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Xin Fang - Publications

Affiliations: 
2020 University of California, San Diego, La Jolla, CA 
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16 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Fang X, Vázquez-Baeza Y, Elijah E, Vargas F, Ackermann G, Humphrey G, Lau R, Weldon KC, Sanders JG, Panitchpakdi M, Carpenter C, Jarmusch AK, Neill J, Miralles A, Dulai P, et al. Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. Inflammatory Bowel Diseases. PMID 33026068 DOI: 10.1093/ibd/izaa262  0.321
2020 Shiratsubaki IS, Fang X, Souza ROO, Palsson BO, Silber AM, Siqueira-Neto JL. Genome-scale metabolic models highlight stage-specific differences in essential metabolic pathways in Trypanosoma cruzi. Plos Neglected Tropical Diseases. 14: e0008728. PMID 33021977 DOI: 10.1371/journal.pntd.0008728  0.44
2020 Fang X, Lloyd CJ, Palsson BO. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nature Reviews. Microbiology. PMID 32958892 DOI: 10.1038/S41579-020-00440-4  0.785
2020 Mih N, Monk JM, Fang X, Catoiu E, Heckmann D, Yang L, Palsson BO. Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. Bmc Bioinformatics. 21: 162. PMID 32349661 DOI: 10.1186/S12859-020-3505-Y  0.765
2020 Jensen CS, Norsigian CJ, Fang X, Nielsen XC, Christensen JJ, Palsson BO, Monk JM. Reconstruction and Validation of a Genome-Scale Metabolic Model of (iCJ415), a Human Commensal and Opportunistic Pathogen. Frontiers in Genetics. 11: 116. PMID 32194617 DOI: 10.3389/Fgene.2020.00116  0.772
2019 Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BO. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nature Protocols. PMID 31863076 DOI: 10.1038/S41596-019-0254-3  0.756
2019 Du B, Yang L, Lloyd CJ, Fang X, Palsson BO. Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli. Plos Computational Biology. 15: e1007525. PMID 31809503 DOI: 10.1371/Journal.Pcbi.1007525  0.793
2019 Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Adaptive laboratory evolution of under acid stress. Microbiology (Reading, England). PMID 31625833 DOI: 10.1099/Mic.0.000867  0.754
2018 Wu X, Yang M, Fang X, Zhen S, Zhang J, Yang X, Qiao L, Yang Y, Zhang C. Expression and regulation of phenol-soluble modulins and enterotoxins in foodborne Staphylococcus aureus. Amb Express. 8: 187. PMID 30467730 DOI: 10.1186/s13568-018-0717-x  0.318
2018 Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, et al. Metagenomics-Based, Strain-Level Analysis of From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology. 9: 2559. PMID 30425690 DOI: 10.3389/Fmicb.2018.02559  0.704
2018 Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nature Communications. 9: 3771. PMID 30218022 DOI: 10.1038/S41467-018-06112-5  0.786
2018 Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655. Nucleic Acids Research. PMID 30137486 DOI: 10.1093/Nar/Gky752  0.721
2018 Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J. A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. Bmc Biology. 16: 91. PMID 30115066 DOI: 10.1186/S12915-018-0555-Y  0.509
2018 Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO. Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa. Bmc Systems Biology. 12: 66. PMID 29890970 DOI: 10.1186/S12918-018-0587-5  0.736
2017 Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874552 DOI: 10.1073/Pnas.1702581114  0.684
2012 Wu XQ, Yuan WM, Tian XJ, Fan B, Fang X, Ye JR, Ding XL. Specific and functional diversity of endophytic bacteria from pine wood nematode bursaphelenchus xylophilus with different virulence International Journal of Biological Sciences. 9: 34-44. PMID 23289015 DOI: 10.7150/ijbs.5071  0.321
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