{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:38:24Z","timestamp":1762522704608,"version":"3.37.3"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,4,30]],"date-time":"2022-04-30T00:00:00Z","timestamp":1651276800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2020YFA0908300"],"award-info":[{"award-number":["2020YFA0908300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project","award":["TSBICIP-PTJS-001"],"award-info":[{"award-number":["TSBICIP-PTJS-001"]}]},{"DOI":"10.13039\/501100004739","name":"Youth Innovation Promotion Association CAS","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004739","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Cellular regulation is inherently complex, and one particular cellular function is often controlled by a cascade of different types of regulatory interactions. For example, the activity of a transcription factor (TF), which regulates the expression level of downstream genes through transcriptional regulation, can be regulated by small molecules through compound\u2013protein interactions. To identify such complex regulatory cascades, traditional relational databases require ineffective additional operations and are computationally expensive. In contrast, graph databases are purposefully developed to execute such deep searches efficiently. Here, we present ERMer (E. coli Regulation Miner), the first cloud platform for mining the regulatory landscape of Escherichia coli based on graph databases. Combining the AWS Neptune graph database, AWS lambda function, and G6 graph visualization engine enables quick search and visualization of complex regulatory cascades\/patterns. Users can also interactively navigate the E. coli regulatory landscape through ERMer. Furthermore, a Q&amp;A module is included to showcase the power of graph databases in answering complex biological questions through simple queries. The backend graph model can be easily extended as new data become available. In addition, the framework implemented in ERMer can be easily migrated to other applications or organisms. ERMer is available at https:\/\/ermer.biodesign.ac.cn\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac288","type":"journal-article","created":{"date-parts":[[2022,4,26]],"date-time":"2022-04-26T13:27:19Z","timestamp":1650979639000},"page":"W298-W304","source":"Crossref","is-referenced-by-count":5,"title":["ERMer: a serverless platform for navigating, analyzing, and visualizing<i>Escherichia coli<\/i>regulatory landscape through graph database"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8160-2585","authenticated-orcid":false,"given":"Zhitao","family":"Mao","sequence":"first","affiliation":[{"name":"Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin \u00a0 300308 , PR China"},{"name":"National Technology Innovation Center of Synthetic Biology , Tianjin \u00a0 300308 , PR\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin \u00a0 300308 , PR China"},{"name":"National Technology Innovation Center of Synthetic Biology , Tianjin \u00a0 300308 , PR\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoran","family":"Li","sequence":"additional","affiliation":[{"name":"Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin \u00a0 300308 , PR China"},{"name":"National Technology Innovation Center of Synthetic Biology , Tianjin \u00a0 300308 , PR\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixin","family":"Huang","sequence":"additional","affiliation":[{"name":"AWS Professional Services , No.576 West Tianshan Road , Shanghai \u00a0 200335 , PR China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"AWS Solution Architect Sector, Amazon Web Service Inc , Beijing \u00a0 100016 , PR China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9852-910X","authenticated-orcid":false,"given":"Xiaoping","family":"Liao","sequence":"additional","affiliation":[{"name":"Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin \u00a0 300308 , PR China"},{"name":"National Technology Innovation Center of Synthetic Biology , Tianjin \u00a0 300308 , PR\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongwu","family":"Ma","sequence":"additional","affiliation":[{"name":"Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin \u00a0 300308 , PR China"},{"name":"National Technology Innovation Center of Synthetic Biology , Tianjin \u00a0 300308 , PR\u00a0China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,4,30]]},"reference":[{"key":"2022070423593040900_B1","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1109\/TAI.2021.3076021","article-title":"Graph learning: a survey","volume":"2","author":"Xia","year":"2021","journal-title":"IEEE Trans. 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