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Rob Knight

University of California San Diego

255H-index
1.8KPaper Count
46.3WCitation Count
Published Papers 693
Publication Date
Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer’s disease
err2026-09-28
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errTim Hensen; Lora Khatib; Lucas Patel; Daniel McDonald; Antonio González; Siamak MahmoudianDehkordi; Colette Blach; Rob Knight; Rima Kaddurah-Daouk; Ines Thiele
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Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation
err2026-09-21
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errLora Khatib; Renee Oles; Alejandra Ríos Hernández; Tyler Myers; Jianshu Zhao; Megha Kumar; Ana Laroya; Veronica Tolosa-Enguis; Nobuko Matsunami; Daisuke Suzuki; Nodoka Chiba; Katharine E. Gilbert; Promi Das; Jon G. Sanders; Lucas Patel; Nicole Litwin; Brent Nowinski; Amanda Birmingham; Sawyer Farmer; Caitriona Brennan; MacKenzie Bryant; Caitlin Tribelhorn; Karenina Sanders-Bodai; Charles Cowart; Oliver Nizet; Edgar A. Diaz; Patrick Veiga; Sudarshan A. Shetty; Jan Knol; Christophe Lay; Hana Koutnikova; Soline Chaumont; Julien Tap; Aurélie Cotillard; Muriel Derrien; Manolo Laiola; Antonio González; Armando R. Tovar; Nimbe Torres; Yolanda Sanz; Takuji Yamada; Daniel McDonald; Se Jin Song; Andrew Bartko; Rob Knight
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Microbial and inflammatory features linked to distal sensory polyneuropathy in people with HIV
err2026-09-09
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PREAI
errLora Khatib; Mohammadsobhan S. Andalibi; Christophe Vanpouille; Azin Tavasoli; Daniel McDonald; Alan Wells; Mattia Trunfio; Jennifer E. Iudicello; Donald Franklin; Antonio Gonzalez; Wendy Fitzgerald; Robert K. Heaton; David J. Moore; Scott L. Letendre; Sara Gianella; Rob Knight; Ronald J. Ellis
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Megascale microbiome analysis with DartUniFrac
err2026-08-28
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errJianshu Zhao; Daniel McDonald; Igor Sfiligoi; Manuel E. Lladser; Lucas Patel; Yuhan Weng; Lora Khatib; Samuel Degregori; Antonio Gonzalez; Catherine A. Lozupone; Rob Knight
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Multi-omics analyses of facial skin in acne identify distinct microbial and metabolic features at lesional and non-lesional sites
err2026-08-06
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errYang Chen; Britta De Pessemier; Tyler Myers; Simone Zuffa; Jasmine Zemlin; Sayeh Pourhamidi; Susi Elaine Dal Belo; Anthony Woo; Magali Moreau; Jolanta Idkowiak-Baldys; Iveta Kalcheva; Paulo Wender Portal Gomes; Chloe Lieng; Samia Almoughrabie; Anna Dan Nguyen; Josh L. Espinoza; Christopher Dupont; Tom Van de Wiele; Chris Callewaert; Daniel McDonald; Karsten Zengler; Andrew Bartko; Luc Aguilar; Philippe Barbarat; Richard L. Gallo; Pieter C. Dorrestein; Qian Zheng; Amina Bouslimani; Se Jin Song; Rob Knight
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Effect of a complementary feeding intervention based on iron- and zinc-biofortified pearl millet on the gut microbiota in 12–18-month-old children: a randomized trial
err2026-07-30
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errSamantha L. Huey; Nathaniel L. Cole; Ioanna Pagani; Antonio González; Julia L. Finkelstein; Jere D. Haas; Shobha A. Udipi; Padmini Ghugre; Ramesh D. Potdar; Rob Knight; Saurabh Mehta
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Applying Artificial Intelligence and machine learning in precision nutrition
err2026-07-06
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errParaskevi Massara; Jonathan Kirkland; Ioanna Pagani; Samantha L. Huey; Haym Hirsh; Daniel McDonald; Lucas Patel; Julia L. Finkelstein; Marie Gantz; Fei Wang; David Erickson; Martin T. Wells; Olivier Elemento; Rob Knight; Saurabh Mehta
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A multi-organ metabolomics atlas reveals molecular dysregulations in Alzheimer's disease mouse models
err2026-06-01
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PREAI
errZuffa, Simone; Allaband, Celeste; Charron-Lamoureux, Vincent; Caraballo-Rodriguez, Andres M.; Patan, Abubaker; Mohanty, Ipsita; Agongo, Julius; Bostick, John W.; Connerly, T. Jaymie; Thron, Taren; Needam, Brittany D.; Fonseca, Matheus de Castro; Benitez, Rodolfo Salido; Hansen, Lauren; Tubb, Helena; Cao, Jennifer; Kalecky, Karel; Bottiglieri, Teodoro; MahmoudianDehkordi, Siamak; Schimmel, Leyla; Kueider-Paisley, Alexandra; Graham, Stewart F.; Siegel, Dionicio; Wang, Mingxun; Knight, Rob; Kaddurah-Daouk, Rima; Dorrestein, Pieter C.; Mazmanian, Sarkis K.
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Insects shape the cadaver decomposition microbiome and postmortem interval estimation accuracy
err2026-05-19
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PREAI
errNieciecki, Victoria; Seitz, Valerie A.; Burcham, Zachary M.; Otto, Kristen; Cantrell, Kalen; Kirkland, Jonathan; Ackermann, Gail; Knight, Rob; Lynne, Aaron; Metcalf, Jessica L.; Bucheli, Sibyl
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Lactic acid bacteria and endogenous ethanol mediate proton pump inhibitor-associated MASLD: a multicohort cross-sectional mediation analysis
err2026-05-03
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errMark Davids; Hilde Herrema; Albert K. Groen; Henrike Galenkamp; Aeilko Zwinderman; Joonatan Palmu; Aki Havulinna; Teemu Niiranen; Rob Knight; Yaïr Acherman; Rutger Franken; Joanne Verheij; Michael Dukas; null; Jasmohan Bajaj; Cristina Llorente; Bernd Schnabl; Max Nieuwdorp; Abraham Meijnikman
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Author Correction: Consuming a modified Mediterranean ketogenic diet reverses the peripheral lipid signature of Alzheimer’s disease in humans
err2026-04-06
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errOAAI
errBryan J. Neth; Kevin Huynh; Corey Giles; Tingting Wang; Natalie A. Mellett; Thy Duong; Colette Blach; Leyla Schimmel; Thomas C. Register; Kaj Blennow; Henrik Zetterberg; Richa Batra; Annalise Schweickart; Amanda Hazel Dilmore; Cameron Martino; Matthias Arnold; Jan Krumsiek; Xianlin Han; Pieter C. Dorrestein; Rob Knight; Peter J. Meikle; Suzanne Craft; Rima Kaddurah-Daouk
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Targeted Microbial Shifts and Metabolite Profiles Were Associated with Clinical Response to an Anti-Inflammatory Diet in Osteoarthritis
err2026-03-03
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errMarta Sala-Climent; Kevin Bu; Roxana Coras; Martha Cedeno; Simone Zuffa; Jessica Murillo-Saich; Helena Mannochio-Russo; Celeste Allaband; Michal K. Hose; Anna Quan; Soo-In Choi; Katherine Nguyen; Shahrokh Golshan; Rebecca B. Blank; Tiffany Holt; Nancy E. Lane; Rob Knight; Jose Scher; Pieter Dorrestein; Jose Clemente; Monica Guma
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Value of Multiomics Over Clinical Risk Factors in Hypertension Prediction
err2026-02-01
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PREAI
errVuori, Matti; Ruuskanen, Matti O.; Jousilahti, Pekka; Salomaa, Veikko; Yeo, Li-Fang; Kauko, Anni; Vaura, Felix; Havulinna, Aki; Liu, Yang; Meric, Guillaume; Inouye, Michael; Knight, Rob; Lahti, Leo; Niiranen, Teemu
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Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats
err2025-12-18
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errHélène Tonnelé; Denghui Chen; Felipe Morillo; Jorge Garcia-Calleja; Apurva S. Chitre; Benjamin B. Johnson; Thiago Missfeldt Sanches; Riyan Cheng; Marc Jan Bonder; Antonio Gonzalez; Tomasz Kosciolek; Anthony M. George; Wenyan Han; Katie Holl; Aidan Horvath; Keita Ishiwari; Christopher P. King; Alexander C. Lamparelli; Connor D. Martin; Angel Garcia Martinez; Alesa H. Netzley; Jordan A. Tripi; Tengfei Wang; Elena Bosch; Peter A. Doris; Oliver Stegle; Hao Chen; Shelly B. Flagel; Paul J. Meyer; Jerry B. Richards; Terry E. Robinson; Leah C. Solberg Woods; Oksana Polesskaya; Rob Knight; Abraham A. Palmer; Amelie Baud
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Environmental and skin–nasal microbiome variation in South African children with atopic dermatitis
err2025-12-12
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errYang Chen; Anna Dan Nguyen; Nonhlanhla Lunjani; Gillian Ndhlovu; Drishti Kaul; Britta De Pessemier; Teruaki Nakatsuji; Murunwa Madzinga; Evgeniya Sovershaeva; Carol Hlela; Michael Levin; Avumile Mankahla; George Hightower; Chris Callewaert; Rob Knight; Richard L. Gallo; Christopher L. Dupont; Felix Dube
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Scikit-bio: a fundamental Python library for biological omic data analysis
err2025-12-11
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PREAI
errMatthew Aton; Daniel McDonald; Jorge Cañardo Alastuey; Raeed Azom; Paarth Batra; Valentyn Bezshapkin; Evan Bolyen; Alexander Cagle; J. Gregory Caporaso; Justine W. Debelius; Kestrel Gorlick; Nirmitha Hamsanipally; Lars Hunger; Aryan Keluskar; Disen Liao; Yang Young Lu; Jose A. Navas-Molina; Anders Pitman; Jai Ram Rideout; Anton Sazonov; Bharath Sathappan; Karen Schwarzberg Lipson; Igor Sfiligoi; Chris Tapo; Yoshiki Vázquez-Baeza; Zijun Wu; Zhenjiang Zech Xu; Mingsong Sam Ye; Jianshu Zhao; Rob Knight; James T. Morton; Qiyun Zhu
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A resource to empirically establish drug exposure records directly from untargeted metabolomics data
err2025-12-09
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errHaoqi Nina Zhao; Kine Eide Kvitne; Corinna Brungs; Siddharth Mohan; Vincent Charron-Lamoureux; Wout Bittremieux; Runbang Tang; Robin Schmid; Santosh Lamichhane; Shipei Xing; Yasin El Abiead; Mohammadsobhan S. Andalibi; Helena Mannochio-Russo; Madison Ambre; Nicole E. Avalon; MacKenzie Bryant; Lindsey A. Burnett; Andrés Mauricio Caraballo-Rodríguez; Martin Casas Maya; Loryn Chin; Lluís Corominas; Ronald J. Ellis; Donald Franklin; Sagan Girod; Paulo Wender P. Gomes; Lauren Hansen; Robert K. Heaton; Jennifer E. Iudicello; Alan K. Jarmusch; Lora Khatib; Scott Letendre; Sarolt Magyari; Daniel McDonald; Ipsita Mohanty; Andrés Cumsille; David J. Moore; Prajit Rajkumar; Dylan H. Ross; Harshada Sapre; Mohammad Reza Zare Shahneh; Ruben Gil-Solsona; Sydney P. Thomas; Caitlin Tribelhorn; Helena M. Tubb; Corinn Walker; Crystal X. Wang; Jasmine Zemlin; Simone Zuffa; David S. Wishart; Pablo Gago-Ferrero; Rima Kaddurah-Daouk; Mingxun Wang; Manuela Raffatellu; Karsten Zengler; Tomáš Pluskal; Libin Xu; Rob Knight; Shirley M. Tsunoda; Pieter C. Dorrestein
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Calculating fast differential genome coverages among metagenomic sources using micov
err2025-11-20
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errOAAI
errYuhan Weng; Caitlin Guccione; Daniel McDonald; Renee Oles; Suzanne Devkota; Evguenia Kopylova; Gregory D. Sepich-Poore; Rodolfo A. Salido; M. Omar Din; Se Jin Song; Kit Curtius; Hiutung Chu; Andrew Bartko; Jeff Hasty; Rob Knight
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Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens
err2025-11-01
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PREAI
errLukacz, Emily S.; Mcdonald, Daniel; Bryant, Mackenzie; Putnam, Sara; Rudser, Kyle; Brennan, Caitriona; Meister, Melanie; Fok, Cynthia S.; Mueller, Margaret G.; Knight, Rob; Brubaker, Linda
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Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos
err2025-10-09
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PREAI
errNatalia Palacios; Scott Gordon; Tao Wang; Robert Burk; Qibin Qi; Curtis Huttenhower; Hector M. Gonzalez; Rob Knight; Charles De Carli; Marta Daviglus; Melissa Lamar; Gregory Telavera; Wassim Tarraf; Tomasz Kosciolek; Jianwen Cai; Robert C Kaplan
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