Michael Hackenberg

25 papers B 1Journal 21Unranked 2
YearRankTypeTitle / Venue / Authors
2023 J jnl
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods.
Nucleic Acids Res.
Chantal Scheepbouwer, Michael Hackenberg, Monique A J. van Eijndhoven, Alan Gerber, Michiel Pegtel, Cristina Gómez-Martín
2023 J jnl
isomiRdb: microRNA expression at isoform resolution.
Nucleic Acids Res.
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges Pierre Schmartz, Tobias Fehlmann, Verena Keller, Annika Engel, Fabian Kern, Michael Hackenberg, Andreas Keller
2022 J jnl
MirGeneDB 2.1: toward a complete sampling of all major animal phyla.
Nucleic Acids Res.
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, Gianvito Urgese, Morten Johansen, Eivind Hovig, Michael Hackenberg, Marc R. Friedländer, Kevin J. Peterson
2022 J jnl
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms.
Nucleic Acids Res.
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
2020 — conf
Applying Feature Selection to Improve Predictive Performance and Explainability in Lung Cancer Detection with Soft Computing.
HICSS
Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernández
2020 J jnl
MirGeneDB 2.0: the metazoan microRNA complement.
Nucleic Acids Res.
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, Kevin J. Peterson
2020 J jnl
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.
Bioinform.
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, Eric Londin, Aristeidis G. Telonis, Elisa Ficarra, Marc R. Friedländer, John H. Postlethwait, Isidore Rigoutsos, Michael Hackenberg, Ioannis S. Vlachos, Marc K. Halushka, Lorena Pantano
2020 J jnl
mirnaQC: a webserver for comparative quality control of miRNA-seq data.
Nucleic Acids Res.
Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Juan Antonio Marchal, Michael Hackenberg
2019 B conf
On the Need of Interpretability for Biomedical Applications: Using Fuzzy Models for Lung Cancer Prediction with Liquid Biopsy.
FUZZ-IEEE
Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernández
2019 J jnl
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies.
Nucleic Acids Res.
Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan Antonio Marchal, Michael Hackenberg
2019 J jnl
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.
Nucleic Acids Res.
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, Michael Hackenberg
2017 — ch.
Error Correction in Methylation Profiling From NGS Bisulfite Protocols.
Algorithms for Next-Generation Sequencing Data
Guillermo Barturen, José L. Oliver, Michael Hackenberg
2017 J jnl
NGSmethDB 2017: enhanced methylomes and differential methylation.
Nucleic Acids Res.
Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro A. Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver
2015 J jnl
sRNAtoolbox: an integrated collection of small RNA research tools.
Nucleic Acids Res.
Antonio Rueda, Guillermo Barturen, Ricardo Lebrón, Cristina Gómez-Martín, Ángel M. Alganza, José L. Oliver, Michael Hackenberg
2014 J jnl
DNA clustering and genome complexity.
Comput. Biol. Chem.
Francisco Dios, Guillermo Barturen, Ricardo Lebrón, Antonio Rueda, Michael Hackenberg, José L. Oliver
2014 J jnl
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.
Nucleic Acids Res.
Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg, José L. Oliver
2013 — conf
Best practices for SNV and methylation calling from bisulfite sequencing data.
IWBBIO
Guillermo Barturen, José L. Oliver, Michael Hackenberg
2011 J jnl
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.
Nucleic Acids Res.
Michael Hackenberg, Guillermo Barturen, José L. Oliver
2011 J jnl
WordCluster: detecting clusters of DNA words and genomic elements.
Algorithms Mol. Biol.
Michael Hackenberg, Pedro Carpena, Pedro A. Bernaola-Galván, Guillermo Barturen, Ángel M. Alganza, José L. Oliver
2011 J jnl
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.
Nucleic Acids Res.
Michael Hackenberg, Naiara Rodríguez-Ezpeleta, Ana M. Aransay
2010 J jnl
TargetSpy: a supervised machine learning approach for microRNA target prediction.
BMC Bioinform.
Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman
2009 J jnl
ContDist: a tool for the analysis of quantitative gene and promoter properties.
BMC Bioinform.
Michael Hackenberg, Gorka Lasso, Rune Matthiesen
2009 J jnl
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.
Nucleic Acids Res.
Michael Hackenberg, Martin Sturm, David Langenberger, Juan Manuel Falcón-Pérez, Ana M. Aransay
2008 J jnl
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists.
Bioinform.
Michael Hackenberg, Rune Matthiesen
2004 J jnl
IsoFinder: computational prediction of isochores in genome sequences.
Nucleic Acids Res.
José L. Oliver, Pedro Carpena, Michael Hackenberg, Pedro A. Bernaola-Galván