Douglas, Daniel M Durall, Claire Duvallet, Christian F Edwardson, Madeleine Ernst, Mehrbod Estaki, Jennifer Fouquier, Julia M Gauglitz, Sean M Gibbons, Deanna L Gibson, Antonio Gonzalez, Kestrel Gorlick, Jiarong Guo, Benjamin Hillmann, Susan P Holmes, Hannes Holste, Curtis Huttenhower, Gavin A Huttley, Stefan Janssen, Alan K Jarmusch, Lingjing Jiang, Benjamin D Kaehler, Kyo-Bin Kang, Christopher R Keefe, Paul Keim, Scott T Kelley, Dan Knights, Irina Koester, Tomasz Kosciolek, Jorden Kreps, Morgan G I Langille, Joslynn Lee, Ruth Ley, Yong-Xin Liu, Erikka Loftfield, Catherine A Lozupone, Massoud Maher, Clarisse A Marotz, Bryan D Martin, Daniel McDonald, Lauren J McIver, Alexey V Melnik, Jessica L Metcalf, Sydney C Morgan, Jamie T Morton, Ahmad Turan Naimey, Jose A Navas-Molina, Louis Felix Nothias, Stephanie B Orchanian, Talima R Pearson, Samuel L Peoples, Daniel Petras, Mary Lai Preuss, Elmar Pruesse, Lasse Buur Rasmussen, Adam R Rivers, Michael Scott Robeson, Patrick Rosenthal, Nicola Segata, Michael Shaffer, Arron Shiffer, Rashmi Sinha, Se Jin Song, John R Spear, Austin D Swafford, Luke R Thompson, Pedro J Torres, Pauline Trinh, Anupriya Tripathi, Peter J Turnbaugh, Sabah Ul-Hasan, Justin Johan Jozias van der Hooft, Fernando Vargas, Yoshiki Vázquez-Baeza, Emily Vogtmann, Max von Hippel, William Walters, Yunhu Wan, Mingxun Wang, Jonathan Warren, Kyle C Weber, Charles H D Williamson, Amy D Willis, Zhenjiang Zech Xu, Jesse R Zaneveld, Yilong Zhang, Qiyun Zhu, Rob Knight, J Gregory Caporaso
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37 (8) (2019)
Luke R Thompson, Mohamed F Haroon, Ahmed A Shibl, Matt J Cahill, David Kamanda Ngugi, Gareth J Williams, James T Morton, Rob Knight, Kelly D Goodwin, Ulrich Stingl
Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes. Applied and environmental microbiology 85 (13) (2019)
Anton Lavrinienko, Tapio Mappes, Eugene Tukalenko, Timothy A Mousseau, Anders P Møller, Rob Knight, James T Morton, Luke R Thompson, Phillip C Watts
Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus. The ISME journal 12 (11) (2018)
Jennifer M Michaud, Luke R Thompson, Drishti Kaul, Josh L Espinoza, R Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M Pham, Charlotte M Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D Burkart, Christopher L Dupont, Kimberly A Prather
Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nature communications 9 (1) (2018)
Eric A Franzosa, Lauren J McIver, Gholamali Rahnavard, Luke R Thompson, Melanie Schirmer, George Weingart, Karen Schwarzberg Lipson, Rob Knight, J Gregory Caporaso, Nicola Segata, Curtis Huttenhower
Species-level functional profiling of metagenomes and metatranscriptomes. Nature methods 15 (11) (2018)
Luke R Thompson, Qinglu Zeng, Sallie W Chisholm
Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage. PloS one 11 (10) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Luke R Thompson