Michael Hackenberg

Publication Activity (10 Years)

Years Active: 2004-2023
Publications (10 Years): 13

Top Topics

Differential Expression

Inductive Databases

Sequenced Genomes

Top Venues

Nucleic Acids Res.

Publications

Chantal Scheepbouwer, Michael Hackenberg, Monique A J. van Eijndhoven, Alan Gerber, Michiel Pegtel, Cristina Gómez-Martín
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. Nucleic Acids Res. 51 (W1) (2023)
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges Pierre Schmartz, Tobias Fehlmann, Verena Keller, Annika Engel, Fabian Kern, Michael Hackenberg, Andreas Keller
isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res. 51 (D1) (2023)
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
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res. 50 (W1) (2022)
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
MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res. 50 (D1) (2022)
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
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinform. 36 (3) (2020)
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
MirGeneDB 2.0: the metazoan microRNA complement. Nucleic Acids Res. 48 (Database-Issue) (2020)
Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernandez
Applying Feature Selection to Improve Predictive Performance and Explainability in Lung Cancer Detection with Soft Computing. HICSS (2020)
Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Juan A. Marchal, Michael Hackenberg
mirnaQC: a webserver for comparative quality control of miRNA-seq data. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Ernesto Aparicio-Puerta, Ricardo Lebrón, Antonio Rueda, Cristina Gómez-Martín, Stavros Giannoukakos, David Jáspez, José María Medina, Andreja Zubkovic, Igor Jurak, Bastian Fromm, Juan A. Marchal, José L. Oliver, Michael Hackenberg
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernandez
On the Need of Interpretability for Biomedical Applications: Using Fuzzy Models for Lung Cancer Prediction with Liquid Biopsy. FUZZ-IEEE (2019)
Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan A. Marchal, Michael Hackenberg
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies. Nucleic Acids Res. 47 (Database-Issue) (2019)
Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver
NGSmethDB 2017: enhanced methylomes and differential methylation. Nucleic Acids Res. 45 (Database-Issue) (2017)
Antonio Rueda, Guillermo Barturen, Ricardo Lebrón, Cristina Gómez-Martín, Ángel M. Alganza, José L. Oliver, Michael Hackenberg
sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg, José L. Oliver
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes. Nucleic Acids Res. 42 (Database-Issue) (2014)
Francisco Dios, Guillermo Barturen, Ricardo Lebrón, Antonio Rueda, Michael Hackenberg, José L. Oliver
DNA clustering and genome complexity. Comput. Biol. Chem. 53 (2014)
Guillermo Barturen, José L. Oliver, Michael Hackenberg
Best practices for SNV and methylation calling from bisulfite sequencing data. IWBBIO (2013)
Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Ángel M. Alganza, José L. Oliver
WordCluster: detecting clusters of DNA words and genomic elements. Algorithms Mol. Biol. 6 (2011)
Michael Hackenberg, Guillermo Barturen, José L. Oliver
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data. Nucleic Acids Res. 39 (Database-Issue) (2011)
Michael Hackenberg, Naiara Rodríguez-Ezpeleta, Ana M. Aransay
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman
TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinform. 11 (2010)
Michael Hackenberg, Martin Sturm, David Langenberger, Juan Manuel Falcón-Pérez, Ana M. Aransay
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Michael Hackenberg, Gorka Lasso, Rune Matthiesen
ContDist: a tool for the analysis of quantitative gene and promoter properties. BMC Bioinform. 10 (2009)
Michael Hackenberg, Rune Matthiesen
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. Bioinform. 24 (11) (2008)
Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza, José L. Oliver
: a distance-based algorithm for CpG-island detection. BMC Bioinform. 7 (2006)
José L. Oliver, Pedro Carpena, Michael Hackenberg, Pedro Bernaola-Galván
IsoFinder: computational prediction of isochores in genome sequences. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)