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Ye Gao - Publications

Affiliations: 
2020 University of California, San Diego, La Jolla, CA 
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22 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
2023 Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn JL, Zielinski DC, Palsson BO. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Research. PMID 37713610 DOI: 10.1093/nar/gkad750  0.802
2023 Gao Y, Poudel S, Seif Y, Shen Z, Palsson BO. Elucidating the CodY regulon in USA300 substrains TCH1516 and LAC. Msystems. e0027923. PMID 37310465 DOI: 10.1128/msystems.00279-23  0.803
2023 Rodionova IA, Lim HG, Rodionov DA, Hutchison Y, Dalldorf C, Gao Y, Monk J, Palsson BO. CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in . Biorxiv : the Preprint Server For Biology. PMID 37292663 DOI: 10.1101/2023.05.16.541025  0.699
2023 Gao Y, Bang I, Seif Y, Kim D, Palsson BO. The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets. Nucleic Acids Research. PMID 37026477 DOI: 10.1093/nar/gkad253  0.794
2023 Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Briefings in Bioinformatics. PMID 36702751 DOI: 10.1093/bib/bbad024  0.64
2022 Poudel S, Hefner Y, Szubin R, Sastry A, Gao Y, Nizet V, Palsson BO. Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains. Msystems. e0048022. PMID 36321827 DOI: 10.1128/msystems.00480-22  0.814
2022 Rodionova IA, Gao Y, Monk J, Hefner Y, Wong N, Szubin R, Lim HG, Rodionov DA, Zhang Z, Saier MH, Palsson BO. A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli. Scientific Reports. 12: 7274. PMID 35508583 DOI: 10.1038/s41598-022-11134-7  0.837
2021 Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan SM, Kim D, Cho BK, Palsson BO. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Research. PMID 34791440 DOI: 10.1093/nar/gkab1043  0.712
2021 Gao Y, Lim HG, Verkler H, Szubin R, Quach D, Rodionova I, Chen K, Yurkovich JT, Cho BK, Palsson BO. Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo. Nucleic Acids Research. PMID 34428301 DOI: 10.1093/nar/gkab735  0.801
2021 Rodionova IA, Gao Y, Sastry A, Hefner Y, Lim HG, Rodionov DA, Saier MH, Palsson BO. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli. Communications Biology. 4: 991. PMID 34413462 DOI: 10.1038/s42003-021-02516-0  0.811
2021 Chen K, Anand A, Olson C, Sandberg TE, Gao Y, Mih N, Palsson BO. Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. Plos Computational Biology. 17: e1008596. PMID 33465077 DOI: 10.1371/journal.pcbi.1008596  0.776
2021 Kim GB, Gao Y, Palsson BO, Lee SY. DeepTFactor: A deep learning-based tool for the prediction of transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33372147 DOI: 10.1073/pnas.2021171118  0.499
2020 Choudhary KS, Kleinmanns JA, Decker K, Sastry AV, Gao Y, Szubin R, Seif Y, Palsson BO. Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships. Msystems. 5. PMID 33172971 DOI: 10.1128/mSystems.00980-20  0.785
2020 Lamoureux CR, Choudhary KS, King ZA, Sandberg TE, Gao Y, Sastry AV, Phaneuf PV, Choe D, Cho BK, Palsson BO. The Bitome: digitized genomic features reveal fundamental genome organization. Nucleic Acids Research. PMID 32976587 DOI: 10.1093/nar/gkaa774  0.766
2019 Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nature Communications. 10: 5536. PMID 31797920 DOI: 10.1038/S41467-019-13483-W  0.813
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  0.771
2019 Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences of the United States of America. PMID 31270234 DOI: 10.1073/Pnas.1905039116  0.635
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  0.786
2018 Kim D, Seo SW, Gao Y, Nam H, Guzman GI, Cho BK, Palsson BO. Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. Nucleic Acids Research. PMID 29394395 DOI: 10.1093/Nar/Gky069  0.792
2017 Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences of the United States of America. 114: 11548-11553. PMID 29073085 DOI: 10.1073/Pnas.1705524114  0.795
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  0.763
2017 Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Scientific Reports. 7: 2181. PMID 28526842 DOI: 10.1038/S41598-017-02110-7  0.82
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