Heladia Salgado

A high-quality genome assembly and integrative data portal (Phabase) for the Mesoamerican black bean (Phaseolus vulgaris cv. Negro Jamapa)

The paper presents a high-quality genome assembly for the Mesoamerican black bean variety Negro Jamapa and introduces Phabase, a database integrating genomic and transcriptomic data for functional genomics and breeding.

A Gold Standard for Transcription Factor Regulatory Interactions in Escherichia coli K-12: Architecture of Evidence Types

The paper analyzes the sources of evidence for transcription factor regulatory interactions in E. coli K-12, classifies them into seven groups, and evaluates confidence levels of interactions using high-throughput data.

Programmatic access to bacterial regulatory networks with regutools

The paper introduces regutools, an R package that enables programmatic access to RegulonDB data for analyzing bacterial regulatory networks within the Bioconductor ecosystem.

MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions

The paper introduces MCO, an ontology for standardized annotation of microbial growth conditions, enabling comparison of gene expression data across experiments.

Towards a unified resource for transcriptional regulation in Escherichia coli K-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB.

The paper expands RegulonDB to integrate high-throughput binding data with existing knowledge on gene regulation in E. coli K-12, enhancing its comprehensiveness and utility.