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Employment (1)

University of California, San Diego: La Jolla, US

Post-doctor (Bioengineering)
Employment
Source: Self-asserted source
Ye Gao

Education and qualifications (3)

University of California, San Diego: La Jolla, US

2014-09-22 to 2020-12-18 | PhD (Biological Sciences)
Education
Source: Self-asserted source
Ye Gao

Northwestern University: Evanston, US

2012-09-20 to 2014-06-23 | Master
Education
Source: Self-asserted source
Ye Gao

Sun Yat-sen University: Guangzhou, CN

2004-09-01 to 2008-06-30 | Bachelor
Education
Source: Self-asserted source
Ye Gao

Professional activities (1)

American Society for Nutrition: Md., Md., US

Membership
Source: Self-asserted source
Ye Gao

Works (25)

A multi-scale expression and regulation knowledge base for <i>Escherichia coli</i>

Nucleic Acids Research
2023-09-15 | Journal article
DOI: 10.1093/nar/gkad750
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Cameron R Lamoureux; Katherine T Decker; Anand V Sastry; Kevin Rychel; Ye Gao; John Luke McConn; Daniel C Zielinski; Bernhard Palsson
Source: Self-asserted source
Ye Gao

Elucidating the CodY regulon in <i>Staphylococcus aureus</i> USA300 substrains TCH1516 and LAC.

mSystems
2023-06-13 | Journal article | Author
DOI: 10.1128/msystems.00279-23
PMID: 37310465
PMC: PMC10470025
Contributors: Ye Gao; Poudel S; Seif Y; Shen Z; Palsson BO
Source: Self-asserted source
Ye Gao

The <i>Escherichia coli</i> Fur pan-regulon has few conserved but many unique regulatory targets

Nucleic Acids Research
2023-05-08 | Journal article
DOI: 10.1093/nar/gkad253
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Ye Gao; Ina Bang; Yara Seif; Donghyuk Kim; Bernhard Palsson
Source: Self-asserted source
Ye Gao

Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling

Briefings in Bioinformatics
2023-03-19 | Journal article
DOI: 10.1093/bib/bbad024
Part of ISSN: 1467-5463
Part of ISSN: 1477-4054
Contributors: Ina Bang; Sang-Mok Lee; Seojoung Park; Joon Young Park; Linh Khanh Nong; Ye Gao; Bernhard O Palsson; Donghyuk Kim
Source: Self-asserted source
Ye Gao

Coordination of CcpA and CodY Regulators in Staphylococcus aureus USA300 Strains.

mSystems
2022-11-02 | Journal article
DOI: 10.1128/msystems.00480-22
PMID: 36321827
PMC: PMC9765215
Contributors: Poudel S; Hefner Y; Szubin R; Sastry A; Gao Y; Nizet V; Palsson BO
Source: Self-asserted source
Ye Gao

A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

Scientific Reports
2022-05-04 | Journal article
DOI: 10.1038/s41598-022-11134-7
Part of ISSN: 2045-2322
Contributors: Irina A. Rodionova; Ye Gao; Jonathan Monk; Ying Hefner; Nicholas Wong; Richard Szubin; Hyun Gyu Lim; Dmitry A. Rodionov; Zhongge Zhang; Milton H. Saier et al.
Source: Self-asserted source
Ye Gao

proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms

Nucleic Acids Research
2022-01-07 | Journal article
DOI: 10.1093/nar/gkab1043
Contributors: Katherine T Decker; Ye Gao; Kevin Rychel; Tahani Al Bulushi; Siddharth M Chauhan; Donghyuk Kim; Byung-Kwan Cho; Bernhard O Palsson
Source: check_circle
Crossref

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

Nucleic Acids Research
2021-09-27 | Journal article
DOI: 10.1093/nar/gkab735
Contributors: Ye Gao; Hyun Gyu Lim; Hans Verkler; Richard Szubin; Daniel Quach; Irina Rodionova; Ke Chen; James T Yurkovich; Byung-Kwan Cho; Bernhard O Palsson
Source: check_circle
Crossref

Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.

Communications biology
2021-08-19 | Journal article
DOI: 10.1038/s42003-021-02516-0
PMID: 34413462
PMC: PMC8376909
Source: Self-asserted source
Ye Gao

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.

PLoS computational biology
2021-01-19 | Journal article
DOI: 10.1371/journal.pcbi.1008596
PMID: 33465077
PMC: PMC7846111
Source: Self-asserted source
Ye Gao

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
2021-01-01 | Journal article
DOI: 10.1073/pnas.2021171118
PMID: 33372147
PMC: PMC7812831
Source: Self-asserted source
Ye Gao

Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships.

mSystems
2020-11-10 | Journal article
DOI: 10.1128/msystems.00980-20
PMID: 33172971
PMC: PMC7657598
Source: Self-asserted source
Ye Gao

The Bitome: digitized genomic features reveal fundamental genome organization.

Nucleic acids research
2020-10-01 | Journal article
DOI: 10.1093/nar/gkaa774
PMID: 32976587
PMC: PMC7544223
Source: Self-asserted source
Ye Gao

The Escherichia coli transcriptome mostly consists of independently regulated modules.

Nature communications
2019-12-04 | Journal article
DOI: 10.1038/s41467-019-13483-w
PMID: 31797920
PMC: PMC6892915
Source: Self-asserted source
Ye Gao

Adaptive laboratory evolution of <i>Escherichia coli</i> under acid stress.

Microbiology (Reading, England)
2019-10-18 | Journal article
DOI: 10.1099/mic.0.000867
PMID: 31625833
PMC: PMC7273327
Source: Self-asserted source
Ye Gao

Cellular responses to reactive oxygen species are predicted from molecular mechanisms.

Proceedings of the National Academy of Sciences of the United States of America
2019-07-03 | Journal article
DOI: 10.1073/pnas.1905039116
PMID: 31270234
PMC: PMC6628673
Source: Self-asserted source
Ye Gao

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Nucleic acids research
2018-11-01 | Journal article
DOI: 10.1093/nar/gky752
PMID: 30137486
PMC: PMC6237786
Source: Self-asserted source
Ye Gao

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.

Nucleic acids research
2018-04-01 | Journal article
DOI: 10.1093/nar/gky069
PMID: 29394395
PMC: PMC5888115
Source: Self-asserted source
Ye Gao

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation.

Proceedings of the National Academy of Sciences of the United States of America
2017-10-10 | Journal article
DOI: 10.1073/pnas.1705524114
PMID: 29073085
PMC: PMC5664499
Source: Self-asserted source
Ye Gao

Global transcriptional regulatory network for <i>Escherichia coli</i> robustly connects gene expression to transcription factor activities.

Proceedings of the National Academy of Sciences of the United States of America
2017-09-05 | Journal article
DOI: 10.1073/pnas.1702581114
PMID: 28874552
PMC: PMC5617254
Source: Self-asserted source
Ye Gao

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655.

Scientific reports
2017-05-19 | Journal article
DOI: 10.1038/s41598-017-02110-7
PMID: 28526842
PMC: PMC5438342
Source: Self-asserted source
Ye Gao

Isolation of novel sequences targeting highly variable viral protein hemagglutinin

MethodsX
2015 | Journal article
DOI: 10.1016/j.mex.2015.02.005
Part of ISSN: 2215-0161
Contributors: Zhiwu Xu; Jieyu Wu; Fan Feng; Xiaoxiao Zhang; Xiaoqian Ma; Man Tang; Yan Huang; Ying Zhang; Yongchang Cao; Weiguo Cao et al.
Source: Self-asserted source
Ye Gao

Generation of Sequence Variants Via Accelerated Molecular Evolution Methods

Recent Patents on DNA &amp; Gene Sequences
2013-07-01 | Journal article
DOI: 10.2174/1872215611307020009
Part of ISSN: 1872-2156
Contributors: Min Fu; Xiaoxiao Zhang; Xingqiang Lai; Xiaoxuan Wu; Fan Feng; Jingli Peng; Hongyu Zhong; Ying Zhang; Yuan Wang; Qingfeng Zhou et al.
Source: Self-asserted source
Ye Gao

The ClpP protease homologue is required for the transmission traits and cell division of the pathogen Legionella pneumophila

BMC Microbiology
2010-12 | Journal article
DOI: 10.1186/1471-2180-10-54
Part of ISSN: 1471-2180
Contributors: Xiang-hui Li; Yong-lun Zeng; Ye Gao; Xiao-cong Zheng; Qin-fen Zhang; Shi-ning Zhou; Yong-jun Lu
Source: Self-asserted source
Ye Gao

The anthracenedione compound bostrycin induces mitochondria-mediated apoptosis in the yeast Saccharomyces cerevisiae

FEMS Yeast Research
2010-04-12 | Journal article
DOI: 10.1111/j.1567-1364.2010.00615.x
Part of ISSN: 1567-1356
Part of ISSN: 1567-1364
Contributors: Chunling Xu; Jiafeng Wang; Ye Gao; Huangyu Lin; Lin Du; Shanshan Yang; Simei Long; Zhigang She; Xiaoling Cai; Shining Zhou et al.
Source: Self-asserted source
Ye Gao
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