Sean M Gibbons (S M Gibbons)

Scopus Author ID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 53

Top Venues

bioRxiv : the preprint server for biology

Nature communications

mSystems

BMC biology

Institute for Systems Biology

University of Chicago (PHD)

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

Affiliation History

Institute for Systems Biology Jun 01 2018

United States

Assistant Professor

Massachusetts Institute of Technology Sep 01 2015 - Jun 01 2018

United States

Postdoctoral Associate :: Biological Engineering

Education History

University of Chicago - Aug 01 2015

United States

PHD :: Biophysical Sciences

Uppsala Universitet

Sweden

MSC :: Microbial Chemistry

University of Montana

United States

BSC :: Microbiology, Molecular Biology, and French

Publications

Jacob J Valenzuela, Selva Rupa Christinal Immanuel, James Wilson, Serdar Turkarslan, Maryann Ruiz, Sean M Gibbons, Kristopher A Hunt, Nejc Stopnisek, Manfred Auer, Marcin Zemla, David A Stahl, Nitin S Baliga
Origin of biogeographically distinct ecotypes during laboratory evolution. Nature communications 15 (1) (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature communications 15 (1) (2024)
Nick Quinn-Bohmann, Tomasz Wilmanski, Katherine Ramos Sarmiento, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Erin M Ostrem, Ophelia S Venturelli, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature microbiology 9 (7) (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. bioRxiv : the preprint server for biology (2024)
Nick Quinn-Bohmann, Jose A Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, Sean M Gibbons
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC biology 22 (1) (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature communications 15 (1) (2024)
Christian Diener, Sean M Gibbons
Metagenomic estimation of dietary intake from human stool. bioRxiv : the preprint server for biology (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature communications 15 (1) (2024)
Nick Quinn-Bohmann, Tomasz Wilmanski, Katherine Ramos Sarmiento, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Erin M Ostrem, Ophelia S Venturelli, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature microbiology 9 (7) (2024)
Christian Diener, Sean M Gibbons
Metagenomic estimation of dietary intake from human stool. bioRxiv : the preprint server for biology (2024)
Christian Diener, Sean M Gibbons
Metagenomic estimation of dietary intake from human stool. bioRxiv : the preprint server for biology (2024)
Nick Quinn-Bohmann, Tomasz Wilmanski, Katherine Ramos Sarmiento, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Erin M Ostrem, Ophelia S Venturelli, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature microbiology (2024)
Nick Quinn-Bohmann, Tomasz Wilmanski, Katherine Ramos Sarmiento, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Erin M Ostrem, Ophelia S Venturelli, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut. Nature microbiology 9 (7) (2024)
Nick Quinn-Bohmann, Jose A Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, Sean M Gibbons
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC biology 22 (1) (2024)
Nick Quinn-Bohmann, Jose A Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, Sean M Gibbons
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC biology 22 (1) (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. bioRxiv : the preprint server for biology (2024)
Alice E Kane, Karthikeyani Chellappa, Michael B Schultz, Matthew Arnold, Jien Li, Joao Amorim, Christian Diener, Dantong Zhu, Sarah J Mitchell, Patrick Griffin, Xiao Tian, Christopher Petty, Ryan Conway, Katie Walsh, Lukas Shelerud, Charlotte Duesing, Amber L Mueller, Karlin Li, Maeve McNamara, Rafaella T Shima, James Mitchell, Michael S Bonkowski, Rafael de Cabo, Sean M Gibbons, Lindsay E Wu, Yuji Ikeno, Joseph A Baur, Luis Rajman, David A Sinclair
Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner. bioRxiv : the preprint server for biology (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. Nature communications 15 (1) (2024)
Jacob J Valenzuela, Selva Rupa Christinal Immanuel, James Wilson, Serdar Turkarslan, Maryann Ruiz, Sean M Gibbons, Kristopher A Hunt, Nejc Stopnisek, Manfred Auer, Marcin Zemla, David A Stahl, Nitin S Baliga
Origin of biogeographically distinct ecotypes during laboratory evolution. Nature communications 15 (1) (2024)
Nick Quinn-Bohmann, Jose A Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, Sean M Gibbons
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease. BMC biology 22 (1) (2024)
Jordy Evan Sulaiman, Jaron Thompson, Yili Qian, Eugenio I Vivas, Christian Diener, Sean M Gibbons, Nasia Safdar, Ophelia S Venturelli
Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes. bioRxiv : the preprint server for biology (2024)
Alex Carr, Nitin S Baliga, Christian Diener, Sean M Gibbons
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. bioRxiv : the preprint server for biology (2023)
Tomasz Wilmanski, Sean M Gibbons, Nathan D Price
Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nature aging 2 (10) (2023)
Alex Carr, Nitin S Baliga, Christian Diener, Sean M Gibbons
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. bioRxiv : the preprint server for biology (2023)
Nick Bohmann, Tomasz Wilmanski, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut. bioRxiv : the preprint server for biology (2023)
Kengo Watanabe, Tomasz Wilmanski, Christian Diener, John C Earls, Anat Zimmer, Briana Lincoln, Jennifer J Hadlock, Jennifer C Lovejoy, Sean M Gibbons, Andrew T Magis, Leroy Hood, Nathan D Price, Noa Rappaport
Multiomic signatures of body mass index identify heterogeneous health phenotypes and responses to a lifestyle intervention. Nature medicine (2023)
Nick Bohmann, Tomasz Wilmanski, Lisa Levy, Johanna W Lampe, Thomas Gurry, Noa Rappaport, Christian Diener, Sean M Gibbons
Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut. bioRxiv : the preprint server for biology (2023)
Christian Diener, Sean M Gibbons
More is Different: Metabolic Modeling of Diverse Microbial Communities. mSystems (2023)
Vanessa Rossetto Marcelino, Caitlin Welsh, Christian Diener, Emily L Gulliver, Emily L Rutten, Remy B Young, Edward M Giles, Sean M Gibbons, Chris Greening, Samuel C Forster
Disease-specific loss of microbial cross-feeding interactions in the human gut. Nature communications 14 (1) (2023)
Alex Carr, Nitin S Baliga, Christian Diener, Sean M Gibbons
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut. bioRxiv : the preprint server for biology (2023)
Katherine Ramos Sarmiento, Alex Carr, Christian Diener, Kenneth J Locey, Sean M Gibbons
Island biogeography theory and the gut: why taller people tend to harbor more diverse gut microbiomes. bioRxiv : the preprint server for biology (2023)
Tomasz Wilmanski, Sean M Gibbons, Nathan D Price
Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nature aging 2 (10) (2023)
Tomasz Wilmanski, Sean M Gibbons, Nathan D Price
Healthy aging and the human gut microbiome: why we cannot just turn back the clock. Nature aging 2 (10) (2023)
Joe L Lim, Christian Diener, James Wilson, Jacob J Valenzuela, Nitin S Baliga, Sean M Gibbons
Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. Nature communications 14 (1) (2023)
James P Johnson, Christian Diener, Anne E Levine, Tomasz Wilmanski, David L Suskind, Alexandra Ralevski, Jennifer J Hadlock, Andrew T Magis, Leroy E Hood, Noa Rappaport, Sean M Gibbons
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function. bioRxiv : the preprint server for biology (2023)
Tomasz Wilmanski, Noa Rappaport, Christian Diener, Sean M Gibbons, Nathan D Price
From taxonomy to metabolic output: what factors define gut microbiome health? Gut microbes 13 (1) (2022)
Christian Diener, Chengzhen L Dai, Tomasz Wilmanski, Priyanka Baloni, Brett Smith, Noa Rappaport, Leroy Hood, Andrew T Magis, Sean M Gibbons
Genome-microbiome interplay provides insight into the determinants of the human blood metabolome. Nature metabolism 4 (11) (2022)
Sean M Gibbons, Thomas Gurry, Johanna W Lampe, Anirikh Chakrabarti, Veerle Dam, Amandine Everard, Almudena Goas, Gabriele Gross, Michiel Kleerebezem, Jonathan Lane, Johanna Maukonen, Ana Lucia Barretto Penna, Bruno Pot, Ana M Valdes, Gemma Walton, Adrienne Weiss, Yoghatama Cindya Zanzer, Naomi V Venlet, Michela Miani
Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions. Advances in nutrition (Bethesda, Md.) 13 (5) (2022)
Christian Diener, Anna C H Hoge, Sean M Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L Moritz, Susan E Erdman, Sean M Gibbons
Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut. Communications biology 4 (1) (2021)
Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gwênlyn Glusman, Max Robinson, Bernhard O Palsson, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, Nathan D Price
Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nature metabolism 3 (2) (2021)
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, José Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, William Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Lynn M Schriml, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, Emiley A Eloe-Fadrosh
Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities". mSystems 6 (3) (2021)
Anne E Otwell, Alex V Carr, Erica L W Majumder, Maryann K Ruiz, Regina L Wilpiszeski, Linh T Hoang, Bill Webb, Serdar Turkarslan, Sean M Gibbons, Dwayne A Elias, David A Stahl, Gary Siuzdak, Nitin S Baliga
Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification. mSystems 6 (1) (2021)
Pajau Vangay, Josephine Burgin, Anjanette Johnston, Kristen L Beck, Daniel C Berrios, Kai Blumberg, Shane Canon, Patrick Chain, John-Marc Chandonia, Danielle Christianson, Sylvain V Costes, Joan Damerow, William D Duncan, José Pablo Dundore-Arias, Kjiersten Fagnan, Jonathan M Galazka, Sean M Gibbons, David Hays, William Judson Hervey, Bin Hu, Bonnie L Hurwitz, Pankaj Jaiswal, Marcin P Joachimiak, Linda Kinkel, Joshua Ladau, Stanton L Martin, Lee Ann McCue, Kayd Miller, Nigel Mouncey, Chris Mungall, Evangelos Pafilis, T B K Reddy, Lorna Richardson, Simon Roux, Lynn M. Schriml, Justin P Shaffer, Jagadish Chandrabose Sundaramurthi, Luke R Thompson, Ruth E Timme, Jie Zheng, Elisha M Wood-Charlson, Emiley A Eloe-Fadrosh
Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. mSystems 6 (1) (2021)
Christian Diener, Shizhen Qin, Yong Zhou, Sushmita Patwardhan, Li Tang, Jennifer C Lovejoy, Andrew T Magis, Nathan D Price, Leroy Hood, Sean M Gibbons
Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans. mSystems 6 (5) (2021)
Roie Levy, Andrew T Magis, John C Earls, Ohad Manor, Tomasz Wilmanski, Jennifer Lovejoy, Sean M Gibbons, Gilbert S Omenn, Leroy E Hood, Nathan D Price
Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. Proceedings of the National Academy of Sciences of the United States of America 117 (24) (2020)
Ohad Manor, Chengzhen L Dai, Sergey A Kornilov, Brett Smith, Nathan D Price, Jennifer C Lovejoy, Sean M Gibbons, Andrew T Magis
Health and disease markers correlate with gut microbiome composition across thousands of people. Nature communications 11 (1) (2020)
Christian Diener, Sean M Gibbons, Resendis-Antonio Osbaldo
MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota. mSystems 5 (1) (2020)
M Poyet, M Groussin, Sean M Gibbons, J Avila-Pacheco, X Jiang, S M Kearney, A R Perrotta, Brittany Berdy, S Zhao, T D Lieberman, P K Swanson, M Smith, S Roesemann, J E Alexander, S A Rich, J Livny, H Vlamakis, Andrew T Chan, K Bullock, A Deik, J Scott, K A Pierce, R J Xavier, Eric John Alm
A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nature medicine 25 (9) (2019)
Alex Carr, Christian Diener, Nitin S Baliga, Sean M Gibbons
Use and abuse of correlation analyses in microbial ecology. The ISME journal 13 (11) (2019)
Sean M Gibbons
Defining Microbiome Health through a Host Lens. mSystems 4 (3) (2019)
Tomasz Wilmanski, Noa Rappaport, John C Earls, Andrew T Magis, Ohad Manor, Jennifer Lovejoy, Gilbert S Omenn, Leroy E Hood, Sean M Gibbons, Nathan D Price
Blood metabolome predicts gut microbiome α-diversity in humans. Nature biotechnology 37 (10) (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)
Sean M Gibbons, Sean M Kearney, Chris S Smillie, Eric J Alm
Two dynamic regimes in the human gut microbiome. PLoS computational biology 13 (2) (2017)

Sean M Gibbons.css-eqlu8i{font-size:small;padding-left:4px;} (S M Gibbons)

Publication Activity (10 Years)

Top Topics

Top Venues

Sean M Gibbons (S M Gibbons)