SDSE: a software package to simulate the evolution of a pair of DNA sequences. - José L. Oliver; A. Marin; Juan-Ramón Medina (Comput. Appl. Biosci., 1989)

Chloroplast genes transferred to the nuclear plant genome have adjusted to nuclear base composition and codon usage. - José L. Oliver; A. Marin; Jose Miguel Martinez-Zapater (Nucleic Acids Res., 1990)

Entropic feature for sequence pattern through iterated function systems. - Ramón Román-Roldán; Pedro Bernaola-Galván; José L. Oliver (Pattern Recognit. Lett., 1994)

Application of information theory to DNA sequence analysis: A review. - Ramón Román-Roldán; Pedro Bernaola-Galván; José L. Oliver (Pattern Recognit., 1996)

SEGMENT: identifying compositional domains in DNA sequences. - José L. Oliver; Ramón Román-Roldán; Javier Pérez; Pedro Bernaola-Galván (Bioinform., 1999)

Isochores merit the prefix 'iso'. - Wentian Li; Pedro Bernaola-Galván; Pedro Carpena; José L. Oliver (Comput. Biol. Chem., 2003)

IsoFinder: computational prediction of isochores in genome sequences. - José L. Oliver; Pedro Carpena; Michael Hackenberg; Pedro Bernaola-Galván (Nucleic Acids Res., 2004)

CpGcluster: a distance-based algorithm for CpG-island detection. - Michael Hackenberg; Christopher Previti; Pedro Luis Luque-Escamilla; Pedro Carpena; José Martínez-Aroza; José L. Oliver (BMC Bioinform., 2006)

WordCluster: detecting clusters of DNA words and genomic elements. - Michael Hackenberg; Pedro Carpena; Pedro Bernaola-Galván; Guillermo Barturen; Ángel M. Alganza; José L. Oliver (Algorithms Mol. Biol., 2011)

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. - Michael Hackenberg; Guillermo Barturen; José L. Oliver (Nucleic Acids Res., 2011)

Best practices for SNV and methylation calling from bisulfite sequencing data. - Guillermo Barturen; José L. Oliver; Michael Hackenberg (IWBBIO, 2013)

DNA clustering and genome complexity. - Francisco Dios; Guillermo Barturen; Ricardo Lebrón; Antonio Rueda; Michael Hackenberg; José L. Oliver (Comput. Biol. Chem., 2014)

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. - Stefanie Geisen; Guillermo Barturen; Ángel M. Alganza; Michael Hackenberg; José L. Oliver (Nucleic Acids Res., 2014)

sRNAtoolbox: an integrated collection of small RNA research tools. - Antonio Rueda; Guillermo Barturen; Ricardo Lebrón; Cristina Gómez-Martín; Ángel M. Alganza; José L. Oliver; Michael Hackenberg (Nucleic Acids Res., 2015)

Error Correction in Methylation Profiling From NGS Bisulfite Protocols. - Guillermo Barturen; José L. Oliver; Michael Hackenberg (Algorithms for Next-Generation Sequencing Data, 2017)

NGSmethDB 2017: enhanced methylomes and differential methylation. - Ricardo Lebrón; Cristina Gómez-Martín; Pedro Carpena; Pedro Bernaola-Galván; Guillermo Barturen; Michael Hackenberg; José L. Oliver (Nucleic Acids Res., 2017)

sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. - Ernesto Aparicio-Puerta; Ricardo Lebrón; Antonio Rueda; Cristina Gómez-Martín; Stavros Giannoukakos; David Jáspez; José María Medina; Andreja Zubkovic; Igor Jurak; Bastian Fromm; Juan Antonio Marchal; José L. Oliver; et al. (Nucleic Acids Res., 2019)

A novel approach to predict the traffic accident assistance based on deep learning. - José-Francisco Vicent; Manuel Curado; José L. Oliver; Luis Pérez-Sala (Neural Comput. Appl., 2025)