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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: velazquez ramirez da. Nucleic Acids Res. 2019 Jan 8;47(D1):D212-D220. doi: 10.1093/nar/gky1077. Nucleic Acids Res. 2019. PMID: 30395280 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. Among authors: velazquez ramirez da. 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.
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: velazquez ramirez da. BMC Biol. 2018 Aug 16;16(1):91. doi: 10.1186/s12915-018-0555-y. BMC Biol. 2018. PMID: 30115066 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.
Hierarchical dynamics of a transcription factors network in E. coli.
Martínez-Antonio A, Velázquez-Ramírez DA, Sánchez-Mondragón J, Santillán M. Martínez-Antonio A, et al. Among authors: velazquez ramirez da. Mol Biosyst. 2012 Nov;8(11):2932-6. doi: 10.1039/c2mb25236h. Mol Biosyst. 2012. PMID: 22907621
Demographic history and genetic structure in pre-Hispanic Central Mexico.
Villa-Islas V, Izarraras-Gomez A, Larena M, Campos EMP, Sandoval-Velasco M, Rodríguez-Rodríguez JE, Bravo-Lopez M, Moguel B, Fregel R, Garfias-Morales E, Medina Tretmanis J, Velázquez-Ramírez DA, Herrera-Muñóz A, Sandoval K, Nieves-Colón MA, Zepeda García Moreno G, Villanea FA, Medina EFV, Aguayo-Haro R, Valdiosera C, Ioannidis AG, Moreno-Estrada A, Jay F, Huerta-Sanchez E, Moreno-Mayar JV, Sánchez-Quinto F, Ávila-Arcos MC. Villa-Islas V, et al. Among authors: velazquez ramirez da. Science. 2023 May 12;380(6645):eadd6142. doi: 10.1126/science.add6142. Epub 2023 May 12. Science. 2023. PMID: 37167382