Rob Knight (R Knight)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 226

Top Venues

mSystems

Nature

Nature communications

bioRxiv : the preprint server for biology

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

Publications

Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene (2024)
Zhendong Mei, FengLei Wang, Amrisha Bhosle, Danyue Dong, Raaj Mehta, Andrew Ghazi, Yancong Zhang, Yuxi Liu, Ehud Rinott, Siyuan Ma, Eric Bruce Rimm, Martha Daviglus, Walter C Willett, Rob Knight, Frank B Hu, Qibin Qi, Andrew T Chan, Meredith Yeager, Meir J Stampfer, Iris Shai, Robert C Kaplan, Curtis Huttenhower, Dong D Wang
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. Nature medicine 30 (8) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43 (15) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43 (15) (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)
Jocelyn Keehner, Shira R Abeles, Christopher A Longhurst, Lucy E Horton, Frank E Myers, Lindsay Riggs-Rodriguez, Mohammed Ahmad, Sally Baxter, Aaron Boussina, Kalen Cantrell, Priscilla Cardenas, Peter De Hoff, Robert El-Kareh, Jennifer Holland, Daryn Ikeda, Kirk Kurashige, Louise C Laurent, null null, Andrew Lucas, David Pride, Shashank Sathe, Allen R Tran, Tetyana I Vasylyeva, Gene W Yeo, Rob Knight, Joel O Wertheim, Francesca J Torriani
Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 78 (5) (2024)
Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thygarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circulation research 134 (7) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thygarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circulation research 134 (7) (2024)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism 6 (7) (2024)
Cassandra Tang-Wing, Ipsita Mohanty, MacKenzie Bryant, Katherine Makowski, Daira Melendez, Pieter C Dorrestein, Rob Knight, Andrés Mauricio Caraballo-Rodriguez, Celeste Allaband, Keith Jenné
Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus ). mSystems (2024)
Jocelyn Keehner, Shira R Abeles, Christopher A Longhurst, Lucy E Horton, Frank E Myers, Lindsay Riggs-Rodriguez, Mohammed Ahmad, Sally Baxter, Aaron Boussina, Kalen Cantrell, Priscilla Cardenas, Peter De Hoff, Robert El-Kareh, Jennifer Holland, Daryn Ikeda, Kirk Kurashige, Louise C Laurent, null null, Andrew Lucas, David Pride, Shashank Sathe, Allen R Tran, Tetyana I Vasylyeva, Gene W Yeo, Rob Knight, Joel O Wertheim, Francesca J Torriani
Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America (2024)
Charlene Enhui Goh, Bruno Bohn, Jeanine M Genkinger, Rebecca L Molinsky, Sumith Roy, Bruce J Paster, Ching-Yuan Chen, Melana Yuzelpolskaya, Paolo C Colombo, Michael Rosenbaum, Rob Knight, Moïse Desvarieux, Panos N Papapanou, David R Jacobs, Ryan T Demmer
Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS). medRxiv : the preprint server for health sciences (2024)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism 6 (7) (2024)
Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thygarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circulation research 134 (7) (2024)
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Gregory D Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Rob Knight
Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature (2024)
Cassandra Tang-Wing, Ipsita Mohanty, MacKenzie Bryant, Katherine Makowski, Daira Melendez, Pieter C Dorrestein, Rob Knight, Andrés Mauricio Caraballo-Rodriguez, Celeste Allaband, Keith Jenné
Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus ). mSystems 9 (8) (2024)
Jocelyn Keehner, Shira R Abeles, Christopher A Longhurst, Lucy E Horton, Frank E Myers, Lindsay Riggs-Rodriguez, Mohammed Ahmad, Sally Baxter, Aaron Boussina, Kalen Cantrell, Priscilla Cardenas, Peter De Hoff, Robert El-Kareh, Jennifer Holland, Daryn Ikeda, Kirk Kurashige, Louise C Laurent, null null, Andrew Lucas, David Pride, Shashank Sathe, Allen R Tran, Tetyana I Vasylyeva, Gene W Yeo, Rob Knight, Joel O Wertheim, Francesca J Torriani
Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America (2024)
Yi Wang, Guo-Chong Chen, Zheng Wang, Kai Luo, Yan-Bo Zhang, Yang Li, Amanda C McClain, Marta M Jankowska, Krista M Perreira, Catherine M Champagne, Carmen R Isasi, Maria M Llabre, Bharat Thygarajan, Martha L Daviglus, Linda V Van Horn, David Goldsztajn Farelo, Luis E Maldonado, Steven R Levine, Bing Yu, Eric Boerwinkle, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi, Brandilyn A Peters
Dietary Acculturation Is Associated With Altered Gut Microbiome, Circulating Metabolites, and Cardiovascular Disease Risk in US Hispanics and Latinos: Results From HCHS/SOL. Circulation 150 (3) (2024)
Caitriona Brennan, Pedro Belda-Ferre, Simone Zuffa, Vincent Charron-Lamoureux, Ipsita Mohanty, Gail Ackermann, Celeste Allaband, Madison Ambre, Tara Boyer, MacKenzie Bryant, Kalen Cantrell, Antonio Gonzalez, Daniel McDonald, Rodolfo A Salido, Se Jin Song, Gillian Wright, Pieter C Dorrestein, Rob Knight
Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies. mSystems (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison C Ea, MacKenzie Bryant, Jocelyn A Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems 9 (7) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Charlene Enhui Goh, Bruno Bohn, Jeanine M Genkinger, Rebecca L Molinsky, Sumith Roy, Bruce J Paster, Ching-Yuan Chen, Melana Yuzelpolskaya, Paolo C Colombo, Michael Rosenbaum, Rob Knight, Moïse Desvarieux, Panos N Papapanou, David R Jacobs, Ryan T Demmer
Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS). medRxiv : the preprint server for health sciences (2024)
Robert S Thompson, Samuel J Bowers, Fernando Vargas, Shelby Hopkins, Tel Kelley, Antonio Gonzalez, Christopher A Lowry, Pieter C Dorrestein, Martha Hotz Vitaterna, Fred W Turek, Rob Knight, Kenneth P Wright, Monika Fleshner
A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats. Nutrients 16 (11) (2024)
Ipsita Mohanty, Celeste Allaband, Helena M Russo, Yasin El Abiead, Lee R Hagey, Rob Knight, Pieter C Dorrestein
The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nature reviews. Gastroenterology & hepatology (2024)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism 6 (7) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison C Ea, MacKenzie Bryant, Jocelyn A Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems 9 (7) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43 (15) (2024)
Cassandra Tang-Wing, Ipsita Mohanty, MacKenzie Bryant, Katherine Makowski, Daira Melendez, Pieter C Dorrestein, Rob Knight, Andrés Mauricio Caraballo-Rodriguez, Celeste Allaband, Keith Jenné
Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus ). mSystems 9 (8) (2024)
Jocelyn Keehner, Shira R Abeles, Christopher A Longhurst, Lucy E Horton, Frank E Myers, Lindsay Riggs-Rodriguez, Mohammed Ahmad, Sally Baxter, Aaron Boussina, Kalen Cantrell, Priscilla Cardenas, Peter De Hoff, Robert El-Kareh, Jennifer Holland, Daryn Ikeda, Kirk Kurashige, Louise C Laurent, null null, Andrew Lucas, David Pride, Shashank Sathe, Allen R Tran, Tetyana I Vasylyeva, Gene W Yeo, Rob Knight, Joel O Wertheim, Francesca J Torriani
Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 78 (5) (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)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism 6 (7) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43 (15) (2024)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism 6 (7) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Correction: Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene (2024)
Ipsita Mohanty, Celeste Allaband, Helena M Russo, Yasin El Abiead, Lee R Hagey, Rob Knight, Pieter C Dorrestein
The changing metabolic landscape of bile acids - keys to metabolism and immune regulation. Nature reviews. Gastroenterology & hepatology 21 (7) (2024)
Robert S Thompson, Samuel J Bowers, Fernando Vargas, Shelby Hopkins, Tel Kelley, Antonio Gonzalez, Christopher A Lowry, Pieter C Dorrestein, Martha Hotz Vitaterna, Fred W Turek, Rob Knight, Kenneth P Wright, Monika Fleshner
A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats. Nutrients 16 (11) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison C Ea, MacKenzie Bryant, Jocelyn A Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene (2024)
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Gregory D Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D Swafford, Rob Knight
Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nature (2024)
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology 9 (3) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison C Ea, MacKenzie Bryant, Jocelyn A Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems (2024)
Zhendong Mei, FengLei Wang, Amrisha Bhosle, Danyue Dong, Raaj Mehta, Andrew Ghazi, Yancong Zhang, Yuxi Liu, Ehud Rinott, Siyuan Ma, Eric Bruce Rimm, Martha Daviglus, Walter C Willett, Rob Knight, Frank B Hu, Qibin Qi, Andrew T Chan, Meredith Yeager, Meir J Stampfer, Iris Shai, Robert C Kaplan, Curtis Huttenhower, Dong D Wang
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. Nature medicine 30 (8) (2024)
Gregory D Sepich-Poore, Daniel McDonald, Evguenia Kopylova, Caitlin Guccione, Qiyun Zhu, George Austin, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciolek, Stefan Janssen, Jessica L Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana R McKay, Sandip Pravin Patel, Austin D Swafford, Tal Korem, Rob Knight
Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 43 (15) (2024)
John W Bostick, Trista J Connerly, Taren Thron, Brittany D Needham, Matheus de Castro Fonseca, Rima Kaddurah-Daouk, Rob Knight, Sarkis K Mazmanian
The microbiome shapes immunity in a sex-specific manner in mouse models of Alzheimer's disease. bioRxiv : the preprint server for biology (2024)
Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thygarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circulation research 134 (7) (2024)
Zhendong Mei, FengLei Wang, Amrisha Bhosle, Danyue Dong, Raaj Mehta, Andrew Ghazi, Yancong Zhang, Yuxi Liu, Ehud Rinott, Siyuan Ma, Eric Bruce Rimm, Martha Daviglus, Walter C Willett, Rob Knight, Frank B Hu, Qibin Qi, Andrew T Chan, Meredith Yeager, Meir J Stampfer, Iris Shai, Robert C Kaplan, Curtis Huttenhower, Dong D Wang
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. Nature medicine (2024)
Charlene Enhui Goh, Bruno Bohn, Jeanine M Genkinger, Rebecca L Molinsky, Sumith Roy, Bruce J Paster, Ching-Yuan Chen, Melana Yuzelpolskaya, Paolo C Colombo, Michael Rosenbaum, Rob Knight, Moïse Desvarieux, Panos N Papapanou, David R Jacobs, Ryan T Demmer
Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS). medRxiv : the preprint server for health sciences (2024)
Jocelyn Keehner, Shira R Abeles, Christopher A Longhurst, Lucy E Horton, Frank E Myers, Lindsay Riggs-Rodriguez, Mohammed Ahmad, Sally Baxter, Aaron Boussina, Kalen Cantrell, Priscilla Cardenas, Peter De Hoff, Robert El-Kareh, Jennifer Holland, Daryn Ikeda, Kirk Kurashige, Louise C Laurent, null null, Andrew Lucas, David Pride, Shashank Sathe, Allen R Tran, Tetyana I Vasylyeva, Gene W Yeo, Rob Knight, Joel O Wertheim, Francesca J Torriani
Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America (2024)
Zhendong Mei, FengLei Wang, Amrisha Bhosle, Danyue Dong, Raaj Mehta, Andrew Ghazi, Yancong Zhang, Yuxi Liu, Ehud Rinott, Siyuan Ma, Eric Bruce Rimm, Martha Daviglus, Walter C Willett, Rob Knight, Frank B Hu, Qibin Qi, Andrew T Chan, Meredith Yeager, Meir J Stampfer, Iris Shai, Robert C Kaplan, Curtis Huttenhower, Dong D Wang
Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. Nature medicine (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison C Ea, MacKenzie Bryant, Jocelyn A Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights. mSystems 9 (7) (2024)
Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thygarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Meredith Yeager, Robert C Kaplan, Qibin Qi
Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes. Circulation research 134 (7) (2024)
Cassandra Tang-Wing, Ipsita Mohanty, MacKenzie Bryant, Katherine Makowski, Daira Melendez, Pieter C Dorrestein, Rob Knight, Andrés Mauricio Caraballo-Rodriguez, Celeste Allaband, Keith Jenné
Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus ). mSystems 9 (8) (2024)
Zachary M Burcham, Aeriel D Belk, Bridget B McGivern, Amina Bouslimani, Parsa Ghadermazi, Cameron Martino, Liat Shenhav, Anru R Zhang, Pixu Shi, Alexandra Emmons, Heather L Deel, Zhenjiang Zech Xu, Victoria Nieciecki, Qiyun Zhu, Michael Shaffer, Morgan Panitchpakdi, Kelly C Weldon, Kalen Cantrell, Asa Ben-Hur, Sasha C Reed, Greg C Humphry, Gail Ackermann, Daniel McDonald, Siu Hung Joshua Chan, Melissa Connor, Derek Boyd, Jake Smith, Jenna M S Watson, Giovanna Vidoli, Dawnie Wolfe Steadman, Aaron M Lynne, Sibyl Bucheli, Pieter C Dorrestein, Kelly C Wrighton, David O Carter, Rob Knight, Jessica L Metcalf
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature microbiology (2024)
Celeste Allaband, Amulya Lingaraju, Stephany Flores Ramos, Tanya Kumar, Haniyeh Javaheri, Maria D Tiu, Ana Carolina Dantas Machado, R Alexander Richter, Emmanuel Elijah, Gabriel G Haddad, Vanessa A Leone, Pieter C Dorrestein, Rob Knight, Amir Zarrinpar
Time of sample collection is critical for the replicability of microbiome analyses. Nature metabolism (2024)
Gibraan Rahman, James T Morton, Cameron Martino, Gregory D Sepich-Poore, Celeste Allaband, Caitlin Guccione, Yang Chen, Daniel Hakim, Mehrbod Estaki, Rob Knight
BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv : the preprint server for biology (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature (2023)
Gibraan Rahman, James T Morton, Cameron Martino, Gregory D Sepich-Poore, Celeste Allaband, Caitlin Guccione, Yang Chen, Daniel Hakim, Mehrbod Estaki, Rob Knight
BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv : the preprint server for biology (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)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Semi Zouiouich, Doratha A Byrd, Xing Hua, Smriti Karwa, Yunhu Wan, Jianxin Shi, Gregory C Humphrey, Gail L Ackermann, Rob Knight, Christian C Abnet, Emily Vogtmann, Rashmi Sinha
Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 32 (3) (2023)
Joseph C Boktor, Gil Sharon, Leonard Verhagen, Deborah A Hall, Phillip A Engen, Zoe Zreloff, Daniel J Hakim, John W Bostick, James A Ousey, Danielle Lange, Gregory Humphrey, Gail L Ackermann, Martha Carlin, Rob Knight, Ali Keshavarzian, Sarkis K Mazmanian
Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Movement disorders : official journal of the Movement Disorder Society 38 (3) (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)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Author Correction: Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 614 (7946) (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 614 (7946) (2023)
Caitriona Brennan, Rodolfo A Salido, Pedro Belda-Ferre, MacKenzie Bryant, Charles Cowart, Maria D Tiu, Antonio González, Daniel McDonald, Caitlin Tribelhorn, Amir Zarrinpar, Rob Knight
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution. mSystems (2023)
Ana Georgina Cobián Güemes, Pooja Ghatbale, Alisha N Blanc, Chase J Morgan, Andrew Garcia, Jesse Leonard, Lina Huang, Grace Kovalick, Marissa Proost, Megan Chiu, Peiting Kuo, Joseph Oh, Smruthi Karthikeyan, Rob Knight, Joe Pogliano, Robert T Schooley, David T Pride
Jumbo phages are active against extensively drug-resistant eyedrop-associated Pseudomonas aeruginosa infections. Antimicrobial agents and chemotherapy (2023)
Tanya Kumar, MacKenzie Bryant, Kalen Cantrell, Se Jin Song, Daniel McDonald, Helena M Tubb, Sawyer Farmer, Amanda Lewis, Emily S Lukacz, Linda Brubaker, Rob Knight
Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses. Microbiology spectrum (2023)
Joseph C Boktor, Gil Sharon, Leonard Verhagen, Deborah A Hall, Phillip A Engen, Zoe Zreloff, Daniel J Hakim, John W Bostick, James A Ousey, Danielle Lange, Gregory Humphrey, Gail L Ackermann, Martha Carlin, Rob Knight, Ali Keshavarzian, Sarkis K Mazmanian
Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Movement disorders : official journal of the Movement Disorder Society 38 (3) (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Caitlin Guccione, Daniel McDonald, Rebecca Fielding-Miller, Kit Curtius, Rob Knight
You are what you excrete. Nature microbiology (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Metin Balaban, Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab
Author Correction: Generation of accurate, expandable phylogenomic trees with uDance. Nature biotechnology (2023)
Semi Zouiouich, Doratha A Byrd, Xing Hua, Smriti Karwa, Yunhu Wan, Jianxin Shi, Gregory C Humphrey, Gail L Ackermann, Rob Knight, Christian C Abnet, Emily Vogtmann, Rashmi Sinha
Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 32 (3) (2023)
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Antonio Gonzalez, James T Morton, Giorgia Nicolaou, Donovan H Parks, Søren M Karst, Mads Albertsen, Philip Hugenholtz, Todd DeSantis, Se Jin Song, Andrew Bartko, Aki Samuli Havulinna, Pekka Jousilahti, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko V Salomaa, Leo Lahti, Siavash Mirarab, Rob Knight
Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology (2023)
Gibraan Rahman, James T Morton, Cameron Martino, Gregory D Sepich-Poore, Celeste Allaband, Caitlin Guccione, Yang Chen, Daniel Hakim, Mehrbod Estaki, Rob Knight
BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv : the preprint server for biology (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Julia Koehler Leman, Pawel Szczerbiak, P Douglas Renfrew, Vladimir Gligorijevic, Daniel Berenberg, Tommi Vatanen, Bryn C Taylor, Chris Chandler, Stefan Janssen, Andras Pataki, Nick Carriero, Ian Fisk, Ramnik J Xavier, Rob Knight, Richard Bonneau, Tomasz Kosciolek
Sequence-structure-function relationships in the microbial protein universe. Nature communications 14 (1) (2023)
Julia Koehler Leman, Pawel Szczerbiak, P Douglas Renfrew, Vladimir Gligorijevic, Daniel Berenberg, Tommi Vatanen, Bryn C Taylor, Chris Chandler, Stefan Janssen, Andras Pataki, Nick Carriero, Ian Fisk, Ramnik J Xavier, Rob Knight, Richard Bonneau, Tomasz Kosciolek
Sequence-structure-function relationships in the microbial protein universe. Nature communications 14 (1) (2023)
Robert M Cooper, Josephine A Wright, Jia Q Ng, Jarrad M Goyne, Nobumi Suzuki, Young-Kyung Lee, Mari Ichinose, Georgette Radford, Feargal Joseph Ryan, Shalni Kumar, Elaine M Thomas, Laura Vrbanac, Rob Knight, Susan L Woods, Daniel L Worthley, Jeff Hasty
Engineered bacteria detect tumor DNA. Science (New York, N.Y.) 381 (6658) (2023)
Semi Zouiouich, Doratha A Byrd, Xing Hua, Smriti Karwa, Yunhu Wan, Jianxin Shi, Gregory C Humphrey, Gail L Ackermann, Rob Knight, Christian C Abnet, Emily Vogtmann, Rashmi Sinha
Stability of the fecal and oral microbiome over two years at -80°C for multiple collection methods. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (2023)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Chia-Yun Hsu, Caitlin Tribelhorn, Pedro Belda Ferre, Allison Ea, MacKenzie Bryant, Jocelyn Young, Hannah C Carrow, William J Sandborn, Parambir S Dulai, Mamata Sivagnanam, David T Pride, Rob Knight, Hiutung Chu
Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv : the preprint server for biology (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)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 614 (7946) (2023)
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, Wen-Hao Zhou, Vassilios Fanos, Valery N Danilenko, Dennis Paul Wall, Paúl Andrés Cárdenas, Manuel E Baldeón, Sebastien 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
Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nature neuroscience (2023)
Metin Balaban, Yueyu Jiang, Qiyun Zhu, Daniel McDonald, Rob Knight, Siavash Mirarab
Generation of accurate, expandable phylogenomic trees with uDance. Nature biotechnology (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 614 (7946) (2023)
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
Dietary weight loss-induced improvements in metabolic function are enhanced by exercise in people with obesity and prediabetes. Nature metabolism (2023)
Zeni Wu, Ruth M Pfeiffer, Doratha A Byrd, Yunhu Wan, Daniel Ansong, Joe-Nat Clegg-Lamptey, Beatrice Wiafe-Addai, Lawrence Edusei, Ernest Adjei, Nicholas Titiloye, Florence Dedey, Francis Aitpillah, Joseph Oppong, Verna Vanderpuye, Ernest Osei-Bonsu, Casey L Dagnall, Kristine Jones, Amy Hutchinson, Belynda D Hicks, Thomas U Ahearn, Rob Knight, Richard Biritwum, Joel Yarney, Seth Wiafe, Baffour Awuah, Kofi Nyarko, Montserrat Garcia-Closas, Rashmi Sinha, Jonine D Figueroa, Louise A Brinton, Britton Trabert, Emily Vogtmann
Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study. Microbiology spectrum (2023)
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
Insulin-regulated serine and lipid metabolism drive peripheral neuropathy. Nature 614 (7946) (2023)

Rob Knight.css-eqlu8i{font-size:small;padding-left:4px;} (R Knight)

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Rob Knight (R Knight)