Austin D Swafford (Austin Swafford)

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 14

Top Topics

Mass Spectrometry

Ankylosing Spondylitis

Interstitial Lung Disease

Top Venues

Science translational medicine

Nature biotechnology

Genome research

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

Publications

R Camille Brewer, Tobias V Lanz, Caryn R Hale, Gregory D Sepich-Poore, Cameron Martino, Austin D Swafford, Thomas S Carroll, Sarah Kongpachith, Lisa K Blum, Serra E Elliott, Nathalie E Blachere, Salina Parveen, John Fak, Vicky Yao, Olga G Troyanskaya, Mayu O Frank, Michelle S Bloom, Shaghayegh Jahanbani, Alejandro M Gomez, Radhika Iyer, Nitya S Ramadoss, Orr Sharpe, Sangeetha Chandrasekaran, Lindsay B Kelmenson, Qian Wang, Heidi Wong, Holly L Torres, Mark Wiesen, Dana T Graves, Kevin D Deane, V Michael Holers, Rob Knight, Robert B Darnell, William H Robinson, Dana E Orange
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Science translational medicine 15 (684) (2023)
R Camille Brewer, Tobias V Lanz, Caryn R Hale, Gregory D Sepich-Poore, Cameron Martino, Austin D Swafford, Thomas S Carroll, Sarah Kongpachith, Lisa K Blum, Serra E Elliott, Nathalie E Blachere, Salina Parveen, John Fak, Vicky Yao, Olga G Troyanskaya, Mayu O Frank, Michelle S Bloom, Shaghayegh Jahanbani, Alejandro M Gomez, Radhika Iyer, Nitya S Ramadoss, Orr Sharpe, Sangeetha Chandrasekaran, Lindsay B Kelmenson, Qian Wang, Heidi Wong, Holly L Torres, Mark Wiesen, Dana T Graves, Kevin D Deane, V Michael Holers, Rob Knight, Robert B Darnell, William H Robinson, Dana E Orange
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Science translational medicine 15 (684) (2023)
R Camille Brewer, Tobias V Lanz, Caryn R Hale, Gregory D Sepich-Poore, Cameron Martino, Austin D Swafford, Thomas S Carroll, Sarah Kongpachith, Lisa K Blum, Serra E Elliott, Nathalie E Blachere, Salina Parveen, John Fak, Vicky Yao, Olga G Troyanskaya, Mayu O Frank, Michelle S Bloom, Shaghayegh Jahanbani, Alejandro M Gomez, Radhika Iyer, Nitya S Ramadoss, Orr Sharpe, Sangeetha Chandrasekaran, Lindsay B Kelmenson, Qian Wang, Heidi Wong, Holly L Torres, Mark Wiesen, Dana T Graves, Kevin D Deane, V Michael Holers, Rob Knight, Robert B Darnell, William H Robinson, Dana E Orange
Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis. Science translational medicine 15 (684) (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)
Stephanie B Orchanian, Julia M Gauglitz, Stephen Wandro, Kelly C Weldon, Megan M Doty, Kristina Stillwell, Shalisa Hansen, Lingjing Jiang, Fernando Vargas, Kyung E Rhee, Julie C Lumeng, Pieter C Dorrestein, Rob Knight, Jae H Kim, Se Jin Song, Austin D Swafford
Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention. Advanced biology 6 (8) (2022)
Justin P Shaffer, Carolina S Carpenter, Cameron Martino, Rodolfo A Salido, Jeremiah J Minich, MacKenzie Bryant, Karenina Sanders, Tara Schwartz, Gregory Humphrey, Austin D Swafford, Rob Knight
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. BioTechniques 73 (1) (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)
Kalen Cantrell, Marcus W Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L Beck, Qiyun Zhu, Erfan Sayyari, James T Morton, George Armstrong, Anupriya Tripathi, Julia M Gauglitz, Clarisse A Marotz, Nathaniel L Matteson, Cameron Martino, Jon G Sanders, Anna Paola Carrieri, Se Jin Song, Austin D Swafford, Pieter C Dorrestein, Kristian G Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. mSystems 6 (2) (2021)
Lingjing Jiang, Niina Haiminen, Anna Paola Carrieri, Shi Huang, Yoshiki Vázquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Austin D Swafford, Rob Knight, Loki Natarajan
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. Biometrics (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)
Mingxun Wang, Alan K Jarmusch, Fernando Vargas, Alexander A Aksenov, Julia M Gauglitz, Kelly C Weldon, Daniel Petras, Ricardo da Silva, Robert Quinn, Alexey V Melnik, Justin Johan Jozias van der Hooft, Andrés Mauricio Caraballo-Rodriguez, Louis Felix Nothias, Christine M Aceves, Morgan Panitchpakdi, Elizabeth Brown, Francesca Di Ottavio, Nicole Sikora, Emmanuel O Elijah, Lara Labarta-Bajo, Emily C Gentry, Shabnam Shalapour, Kathleen E Kyle, Sara P Puckett, Jeramie D Watrous, Carolina S Carpenter, Amina Bouslimani, Madeleine Ernst, Austin D Swafford, Elina I Zúñiga, Marcy J Balunas, Jonathan L Klassen, Rohit Loomba, Rob Knight, Nuno Bandeira, Pieter C Dorrestein
Mass spectrometry searches using MASST. Nature biotechnology 38 (1) (2020)
Jeremiah J Minich, Farhana Ali, Clarisse A Marotz, Pedro Belda Ferre, Leslie Chiang, Justin P Shaffer, Carolina S Carpenter, Daniel McDonald, Jack A Gilbert, Sarah M Allard, Eric E Allen, Rob Knight, Daniel A Sweeney, Austin D Swafford
Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. medRxiv : the preprint server for health sciences (2020)
Lara Labarta-Bajo, Anna Gramalla-Schmitz, Romana Raphaela Gerner, Katelynn R Kazane, Gregory Humphrey, Tara Schwartz, Karenina Sanders, Austin D Swafford, Rob Knight, Manuela Raffatellu, Elina I Zúñiga
CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection. Proceedings of the National Academy of Sciences of the United States of America 117 (40) (2020)
Igor Maricic, Idania Marrero, Akiko Eguchi, Ryota Nakamura, Casey D Johnson, Suryasarathi Dasgupta, Carolyn D Hernandez, Phirum Sam Nguyen, Austin D Swafford, Rob Knight, Ariel E Feldstein, Stephen Caldwell, Vipin Kumar
Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. Journal of immunology (Baltimore, Md. : 1950) 201 (10) (2018)