| American gut: an open platform for citizen science microbiome research D McDonald, E Hyde, JW Debelius, JT Morton, A Gonzalez, G Ackermann, ... Msystems 3 (3), 10.1128/msystems. 00031-18, 2018 | 678 | 2018 |
| Reconstructing organisms in silico: genome-scale models and their emerging applications X Fang, CJ Lloyd, BO Palsson Nature Reviews Microbiology 18 (12), 731-743, 2020 | 202 | 2020 |
| Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits Y Seif, E Kavvas, JC Lachance, JT Yurkovich, SP Nuccio, X Fang, ... Nature communications 9 (1), 3771, 2018 | 116 | 2018 |
| Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities X Fang, A Sastry, N Mih, D Kim, J Tan, JT Yurkovich, CJ Lloyd, Y Gao, ... Proceedings of the National Academy of Sciences 114 (38), 10286-10291, 2017 | 107 | 2017 |
| Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 Y Gao, JT Yurkovich, SW Seo, I Kabimoldayev, A Dräger, K Chen, ... Nucleic acids research 46 (20), 10682-10696, 2018 | 96 | 2018 |
| A workflow for generating multi-strain genome-scale metabolic models of prokaryotes CJ Norsigian, X Fang, Y Seif, JM Monk, BO Palsson Nature protocols 15 (1), 1-14, 2020 | 63 | 2020 |
| Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient X Fang, JM Monk, S Nurk, M Akseshina, Q Zhu, C Gemmell, ... Frontiers in microbiology 9, 2559, 2018 | 50 | 2018 |
| Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli B Du, L Yang, CJ Lloyd, X Fang, BO Palsson PLoS computational biology 15 (12), e1007525, 2019 | 45 | 2019 |
| A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 A Santos-Zavaleta, M Sánchez-Pérez, H Salgado, ... BMC biology 16 (1), 1-12, 2018 | 45 | 2018 |
| Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa X Fang, JM Monk, N Mih, B Du, AV Sastry, E Kavvas, Y Seif, L Smarr, ... BMC systems biology 12, 1-10, 2018 | 45 | 2018 |
| Adaptive laboratory evolution of Escherichia coli under acid stress B Du, CA Olson, AV Sastry, X Fang, PV Phaneuf, K Chen, M Wu, R Szubin, ... Microbiology 166 (2), 141, 2020 | 38 | 2020 |
| Gastrointestinal surgery for inflammatory bowel disease persistently lowers microbiome and metabolome diversity X Fang, Y Vázquez-Baeza, E Elijah, F Vargas, G Ackermann, ... Inflammatory bowel diseases 27 (5), 603-616, 2021 | 32 | 2021 |
| Pangenome flux balance analysis toward panphenomes CJ Norsigian, X Fang, BO Palsson, JM Monk The pangenome: diversity, dynamics and evolution of genomes, 219-232, 2020 | 14 | 2020 |
| Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi IS Shiratsubaki, X Fang, ROO Souza, BO Palsson, AM Silber, ... PLoS neglected tropical diseases 14 (10), e0008728, 2020 | 13 | 2020 |
| Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen CS Jensen, CJ Norsigian, X Fang, XC Nielsen, JJ Christensen, ... Frontiers in Genetics 11, 116, 2020 | 13 | 2020 |
| 23ME-00610, a genetically informed, first-in-class antibody targeting CD200R1 to enhance antitumor T cell function J Fenaux, X Fang, Y Huang, C Melero, C Bonnans, EL Lowe, T Palumbo, ... Oncoimmunology 12 (1), 2217737, 2023 | 8 | 2023 |
| Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes N Mih, JM Monk, X Fang, E Catoiu, D Heckmann, L Yang, BO Palsson BMC bioinformatics 21, 1-23, 2020 | 8 | 2020 |
| Discovery of CD200R1 as a novel immuno-oncology target using pleiotropic signals from 23andme’s genetic and health survey database X Fang, WJ Chung, J Fenaux, A Chen, N Batada, M Schmidt, SR Majeed, ... AACR Annual Meeting, 2022 | 3 | 2022 |
| Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity (vol 27, pg 1368, 2021) X Fang, Y Vazquez-Baeza, E Elijah, F Vargas, G Ackermann, ... INFLAMMATORY BOWEL DISEASES 27 (8), 1368-1368, 2021 | 3 | 2021 |
| Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic … A Santos-Zavaleta, M Sánchez-Pérez, H Salgado, ... bioRxiv, 219006, 2017 | 1 | 2017 |
