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Items: 6

1.

Using RegulonDB, the Escherichia coli K-12 Gene Regulatory Transcriptional Network Database.

Salgado H, Martínez-Flores I, Bustamante VH, Alquicira-Hernández K, García-Sotelo JS, García-Alonso D, Collado-Vides J.

Curr Protoc Bioinformatics. 2018 Mar;61(1):1.32.1-1.32.30. doi: 10.1002/cpbi.43.

PMID:
30040192
2.

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

Palacios-Flores K, García-Sotelo J, Castillo A, Uribe C, Aguilar L, Morales L, Gómez-Romero L, Reyes J, Garciarubio A, Boege M, Dávila G.

Genetics. 2018 Apr;208(4):1631-1641. doi: 10.1534/genetics.117.300589. Epub 2018 Jan 24.

3.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo JS, Alquicira-Hernández K, Martínez-Flores I, Pannier L, Castro-Mondragón JA, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Pérez-Rueda E, Alquicira-Hernández S, Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, Del Moral-Chávez V, Rinaldi F, Collado-Vides J.

Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43. doi: 10.1093/nar/gkv1156. Epub 2015 Nov 2.

4.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29.

5.

Extracting regulatory networks of Escherichia coli from RegulonDB.

Salgado H, Martínez-Flores I, López-Fuentes A, García-Sotelo JS, Porrón-Sotelo L, Solano H, Muñiz-Rascado L, Collado-Vides J.

Methods Mol Biol. 2012;804:179-95. doi: 10.1007/978-1-61779-361-5_10.

PMID:
22144154
6.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

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