Yalbi I. Balderas-Martinez

Publications (2) View all

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

  Heladia Salgado, Martin Peralta-Gil, Socorro Gama-Castro, Alberto Santos-Zavaleta, Luis Muñiz-Rascado, Jair S García-Sotelo, Verena Weiss, Hilda Solano-Lira, Irma Martínez-Flores, Alejandra Medina-Rivera, [......], Yalbi I Balderas-Martínez, Lucia Pannier, Maricela Olvera, Aurora Labastida, Verónica Jiménez-Jacinto, Leticia Vega-Alvarado, Victor Del Moral-Chávez, Alfredo Hernández-Alvarez, Enrique Morett, Julio Collado-Vides
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  ABSTRACT: This article summarizes our progress with RegulonDB (http://regulondb.ccg.unam.mx/) during the past 2 years. We have kept up-to-date the knowledge from the published literature regarding transcriptional regulation in Escherichia coli K-12. We have maintained and expanded our curation efforts to improve the breadth and quality of the encoded experimental knowledge, and we have implemented criteria for the quality of our computational predictions. Regulatory phrases now provide high-level descriptions of regulatory regions. We expanded the assignment of quality to various sources of evidence, particularly for knowledge generated through high-throughput (HT) technology. Based on our analysis of most relevant methods, we defined rules for determining the quality of evidence when multiple independent sources support an entry. With this latest release of RegulonDB, we present a new highly reliable larger collection of transcription start sites, a result of our experimental HT genome-wide efforts. These improvements, together with several novel enhancements (the tracks display, uploading format and curational guidelines), address the challenges of incorporating HT-generated knowledge into RegulonDB. Information on the evolutionary conservation of regulatory elements is also available now. Altogether, RegulonDB version 8.0 is a much better home for integrating knowledge on gene regulation from the sources of information currently available.
  Nucleic Acids Research 11/2012; · 8.03 Impact Factor
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  Available from: Yalbi I. Balderas-Martinez

  Article: Regulation by transcription factors in bacteria: beyond description.

  Enrique Balleza, Lucia N López-Bojorquez, Agustino Martínez-Antonio, Osbaldo Resendis-Antonio, Irma Lozada-Chávez, Yalbi I Balderas-Martínez, Sergio Encarnación, Julio Collado-Vides
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  ABSTRACT: Transcription is an essential step in gene expression and its understanding has been one of the major interests in molecular and cellular biology. By precisely tuning gene expression, transcriptional regulation determines the molecular machinery for developmental plasticity, homeostasis and adaptation. In this review, we transmit the main ideas or concepts behind regulation by transcription factors and give just enough examples to sustain these main ideas, thus avoiding a classical ennumeration of facts. We review recent concepts and developments: cis elements and trans regulatory factors, chromosome organization and structure, transcriptional regulatory networks (TRNs) and transcriptomics. We also summarize new important discoveries that will probably affect the direction of research in gene regulation: epigenetics and stochasticity in transcriptional regulation, synthetic circuits and plasticity and evolution of TRNs. Many of the new discoveries in gene regulation are not extensively tested with wetlab approaches. Consequently, we review this broad area in Inference of TRNs and Dynamical Models of TRNs. Finally, we have stepped backwards to trace the origins of these modern concepts, synthesizing their history in a timeline schema.
  FEMS Microbiology Reviews 02/2009; 33(1):133-51. · 10.96 Impact Factor