Daniel McDonald

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 24

Top Venues

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

Publications

Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Alexander Butyaev, Timothy Keding, Eddie Cai, Jiayue Zheng, Renata Mutalova, Julien Mounthanyvong, Yuxue Zhu, Elena Nazarova, Chrisostomos Drogaris, Kornél Erhart, null null, null null, Amélie Brouillette, Gabriel Richard, Randy Pitchford, Sébastien Caisse, Mathieu Blanchette, Daniel McDonald, Rob Knight, Attila Szantner, Jérôme Waldispühl
Improving microbial phylogeny with citizen science within a mass-market video game. Nature biotechnology (2024)
Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Alexander Butyaev, Timothy Keding, Eddie Cai, Jiayue Zheng, Renata Mutalova, Julien Mounthanyvong, Yuxue Zhu, Elena Nazarova, Chrisostomos Drogaris, Kornél Erhart, null null, null null, Amélie Brouillette, Gabriel Richard, Randy Pitchford, Sébastien Caisse, Mathieu Blanchette, Daniel McDonald, Rob Knight, Attila Szantner, Jérôme Waldispühl
Improving microbial phylogeny with citizen science within a mass-market video game. Nature biotechnology (2024)
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira da Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, David J Gonzalez, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein
Author Correction: Enhancing untargeted metabolomics using metadata-based source annotation. Nature biotechnology (2023)
Gibraan Rahman, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Lingjing Jiang, Climent Casals-Pascual, Daniel Hakim, Amanda Hazel Dilmore, Brent Nowinski, Shyamal Das Peddada, Rob Knight
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Genes 14 (6) (2023)
Gibraan Rahman, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Lingjing Jiang, Climent Casals-Pascual, Daniel Hakim, Amanda Hazel Dilmore, Brent Nowinski, Shyamal Das Peddada, Rob Knight
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Genes 14 (6) (2023)
Julien Tap, Franck Lejzerowicz, Aurélie Cotillard, Matthieu Pichaud, Daniel McDonald, Se Jin Song, Rob Knight, Patrick Veiga, Muriel Derrien
Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nature communications 14 (1) (2023)
Gibraan Rahman, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Lingjing Jiang, Climent Casals-Pascual, Daniel Hakim, Amanda Hazel Dilmore, Brent Nowinski, Shyamal Das Peddada, Rob Knight
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Genes 14 (6) (2023)
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford, Promi Das, Justin P Shaffer, Franck Lejzerowicz, Pedro Belda Ferre, Aki Samuli Havulinna, Guillaume Méric, Teemu J Niiranen, Leo Lahti, Veikko V Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A Gilbert, Rob Knight
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems 7 (2) (2022)
Jeremiah J Minich, Andreas Härer, Joseph Vechinski, Benjamin W Frable, Zachary R Skelton, Emily Kunselman, Michael A Shane, Daniela S Perry, Antonio Gonzalez, Daniel McDonald, Rob Knight, Todd P Michael, Eric E Allen
Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nature communications 13 (1) (2022)
Julia M Gauglitz, Kiana A West, Wout Bittremieux, Candace L Williams, Kelly C Weldon, Morgan Panitchpakdi, Francesca Di Ottavio, Christine M Aceves, Elizabeth Brown, Nicole C Sikora, Alan K Jarmusch, Cameron Martino, Anupriya Tripathi, Michael J Meehan, Kathleen Dorrestein, Justin P Shaffer, Roxana Coras, Fernando Vargas, Lindsay DeRight Goldasich, Tara Schwartz, MacKenzie Bryant, Gregory Humphrey, Abigail J Johnson, Katharina Spengler, Pedro Belda Ferre, Edgar Diaz, Daniel McDonald, Qiyun Zhu, Emmanuel O Elijah, Mingxun Wang, Clarisse Marotz, Kate E Sprecher, Daniela Vargas-Robles, Dana Withrow, Gail Ackermann, Lourdes Herrera, Barry J Bradford, Lucas Maciel Mauriz Marques, Juliano Geraldo Amaral, Rodrigo Moreira da Silva, Flavio Protasio Veras, Thiago Mattar Cunha, Rene Donizeti Ribeiro Oliveira, Paulo Louzada-Junior, Robert H Mills, Paulina K Piotrowski, Stephanie L Servetas, Sandra M Da Silva, Christina M Jones, Nancy J Lin, Katrice A Lippa, Scott A Jackson, Rima Kaddurah Daouk, Douglas Galasko, Parambir S Dulai, Tatyana I Kalashnikova, Curt Wittenberg, Robert Terkeltaub, Megan M Doty, Jae H Kim, David J Gonzalez, Julia Beauchamp-Walters, Kenneth P Wright, Maria Gloria Dominguez Bello, Mark Manary, Michelli F Oliveira, Brigid S Boland, Norberto Peporine Lopes, Monica Guma, Austin D Swafford, Rachel J Dutton, Rob Knight, Pieter C Dorrestein
Enhancing untargeted metabolomics using metadata-based source annotation. Nature biotechnology (2022)
Smruthi Karthikeyan, Joshua I Levy, Peter De Hoff, Greg Humphrey, Amanda Birmingham, Kristen Jepsen, Sawyer Farmer, Helena M Tubb, Tommy Valles, Caitlin E Tribelhorn, Rebecca Tsai, Stefan Aigner, Shashank Sathe, Niema Moshiri, Benjamin Henson, Adam M Mark, Abbas Hakim, Nathan A Baer, Tom Barber, Pedro Belda-Ferre, Marisol Chacón, Willi Cheung, Evelyn S Cresini, Emily R Eisner, Alma L Lastrella, Elijah S Lawrence, Clarisse A Marotz, Toan T Ngo, Tyler Ostrander, Ashley Plascencia, Rodolfo A Salido, Phoebe Seaver, Elizabeth W Smoot, Daniel McDonald, Robert M Neuhard, Angela L Scioscia, Alysson M Satterlund, Elizabeth H Simmons, Dismas B Abelman, David Brenner, Judith C Bruner, Anne Buckley, Michael Ellison, Jeffrey Gattas, Steven L Gonias, Matt Hale, Faith Hawkins, Lydia Ikeda, Hemlata Jhaveri, Ted Johnson, Vince Kellen, Brendan Kremer, Gary Matthews, Ronald W McLawhon, Pierre Ouillet, Daniel Park, Allorah Pradenas, Sharon Reed, Lindsay Riggs, Alison Sanders, Bradley Sollenberger, Angela Song, Benjamin White, Terri Winbush, Christine M Aceves, Catelyn Anderson, Karthik Gangavarapu, Emory Hufbauer, Ezra Kurzban, Justin Lee, Nathaniel L Matteson, Edyth Parker, Sarah A Perkins, Karthik S Ramesh, Refugio Robles-Sikisaka, Madison A Schwab, Emily Spencer, Shirlee Wohl, Laura Nicholson, Ian H McHardy, David P Dimmock, Charlotte A Hobbs, Omid Bakhtar, Aaron Harding, Art Mendoza, Alexandre Bolze, David Becker, Elizabeth T Cirulli, Magnus Isaksson, Kelly M Schiabor Barrett, Nicole L Washington, John D Malone, Ashleigh Murphy Schafer, Nikos Gurfield, Sarah Stous, Rebecca Fielding-Miller, Richard S Garfein, Tommi Gaines, Cheryl Anderson, Natasha K Martin, Robert T Schooley, Brett Austin, Duncan R MacCannell, Stephen F Kingsmore, William Lee, Seema Shah, Eric McDonald, Alexander T Yu, Mark Zeller, Kathleen M Fisch, Christopher Longhurst, Patty Maysent, David Pride, Pradeep K Khosla, Louise C Laurent, Gene W Yeo, Kristian G Andersen, Rob Knight
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 609 (7925) (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)
Søren Michael Karst, Ryan M Ziels, Rasmus Hansen Kirkegaard, Emil Aarre Sørensen, Daniel McDonald, Qiyun Zhu, Rob Knight, Mads Albertsen
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nature methods 18 (2) (2021)
George Armstrong, Kalen Cantrell, Shi Huang, Daniel McDonald, Niina Haiminen, Anna Paola Carrieri, Qiyun Zhu, Antonio Gonzalez, Imran McGrath, Kristen L Beck, Daniel Hakim, Aki Samuli Havulinna, Guillaume Méric, Teemu J Niiranen, Leo Lahti, Veikko V Salomaa, Mohit Jain, Michael Inouye, Austin D Swafford, Ho-Cheol Kim, Laxmi Parida, Yoshiki Vázquez-Baeza, Rob Knight
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. Genome research 31 (11) (2021)
Amanda Hazel Dilmore, Daniel McDonald, Tanya T Nguyen, James B Adams, Rosa Krajmalnik-Brown, Emmanuel Elijah, Pieter C Dorrestein, Rob Knight
The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder. mSystems (2021)
Bryn C Taylor, Kelly C Weldon, Ronald J Ellis, Donald Franklin, Tobin Groth, Emily C Gentry, Anupriya Tripathi, Daniel McDonald, Gregory Humphrey, MacKenzie Bryant, Julia Toronczak, Tara Schwartz, Michelli F Oliveira, Robert Heaton, Igor Grant, Sara Gianella, Scott Letendre, Austin Swafford, Pieter C Dorrestein, Rob Knight
Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems 5 (5) (2020)
Samantha Lee Huey, Lingjing Jiang, Marcus W Fedarko, Daniel McDonald, Cameron Martino, Farhana Ali, David G Russell, Shobha A Udipi, Aparna Thorat, Varsha Thakker, Padmini Ghugre, R D Potdar, Harsha Chopra, Kripa Rajagopalan, Jere D Haas, Julia Leigh Finkelstein, Rob Knight, Saurabh Mehta
Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India. mSphere 5 (5) (2020)
Jennifer B H Martiny, Katrine L Whiteson, Brendan J M Bohannan, Lawrence A David, Nicole A Hynson, Margaret McFall-Ngai, John F Rawls, Thomas M Schmidt, Zaid Abdo, Martin J Blaser, Seth R Bordenstein, Christian Bréchot, Carolee T Bull, Pieter C Dorrestein, Jonathan A Eisen, Ferran Garcia-Pichel, Jack Gilbert, Kirsten S Hofmockel, Mary L Holtz, Rob Knight, David B Mark Welch, Daniel McDonald, Barbara Methé, Nigel J Mouncey, Noel T Mueller, Catherine A Pfister, Lita Proctor, Joel L Sachs
The emergence of microbiome centres. Nature microbiology 5 (1) (2020)
Bryn C Taylor, Franck Lejzerowicz, Marion Poirel, Justin P Shaffer, Lingjing Jiang, Alexander A Aksenov, Nicole Litwin, Gregory Humphrey, Cameron Martino, Sandrine Miller-Montgomery, Pieter C Dorrestein, Patrick Veiga, Se Jin Song, Daniel McDonald, Muriel Derrien, Rob Knight
Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems 5 (2) (2020)
Daniel McDonald, Benjamin Kaehler, Antonio Gonzalez, Jeff DeReus, Gail Ackermann, Clarisse Marotz, Gavin Huttley, Rob Knight
redbiom: a Rapid Sample Discovery and Feature Characterization System. mSystems 4 (4) (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)
Jacobo de la Cuesta-Zuluaga, Scott T Kelley, Yingfeng Chen, Juan S Escobar, Noel T Mueller, Ruth E Ley, Daniel McDonald, Shi Huang, Austin D Swafford, Rob Knight, Varykina G Thackray
Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. mSystems 4 (4) (2019)
Philip Strandwitz, Ki Hyun Kim, Darya Terekhova, Joanne K Liu, Anukriti Sharma, Jennifer Levering, Daniel McDonald, David Dietrich, Timothy R Ramadhar, Asama Lekbua, Nader Mroue, Conor Liston, Eric J Stewart, Marc J Dubin, Karsten Zengler, Rob Knight, Jack A Gilbert, Jon Clardy, Kim Lewis
GABA-modulating bacteria of the human gut microbiota. Nature microbiology 4 (3) (2018)
Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, null null, Rob Knight
American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3 (3) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Daniel McDonald