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RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.
Santos-Zavaleta A, Salgado H, Gama-Castro S, Sánchez-Pérez M, Gómez-Romero L, Ledezma-Tejeida D, García-Sotelo JS, Alquicira-Hernández K, Muñiz-Rascado LJ, Peña-Loredo P, Ishida-Gutiérrez C, Velázquez-Ramírez DA, Del Moral-Chávez V, Bonavides-Martínez C, Méndez-Cruz CF, Galagan J, Collado-Vides J. Santos-Zavaleta A, et al. Among authors: galagan j. Nucleic Acids Res. 2019 Jan 8;47(D1):D212-D220. doi: 10.1093/nar/gky1077. Nucleic Acids Res. 2019. PMID: 30395280 Free PMC article.
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.
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. Santos-Zavaleta A, et al. Among authors: galagan je. BMC Biol. 2018 Aug 16;16(1):91. doi: 10.1186/s12915-018-0555-y. BMC Biol. 2018. PMID: 30115066 Free PMC article.
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.
Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. Tierrafría VH, et al. Among authors: galagan je. Microb Genom. 2022 May;8(5):mgen000833. doi: 10.1099/mgen.0.000833. Microb Genom. 2022. PMID: 35584008 Free PMC article.
Redefining fundamental concepts of transcription initiation in bacteria.
Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Mejía-Almonte C, et al. Among authors: galagan je. Nat Rev Genet. 2020 Nov;21(11):699-714. doi: 10.1038/s41576-020-0254-8. Epub 2020 Jul 14. Nat Rev Genet. 2020. PMID: 32665585 Free PMC article. Review.
Coordinated regulation of acid resistance in Escherichia coli.
Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE. Aquino P, et al. Among authors: galagan je. BMC Syst Biol. 2017 Jan 6;11(1):1. doi: 10.1186/s12918-016-0376-y. BMC Syst Biol. 2017. PMID: 28061857 Free PMC article.
The Mycobacterium tuberculosis regulatory network and hypoxia.
Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, Krueger A, Jaini S, Honda B, Yu WH, Hickey MJ, Zucker J, Garay C, Weiner B, Sisk P, Stolte C, Winkler JK, Van de Peer Y, Iazzetti P, Camacho D, Dreyfuss J, Liu Y, Dorhoi A, Mollenkopf HJ, Drogaris P, Lamontagne J, Zhou Y, Piquenot J, Park ST, Raman S, Kaufmann SH, Mohney RP, Chelsky D, Moody DB, Sherman DR, Schoolnik GK. Galagan JE, et al. Nature. 2013 Jul 11;499(7457):178-83. doi: 10.1038/nature12337. Epub 2013 Jul 3. Nature. 2013. PMID: 23823726 Free PMC article.
Transcription Factor Binding Site Mapping Using ChIP-Seq.
Jaini S, Lyubetskaya A, Gomes A, Peterson M, Tae Park S, Raman S, Schoolnik G, Galagan J. Jaini S, et al. Among authors: galagan j. Microbiol Spectr. 2014 Apr;2(2). doi: 10.1128/microbiolspec.MGM2-0035-2013. Microbiol Spectr. 2014. PMID: 26105820 Free article. Review.
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