Here are the papers to which I’ve contributed.
(*) denotes equal contribution
2023
Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression
Cell Reports 2023
doi: https://doi.org/10.1016/j.celrep.2023.112997
Ting Fu*, Tao Huan*, Gibraan Rahman*, Hui Zhi, Zhenjiang Xu, Tae Gyu Oh, Jian Guo, Sally Coulter, Anupriya Tripathi, Cameron Martino, Justin L. McCarville, Qiyun Zhu, Fritz Cayabyab, Brian Low, Mingxiao He, Shipei Xing, Fernando Vargas, Ruth T. Yu, Annette Atkins, Christopher Liddle, Janelle Ayres, Manuela Raffatellu, Pieter C. Dorrestein, Michael Downes, Rob Knight, Ronald M. Evans
Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles
Nature Neuroscience 2023
doi: https://doi.org/10.1038/s41593-023-01361-0
James T Morton, Dong-Min Jin, Robert H Mills, Yan Shao, Gibraan Rahman, Daniel McDonald, Qiyun Zhu, Metin Balaban, Yueyu Jiang, Kalen Cantrell, Antonio Gonzalez, Julie Carmel, Linoy Mia Frankiensztajn, Sandra Martin-Brevet, Kirsten Berding, Brittany D Needham, María Fernanda Zurita, Maude David, Olga V Averina, Alexey S Kovtun, Antonio Noto, Michele Mussap, Mingbang Wang, Daniel N Frank, Ellen Li, Wenhao Zhou, Vassilios Fanos, Valery N Danilenko, Dennis P Wall, Paúl Cárdenas, Manuel E Baldeón, Sébastien Jacquemont, Omry Koren, Evan Elliott, Ramnik J Xavier, Sarkis K Mazmanian, Rob Knight, Jack A Gilbert, Sharon M Donovan, Trevor D Lawley, Bob Carpenter, Richard Bonneau, Gaspar Taroncher-Oldenburg
Dietary weight loss-induced improvements in metabolic function are enhanced by exercise in people with obesity and prediabetes
Nature Metabolism 2023
doi: https://doi.org/10.1038/s42255-023-00829-4
Joseph W Beals, Brandon D Kayser, Gordon I Smith, George G Schweitzer, Kyleigh Kirbach, Monica L Kearney, Jun Yoshino, Gibraan Rahman, Rob Knight, Bruce W Patterson, Samuel Klein
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases
Genes 2023
doi: https://doi.org/10.3390/genes14061239
Gibraan Rahman, Daniel McDonald, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Lingjing Jiang, Climent Casals-Pascual, Daniel Hakim, Amanda Hazel Dilmore, Brent Nowinski, Shyamal Peddada, Rob Knight
Effects of a Ketogenic and Low Fat Diet on the Human Metabolome, Microbiome and Food-ome in Adults at Risk for Alzheimer’s Disease
Alzheimer’s & Dementia 2023
doi: https://doi.org/10.1002/alz.13007
Amanda Hazel Dilmore*, Cameron Martino*, Bryan J. Neth, Kiana A West, Jasmine Zemlin, Gibraan Rahman, Morgan Panitchpakdi, Michael J Meehan, Kelly C Weldon, Colette Blach, Leyla Schimmel, Rima Kaddurah-Daouk, Pieter Dorrestein, Rob Knight, Suzanne Craft, Alzheimer’s Gut Microbiome Project Consortium
BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations
bioRxiv 2023
doi: https://doi.org/10.1101/2023.01.30.526328
Gibraan Rahman, James T Morton, Cameron Martino, Gregory D Sepich-Poore, Celeste Allaband, Caitlin Guccione, Yang Chen, Daniel Hakim, Mehrbod Estaki, Rob Knight
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy
Nature 2023
doi: https://doi.org/10.1038/s41586-022-05637-6
Michal K Handzlik, Jivani M Gengatharan, Katie E Frizzi, Grace H McGregor, Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Ana M Moreno, Courtney R Green, Lucie S Guernsey, Terry Lin, Patrick Tseng, Yoichiro Ideguchi, Regis J Fallon, Amandine Chaix, Satchidananda Panda, Prashant Mali, Martina Wallace, Rob Knight, Marin L Gantner, Nigel A Calcutt, Christian M Metallo
2022
Compositionally aware phylogenetic beta-diversity measures better resolve microbiomes associated with phenotype
mSystems 2022
doi: https://doi.org/10.1128/msystems.00050-22
Cameron Martino, Daniel McDonald, Kalen Cantrell, Amanda Hazel Dilmore, Yoshiki Vázquez-Baeza, Liat Shenhav, Justin P. Shaffer, Gibraan Rahman, George Armstrong, Celeste Allaband, Se Jin Song, Rob Knight
Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations
bioRxiv 2022
doi: https://doi.org/10.1101/2022.02.23.481658
Rodolfo A Salido, Cameron Martino, Smruthi Karthikeyan, Shi Huang, Gibraan Rahman, Antonio Gonzalez, Livia S. Zaramela, Kristen L Beck, Shrikant Bhute, Kalen Cantrell, Anna Paola Carrieri, Sawyer Farmer, Niina Haiminen, Greg Humphrey, Ho-Cheol Kim, Laxmi Parida, Alex Richter, Yoshiki Vázquez-Baeza, Karsten Zengler, Austin D. Swafford, Andrew Bartko, Rob Knight
Applications and comparison of dimensionality reduction methods for microbiome data
Frontiers in Bioinformatics 2022
doi: https://doi.org/10.3389/fbinf.2022.821861
George Armstrong*, Gibraan Rahman*, Cameron Martino, Daniel McDonald, Antonio Gonzalez, Gal Mishne, Rob Knight
2021
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.
medRxiv 2021
doi: https://dx.doi.org/10.1101%2F2021.12.06.21267101
Victor Cantú*, Rodolfo Salido*, Shi Huang, Gibraan Rahman, Rebecca Tsai, Holly Valentine, Celestine Magallanes, Stefan Aigner, Nathan Baer, Tom Barber, Pedro Belda-Ferre, Maryan Betty, MacKenzie Bryant, Martín Casas Maya, Anelizze Castro-Martínez, Marisol Chacón, Willi Cheung, Evelyn Crescini, Peter De Hoff, Emily Eisner, Sawyer Farmer, Abbas Hakim, Laura Kohn, Alma Lastrella, Elijah Lawrence, Sydney Morgan, Toan Ngo, Alhakam Nouri, R. Ostrander, Ashley Plascencia, Christopher Ruiz, Shashank Sathe, Phoebe Seaver, Tara Schwartz, Elizabeth Smoot, Thomas Valles, Gene Yeo, Louise Laurent, Rebecca Fielding-Miller, Rob Knight
Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data
mSystems 2021
doi: https://doi.org/10.1128/mSystems.00691-21
George Armstrong, Cameron Martino, Gibraan Rahman, Antonio Gonzalez, Yoshiki Vázquez-Baeza, Gal Mishne, Rob Knight
Reduced gut microbiome diversity in people with HIV who have distal neuropathic pain
The Journal of Pain 2021
doi: https://doi.org/10.1016/j.jpain.2021.08.006
Ronald J.Ellis, Robert K.Heaton, Sara Gianella, Gibraan Rahman, Rob Knight
SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment
Microbiome 2021
doi: https://doi.org/10.1186/s40168-021-01083-0
Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E. Diner, Gibraan Rahman, Daniel McDonald, George Armstrong, Sho Kodera, Sonya Donato, Gertrude Ecklu-Mensah, Neil Gottel, Mariana C. Salas Garcia, Leslie Y. Chiang, Rodolfo A. Salido, Justin P. Shaffer, Mac Kenzie Bryant, Karenina Sanders, Greg Humphrey, Gail Ackermann, Niina Haiminen, Kristen L. Beck, Ho-Cheol Kim, Anna Paola Carrieri, Laxmi Parida, Yoshiki Vázquez-Baeza, Francesca J. Torriani, Rob Knight, Jack Gilbert, Daniel A. Sweeney & Sarah M. Allard
Non-alcoholic Steatohepatitis and HCC in a Hyperphagic Mouse Accelerated by Western Diet
Cellular and Molecular Gastroenterology and Hepatology 2021
doi: https://doi.org/10.1016/j.jcmgh.2021.05.010
Souradipta Ganguly, German Aleman Muench, Linshan Shang, Sara Brin Rosenthal, Gibraan Rahman, Ruoyu Wang, Yanhan Wang, Hyeok Choon Kwon, Anthony M. Diomino, Tatiana Kisseleva, Pejman Soorosh, Mojgan Hosseini, Rob Knight, Bernd Schnabl, David A. Brenner, Debanjan Dhar
EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets
mSystems 2021
doi: https://doi.org/10.1128/mSystems.01216-20
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, Jamie Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
2020
Visualizing ’omic feature rankings and log-ratios using Qurro
NAR Genomics and Bioinformatics 2020
doi: https://doi.org/10.1093/nargab/lqaa023
Marcus W. Fedarko, Cameron Martino, James T. Morton, Antonio González, Gibraan Rahman, Clarisse A. Marotz, Jeremiah J. Minich, Eric E. Allen, Rob Knight