Predicting synchronized gene coexpression patterns from fibration symmetries in gene regulatory networks in bacteria

Autor: Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida, Hernán A. Makse

Publikováno v: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-34 (2021)

Abstract Background Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the ques

Externí odkaz: https://doaj.org/article/42e2a102255c4f6a82d69c2726afb415

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Autor: Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, David A. Velázquez-Ramírez, Socorro Gama-Castro, Víctor H. Tierrafría, Stephen J. W. Busby, Patricia Aquino, Xin Fang, Bernhard O. Palsson, James E. Galagan, Julio Collado-Vides

Publikováno v: BMC Biology, Vol 16, Iss 1, Pp 1-12 (2018)

Abstract Background Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors and gene expression pro

Externí odkaz: https://doaj.org/article/62842013a20a414b8d96469a17759c51

Pseudocrossidium replicatum (Taylor) R.H. Zander is a fully desiccation-tolerant moss that expresses an inducible molecular mechanism in response to severe abiotic stress

Autor: Claudio Delgadillo, Martha Bibbins-Martínez, Mario Alberto Martínez-Núñez, Selma Ríos-Meléndez, Emmanuel Valadez-Hernández, Luis Cárdenas, Ignacio E. Maldonado-Mendoza, Mishael Sánchez-Pérez, José L. Martínez-y-Pérez, Maria Lorena Luna-Guevara, Analilia Arroyo-Becerra, Miguel Angel Villalobos-López

Publikováno v: Plant Molecular Biology

Key message The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore tissues. Abstract Desiccation tolerance (DT) is the ability of cell

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::044e196c891af16af4a7d1e44de40f24
https://doi.org/10.1007/s11103-021-01167-3

RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12

Autor: James E. Galagan, Cecilia Ishida-Gutiérrez, Julio Collado-Vides, Socorro Gama-Castro, Kevin Alquicira-Hernández, César Bonavides-Martínez, Jair S. García-Sotelo, Alberto Santos-Zavaleta, Heladia Salgado, Luis Muñiz-Rascado, David A. Velázquez-Ramírez, Laura Gómez-Romero, Víctor Del Moral-Chávez, Carlos-Francisco Méndez-Cruz, Mishael Sánchez-Pérez, Pablo Peña-Loredo, Daniela Ledezma-Tejeida

Publikováno v: Nucleic Acids Research

RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-th

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::110e2d03ec9378fc567540767d3b1846
https://pubmed.ncbi.nlm.nih.gov/30395280

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Autor: James E. Galagan, Bernhard O. Palsson, Socorro Gama-Castro, Alberto Santos-Zavaleta, Stephen J. W. Busby, Víctor H. Tierrafría, Julio Collado-Vides, Heladia Salgado, Mishael Sánchez-Pérez, Patricia Aquino, Xin Fang, David A. Velázquez-Ramírez

Publikováno v: Santos-Zavaleta, A, Sanchez-Perez, M, Salgado, H, Velazquez-Ramirez, D A, Gama-Castro, S, Tierrafria, V H, Busby, S J W, Aquino, P, Fang, X, Palsson, B O, Galagan, J E & Collado-Vides, J 2018, ' A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0 ', B M C Biology, vol. 16, 91 . https://doi.org/10.1186/s12915-018-0555-y
BMC Biology
BMC Biology, Vol 16, Iss 1, Pp 1-12 (2018)

Background: Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors and gene expression profiles. I

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6d400758903e01ef090ab522a7664f94
https://doi.org/10.1186/s12915-018-0555-y