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Page 1
The EcoCyc Database in 2021.
Keseler IM, Gama-Castro S, Mackie A, Billington R, Bonavides-Martínez C, Caspi R, Kothari A, Krummenacker M, Midford PE, Muñiz-Rascado L, Ong WK, Paley S, Santos-Zavaleta A, Subhraveti P, Tierrafría VH, Wolfe AJ, Collado-Vides J, Paulsen IT, Karp PD. Keseler IM, et al. Front Microbiol. 2021 Jul 28;12:711077. doi: 10.3389/fmicb.2021.711077. eCollection 2021. Front Microbiol. 2021. PMID: 34394059 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. 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.
Integrating Bacterial ChIP-seq and RNA-seq Data With SnakeChunks.
Rioualen C, Charbonnier-Khamvongsa L, Collado-Vides J, van Helden J. Rioualen C, et al. Curr Protoc Bioinformatics. 2019 Jun;66(1):e72. doi: 10.1002/cpbi.72. Epub 2019 Feb 20. Curr Protoc Bioinformatics. 2019. PMID: 30786165 Free PMC article.
Similarity corpus on microbial transcriptional regulation.
Lithgow-Serrano O, Gama-Castro S, Ishida-Gutiérrez C, Mejía-Almonte C, Tierrafría VH, Martínez-Luna S, Santos-Zavaleta A, Velázquez-Ramírez D, Collado-Vides J. Lithgow-Serrano O, et al. J Biomed Semantics. 2019 May 22;10(1):8. doi: 10.1186/s13326-019-0200-x. J Biomed Semantics. 2019. PMID: 31118102 Free PMC article.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD. Keseler IM, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899573 Free PMC article.
Strategies towards digital and semi-automated curation in RegulonDB.
Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. Rinaldi F, et al. Database (Oxford). 2017 Jan 1;2017(1):bax012. doi: 10.1093/database/bax012. Database (Oxford). 2017. PMID: 28365731 Free PMC article.
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. Nucleic Acids Res. 2019 Jan 8;47(D1):D212-D220. doi: 10.1093/nar/gky1077. Nucleic Acids Res. 2019. PMID: 30395280 Free PMC article.
20 results