Genomics of Gene Regulation: The View from Escherichia coli. - Julio Collado-Vides; Gabriel Moreno-Hagelsieb; Ernesto Pérez-Rueda; Heladia Salgado; Araceli M. Huerta; Rosa María Gutiérrez; David A. Rosenblueth; Andrés Christen; Esperanza Benítez-Bellón; Arturo Medrano-Soto; Socorro Gama-Castro; Alberto Santos-Zavaleta; et al. (Gene Regulations and Metabolism, 2002)

A powerful non-homology method for the prediction of operons in prokaryotes. - Gabriel Moreno-Hagelsieb; Julio Collado-Vides (ISMB, 2002)

Operon conservation from the point of view of Escherichia coli, and inference of functional inter-dependence of gene products from genome context. - Gabriel Moreno-Hagelsieb; Julio Collado-Vides (Silico Biol., 2002)

Modelling Dynamics of Genetic Networks as a Multiscale Process. - Xilin Wei; Roderick V. N. Melnik; Gabriel Moreno-Hagelsieb (International Conference on Computational Science (3), 2005)

Choosing BLAST options for better detection of orthologs as reciprocal best hits. - Gabriel Moreno-Hagelsieb; Kristen Latimer (Bioinform., 2008)

GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways. - Cristian E. Martinez-Guerrero; Ricardo Ciria; Cei Abreu-Goodger; Gabriel Moreno-Hagelsieb; Enrique Merino (Nucleic Acids Res., 2008)

Phylogenomic clustering for selecting non-redundant genomes for comparative genomics. - Gabriel Moreno-Hagelsieb; Zilin Wang; Stephanie Walsh; Aisha ElSherbiny (Bioinform., 2013)

The functional landscape bound to the transcription factors of Escherichia coli K-12. - Ernesto Pérez-Rueda; Silvia Tenorio-Salgado; Alejandro Huerta-Saquero; Yalbi I. Balderas-Martínez; Gabriel Moreno-Hagelsieb (Comput. Biol. Chem., 2015)

The Transporter Classification Database (TCDB): recent advances. - Milton H. Saier Jr.; Vamsee S. Reddy; Brian V. Tsu; Muhammad Saad Ahmed; Chun Li; Gabriel Moreno-Hagelsieb (Nucleic Acids Res., 2016)

The Transporter Classification Database (TCDB): 2021 update. - Milton H. Saier Jr.; Vamsee S. Reddy; Gabriel Moreno-Hagelsieb; Kevin J. Hendargo; Yichi Zhang; Vasu Iddamsetty; Katie Jing Kay Lam; Nuo Tian; Steven Russum; Jianing Wang; Arturo Medrano-Soto (Nucleic Acids Res., 2021)

Gene function prediction using an AnnoTree-based genomic language model. - Huagang Tan; Gabriel Moreno-Hagelsieb; Andrew C. Doxey (BIBM, 2024)

Transcription Factors Across the Escherichia coli Pangenome: A 3D Perspective. - Gabriel Moreno-Hagelsieb (RECOMB-CG, 2024)

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods. - Xin Wei; Huagang Tan; Briallen Lobb; William Zhen; Zijing Wu; Donovan H. Parks; Josh D. Neufeld; Gabriel Moreno-Hagelsieb; Andrew C. Doxey (Briefings Bioinform., 2024)