Academic lineage
- Bernhard Ø Palsson - Ph.D. student
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity
- Xin Fang, Yoshiki Vázquez-Baeza, Emmanuel Elijah, …, William J Sandborn, Rob Knight, Brigid S Boland
- Inflamm Bowel Dis, 10.1093/ibd/izaa262
Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi
- Isabel S Shiratsubaki, Xin Fang, Rodolpho O O Souza, Bernhard O Palsson, Ariel M Silber, Jair L Siqueira-Neto
- PLoS Negl Trop Dis, 10.1371/journal.pntd.0008728
Reconstructing organisms in silico: genome-scale models and their emerging applications
- Xin Fang, Colton J Lloyd, Bernhard O Palsson
- Nat Rev Microbiol, 10.1038/s41579-020-00440-4
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
- Nathan Mih, Jonathan M Monk, Xin Fang, …, David Heckmann, Laurence Yang, Bernhard O Palsson
- BMC Bioinformatics, 10.1186/s12859-020-3505-y
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen
- Christian S Jensen, Charles J Norsigian, Xin Fang, …, Jens Jørgen Christensen, Bernhard O Palsson, Jonathan M Monk
- None, 10.3389/fgene.2020.00116
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes
- Charles J Norsigian, Xin Fang, Yara Seif, Jonathan M Monk, Bernhard O Palsson
- Nat Protoc, 10.1038/s41596-019-0254-3
Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli
- Bin Du, Laurence Yang, Colton J Lloyd, Xin Fang, Bernhard O Palsson
- PLoS Comput Biol, 10.1371/journal.pcbi.1007525
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits
- Yara Seif, Erol Kavvas, Jean-Christophe Lachance, …, Manuela Raffatellu, Bernhard O Palsson, Jonathan M Monk
- Nat Commun, 10.1038/s41467-018-06112-5
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
- Ye Gao, James T Yurkovich, Sang Woo Seo, …, Byung-Kwan Cho, Donghyuk Kim, Bernhard O Palsson
- Nucleic Acids Res, 10.1093/nar/gky752
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
- Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, …, Bernhard O Palsson, James E Galagan, Julio Collado-Vides
- BMC Biol, 10.1186/s12915-018-0555-y
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
- Xin Fang, Jonathan M Monk, Nathan Mih, …, Yara Seif, Larry Smarr, Bernhard O Palsson
- None, 10.1186/s12918-018-0587-5
American Gut: an Open Platform for Citizen Science Microbiome Research
- Daniel McDonald, Embriette Hyde, Justine W Debelius, …, Elaine Wolfe, Qiyun Zhu, Rob Knight
- mSystems, 10.1128/msystems.00031-18