2026
Antisense transcription reveals disease-associated adaptations in the human gut microbiome
Marie-Madlen Pust, Ahmed M. T. Mohamed, Martin Stražar, Aranzazu Arias-Rojas, Edward Cunningham-Oakes, Eric M. Brown, Amanda Bumber, Gleb Pishchany, Chenhao Li, Ashwin N. Ananthakrishnan, Alistair C. Darby, Hera Vlamakis, Damian R. Plichta, Ramnik J. Xavier
Nature Microbiology 11, 2464-2477
2025
Protein language models uncover carbohydrate-active enzyme function in metagenomics
Kumar Thurimella, Ahmed MT Mohamed, Chenhao Li, Tommi Vatanen, Daniel B Graham, Róisín M Owens, Sabina Leanti La Rosa, Damian R Plichta, Sergio Bacallado, Ramnik J Xavier
BMC bioinformatics 26, 285
Discovery of the metalloenzyme IsmB revises a pathway for coprostanol formation by the human gut microbiome
Antonio Tinoco, Chenhao Li, Jai K Khurana, Bryan Bañuelos Jara, Damian R Plichta, Douglas J Kenny, Ramnik J Xavier, Emily P Balskus
bioRxiv , 2025.12. 29.696961
Autoimmune disease risk gene ANKRD55 promotes TH17 effector function through metabolic modulation
Jinjin Xu, Lingjia Kong, Elizabeth A Creasey, Sneha Rath, Lei Deng, Julian Avila-Pacheco, Chenhao Li, Blayne A Oliver, Tyler T Dao, Angela R Shih, Mark J Daly, Alex K Shalek, Clary B Clish, Daniel B Graham, Jacques Deguine, Ramnik J Xavier
Journal of Experimental Medicine 222, e20250185
2024
Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria
Chenhao Li, Martin Stražar, Ahmed MT Mohamed, Julian A Pacheco, Rebecca L Walker, Tina Lebar, Shijie Zhao, Julia Lockart, Andrea Dame, Kumar Thurimella, Sarah Jeanfavre, Eric M Brown, Qi Yan Ang, Brittany Berdy, Dallis Sergio, Rachele Invernizzi, Antonio Tinoco, Gleb Pishchany, Ramachandran S Vasan, Emily Balskus, Curtis Huttenhower, Hera Vlamakis, Clary Clish, Stanley Y Shaw, Damian R Plichta, Ramnik J Xavier
Cell 187, 1834-1852. e19
Spatially restricted immune and microbiota-driven adaptation of the gut
Toufic Mayassi, Chenhao Li, Åsa Segerstolpe, Eric M Brown, Rebecca Weisberg, Toru Nakata, Hiroshi Yano, Paula Herbst, David Artis, Daniel B Graham, Ramnik J Xavier
Nature 636, 447-456
Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
Aarthi Ravikrishnan, Indrik Wijaya, Eileen Png, Kern Rei Chng, Eliza Xin Pei Ho, Amanda Hui Qi Ng, Ahmad Nazri Mohamed Naim, Jean-Sebastien Gounot, Shou Ping Guan, Jasinda Lee Hanqing, Lihuan Guan, Chenhao Li, Jia Yu Koh, Paola Florez de Sessions, Woon-Puay Koh, Lei Feng, Tze Pin Ng, Anis Larbi, Andrea B Maier, Brian K Kennedy, Niranjan Nagarajan
Nature Communications 15, 7751
2023
Genetic vulnerability to Crohn’s disease reveals a spatially resolved epithelial restitution program
Toru Nakata, Chenhao Li, Toufic Mayassi, Helen Lin, Koushik Ghosh, Åsa Segerstolpe, Emma L Diamond, Paula Herbst, Tommaso Biancalani, Shreya Gaddam, Saurabh Parkar, Ziqing Lu, Alok Jaiswal, Bihua Li, Elizabeth A Creasey, Ariel Lefkovith, Mark J Daly, Daniel B Graham, Ramnik J Xavier
Science translational medicine 15, eadg5252