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)

Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. - Michael Hackenberg; Rune Matthiesen (Bioinform., 2008)

ContDist: a tool for the analysis of quantitative gene and promoter properties. - Michael Hackenberg; Gorka Lasso; Rune Matthiesen (BMC Bioinform., 2009)

miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. - Michael Hackenberg; Martin Sturm; David Langenberger; Juan Manuel Falcón-Pérez; Ana M. Aransay (Nucleic Acids Res., 2009)

TargetSpy: a supervised machine learning approach for microRNA target prediction. - Martin Sturm; Michael Hackenberg; David Langenberger; Dmitrij Frishman (BMC Bioinform., 2010)

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)

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. - Michael Hackenberg; Naiara Rodríguez-Ezpeleta; Ana M. Aransay (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)

On the Need of Interpretability for Biomedical Applications: Using Fuzzy Models for Lung Cancer Prediction with Liquid Biopsy. - Nicolas Potie; Stavros Giannoukakos; Michael Hackenberg; Alberto Fernández 001 (FUZZ-IEEE, 2019)

liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies. - Ernesto Aparicio-Puerta; David Jáspez; Ricardo Lebrón; Danijela Koppers-Lalic; Juan Antonio Marchal; Michael Hackenberg (Nucleic Acids Res., 2019)

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)

Applying Feature Selection to Improve Predictive Performance and Explainability in Lung Cancer Detection with Soft Computing. - Nicolas Potie; Stavros Giannoukakos; Michael Hackenberg; Alberto Fernández 001 (HICSS, 2020)

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. - Thomas Desvignes; Phillipe Loher; Karen Eilbeck; Jeffery Ma; Gianvito Urgese; Bastian Fromm; Jason Sydes; Ernesto Aparicio-Puerta; Víctor Barrera; Roderic Espín; Florian Thibord; Xavier Bofill-De Ros; et al. (Bioinform., 2020)

mirnaQC: a webserver for comparative quality control of miRNA-seq data. - Ernesto Aparicio-Puerta; Cristina Gómez-Martín; Stavros Giannoukakos; José María Medina; Juan Antonio Marchal; Michael Hackenberg (Nucleic Acids Res., 2020)

MirGeneDB 2.0: the metazoan microRNA complement. - Bastian Fromm; Diana Domanska; Eirik Høye; Vladimir Ovchinnikov; Wenjing Kang; Ernesto Aparicio-Puerta; Morten Johansen; Kjersti Flatmark; Anthony Mathelier; Eivind Hovig; Michael Hackenberg; Marc R. Friedländer; et al. (Nucleic Acids Res., 2020)

sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. - Ernesto Aparicio-Puerta; Cristina Gómez-Martín; Stavros Giannoukakos; José María Medina; Chantal Scheepbouwer; Adrián García-Moreno; Pedro Carmona-Saez; Bastian Fromm; Michiel Pegtel; Andreas Keller; Juan Antonio Marchal; Michael Hackenberg (Nucleic Acids Res., 2022)

MirGeneDB 2.1: toward a complete sampling of all major animal phyla. - Bastian Fromm; Eirik Høye; Diana Domanska; Xiangfu Zhong; Ernesto Aparicio-Puerta; Vladimir Ovchinnikov; Sinan U. Umu; Peter J. Chabot; Wenjing Kang; Morteza Aslanzadeh; Marcel Tarbier; Emilio Mármol-Sánchez; et al. (Nucleic Acids Res., 2022)

isomiRdb: microRNA expression at isoform resolution. - Ernesto Aparicio-Puerta; Pascal Hirsch; Georges Pierre Schmartz; Tobias Fehlmann; Verena Keller; Annika Engel; Fabian Kern; Michael Hackenberg; Andreas Keller (Nucleic Acids Res., 2023)

NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. - Chantal Scheepbouwer; Michael Hackenberg; Monique A J. van Eijndhoven; Alan Gerber; Michiel Pegtel; Cristina Gómez-Martín (Nucleic Acids Res., 2023)