Michael Hackenberg

Summary

Publications

  1. pmc Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes
    Maria Jose Ferreiro
    Developmental Neurobiology, IIBCE, Montevideo, Uruguay
    BMC Genomics 13:483. 2012
  2. doi request reprint Clustering of DNA words and biological function: a proof of principle
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada, Spain
    J Theor Biol 297:127-36. 2012
  3. pmc NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
    Nucleic Acids Res 39:D75-9. 2011
  4. pmc miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
    Michael Hackenberg
    Departmento de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada, Spain
    Nucleic Acids Res 39:W132-8. 2011
  5. pmc Prediction of CpG-island function: CpG clustering vs. sliding-window methods
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071, Granada, Spain
    BMC Genomics 11:327. 2010
  6. pmc ContDist: a tool for the analysis of quantitative gene and promoter properties
    Michael Hackenberg
    Bioinformatics Group, CIC bioGUNE, CIBER HEPAD, Technology Park of Bizkaia, Spain
    BMC Bioinformatics 10:7. 2009
  7. pmc TargetSpy: a supervised machine learning approach for microRNA target prediction
    Martin Sturm
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:292. 2010
  8. pmc CpGcluster: a distance-based algorithm for CpG-island detection
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    BMC Bioinformatics 7:446. 2006
  9. pmc WordCluster: detecting clusters of DNA words and genomic elements
    Michael Hackenberg
    Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada and Lab, de Bioinformática, Centro de Investigacion Biomedica, PTS, Avda, del Conocimiento s n, 18100 Granada, Spain
    Algorithms Mol Biol 6:2. 2011
  10. ncbi request reprint The biased distribution of Alus in human isochores might be driven by recombination
    Michael Hackenberg
    Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    J Mol Evol 60:365-77. 2005

Collaborators

Detail Information

Publications18

  1. pmc Whole transcriptome analysis of a reversible neurodegenerative process in Drosophila reveals potential neuroprotective genes
    Maria Jose Ferreiro
    Developmental Neurobiology, IIBCE, Montevideo, Uruguay
    BMC Genomics 13:483. 2012
    ..To identify genes associated to neurodegeneration and neuroprotection, we used mRNA-Seq to compare the transcriptome of Drosophila sall mutant and wild type embryos from neurodegeneration and reversal stages...
  2. doi request reprint Clustering of DNA words and biological function: a proof of principle
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada, Spain
    J Theor Biol 297:127-36. 2012
    ....
  3. pmc NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
    Nucleic Acids Res 39:D75-9. 2011
    ..Dump downloads for three coverage levels (1, 5 or 10 reads) are available. NGSmethDB will be useful for experimental researchers, as well as for bioinformaticians, who might use the data as input for further research...
  4. pmc miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
    Michael Hackenberg
    Departmento de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada, Spain
    Nucleic Acids Res 39:W132-8. 2011
    ..miRanalyzer is available at http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php...
  5. pmc Prediction of CpG-island function: CpG clustering vs. sliding-window methods
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071, Granada, Spain
    BMC Genomics 11:327. 2010
    ..Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence...
  6. pmc ContDist: a tool for the analysis of quantitative gene and promoter properties
    Michael Hackenberg
    Bioinformatics Group, CIC bioGUNE, CIBER HEPAD, Technology Park of Bizkaia, Spain
    BMC Bioinformatics 10:7. 2009
    ..However, so far the subsequent analysis of such experiments (e.g. the resulting gene lists) have been hampered by the fact that currently no tool exists for a detailed analysis of the promoter regions...
  7. pmc TargetSpy: a supervised machine learning approach for microRNA target prediction
    Martin Sturm
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:292. 2010
    ..Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites...
  8. pmc CpGcluster: a distance-based algorithm for CpG-island detection
    Michael Hackenberg
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    BMC Bioinformatics 7:446. 2006
    ....
  9. pmc WordCluster: detecting clusters of DNA words and genomic elements
    Michael Hackenberg
    Dpto, de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s n, 18071 Granada and Lab, de Bioinformática, Centro de Investigacion Biomedica, PTS, Avda, del Conocimiento s n, 18100 Granada, Spain
    Algorithms Mol Biol 6:2. 2011
    ..abstract:..
  10. ncbi request reprint The biased distribution of Alus in human isochores might be driven by recombination
    Michael Hackenberg
    Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    J Mol Evol 60:365-77. 2005
    ..Other evolutionary factors, such as population bottlenecks during primate speciation, may have accelerated the fast accumulation of Alus in GC-rich isochores...
  11. doi request reprint NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes
    Stefanie Geisen
    Facultad de Ciencias, Departmento de Genetica, Universidad de Granada, 18071 Granada, Spain and Laboratorio de Bioinformática, Instituto de Biotecnologia, Centro de Investigacion Biomedica, 18100 Granada, Spain
    Nucleic Acids Res 42:D53-9. 2014
    ..NGSmethDB methylomes are also available as native tracks through a UCSC hub, which allows comparison with a wide range of third-party annotations, in particular phenotype or disease annotations. ..
  12. pmc Phylogenetic distribution of large-scale genome patchiness
    Jose L Oliver
    Dpto de Genetica, Facultad de Ciencias, Universidad de Granada, Spain
    BMC Evol Biol 8:107. 2008
    ....
  13. pmc IsoFinder: computational prediction of isochores in genome sequences
    Jose L Oliver
    Departamento de Genetica, Instituto de Biotecnologia, Facultad de Ciencias, Universidad de Granada, Spain
    Nucleic Acids Res 32:W287-92. 2004
    ..The resulting isochore maps are available at our web site (http://bioinfo2.ugr.es/isochores/), and also at the UCSC Genome Browser (http://genome.cse.ucsc.edu/)...
  14. pmc miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
    Michael Hackenberg
    Functional Genomics Unit, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
    Nucleic Acids Res 37:W68-76. 2009
    ..miRanalyzer is available at http://web.bioinformatics.cicbiogune.es/microRNA/...
  15. doi request reprint Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists
    Michael Hackenberg
    Bioinformatics Group, CIC bioGUNE, CIBER HEPAD, Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain
    Bioinformatics 24:1386-93. 2008
    ..For a more complete and correct interpretation of these experiments, it is important to extend substantially the number of annotations, adapting the ontological analysis to the new emerging techniques...
  16. ncbi request reprint Isochore chromosome maps of the human genome
    Jose L Oliver
    Departamento de Genetica, Instituto de Biotecnologia, Universidad de Granada, Granada, Spain
    Gene 300:117-27. 2002
    ..The coordinates for the LHGRs identified in all the contigs longer than 2 Mb in the human genome sequence are available at the online resource on isochore mapping: http://bioinfo2.ugr.es/isochores...
  17. pmc CpGislandEVO: a database and genome browser for comparative evolutionary genomics of CpG islands
    Guillermo Barturen
    Departamento de Genetica, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain Laboratório de Bioinformática, Instituto de Biotecnologia, Centro de Investigacion Biomedica, 18100 Granada, Spain
    Biomed Res Int 2013:709042. 2013
    ..The resulting CpGislandEVO database, linking together CGIs and single-cytosine DNA methylation data from several mammalian species, is freely available at our website. ..
  18. pmc A transgenic transcription factor (TaDREB3) in barley affects the expression of microRNAs and other small non-coding RNAs
    Michael Hackenberg
    Department of Genetics, University of Granada, Granada, Granada, Spain
    PLoS ONE 7:e42030. 2012
    ..All the predicted novel miRNA targets were validated using a degradome library. Our data provide an insight into the effect of TF on the expression of sRNAs in barley...