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2020 – today
- 2023
[j22]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): 179-185 (2023)- [j21]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): 372-378 (2023) - 2022
- [j20]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): 204-210 (2022) - [j19]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): 710-717 (2022) - 2020
- [j18]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): 698-703 (2020) - [j17]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): D132-D141 (2020) - [j16]Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Juan Antonio Marchal, Michael Hackenberg:
mirnaQC: a webserver for comparative quality control of miRNA-seq data. Nucleic Acids Res. 48(Webserver-Issue): W262-W267 (2020) - [c3]Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernández:
Applying Feature Selection to Improve Predictive Performance and Explainability in Lung Cancer Detection with Soft Computing. HICSS 2020: 1-10
2010 – 2019
- 2019
- [j15]Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan Antonio Marchal, Michael Hackenberg:
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies. Nucleic Acids Res. 47(Database-Issue): D113-D120 (2019) - [j14]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:
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression. Nucleic Acids Res. 47(Webserver-Issue): W530-W535 (2019) - [c2]Nicolas Potie, Stavros Giannoukakos, Michael Hackenberg, Alberto Fernández:
On the Need of Interpretability for Biomedical Applications: Using Fuzzy Models for Lung Cancer Prediction with Liquid Biopsy. FUZZ-IEEE 2019: 1-6 - 2017
- [j13]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): D97-D103 (2017) - [p1]Guillermo Barturen, José L. Oliver, Michael Hackenberg:
Error Correction in Methylation Profiling From NGS Bisulfite Protocols. Algorithms for Next-Generation Sequencing Data 2017: 167-183 - 2015
- [j12]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): W467-W473 (2015) - 2014
- [j11]Francisco Dios, Guillermo Barturen, Ricardo Lebrón, Antonio Rueda, Michael Hackenberg, José L. Oliver:
DNA clustering and genome complexity. Comput. Biol. Chem. 53: 71-78 (2014) - [j10]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): 53-59 (2014) - 2013
- [c1]Guillermo Barturen, José L. Oliver, Michael Hackenberg:
Best practices for SNV and methylation calling from bisulfite sequencing data. IWBBIO 2013: 125 - 2011
- [j9]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: 2 (2011) - [j8]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): 75-79 (2011) - [j7]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): 132-138 (2011) - 2010
- [j6]Martin Sturm, Michael Hackenberg, David Langenberger, Dmitrij Frishman:
TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinform. 11: 292 (2010)
2000 – 2009
- 2009
- [j5]Michael Hackenberg, Gorka Lasso, Rune Matthiesen:
ContDist: a tool for the analysis of quantitative gene and promoter properties. BMC Bioinform. 10 (2009) - [j4]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): 68-76 (2009) - 2008
- [j3]Michael Hackenberg, Rune Matthiesen:
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists. Bioinform. 24(11): 1386-1393 (2008) - 2006
- [j2]Michael Hackenberg, Christopher Previti, Pedro Luis Luque-Escamilla, Pedro Carpena, José Martínez-Aroza, José L. Oliver:
CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinform. 7: 446 (2006) - 2004
- [j1]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): 287-292 (2004)
Coauthor Index
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