Heiko Muller

Summary

Affiliation: European Institute of Oncology
Country: Italy

Publications

  1. pmc Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME
    Giacomo Finocchiaro
    The FIRC Institute of Molecular Oncology Foundation, Milan, Italy
    Nucleic Acids Res 35:2343-55. 2007
  2. pmc Localizing hotspots of antisense transcription
    Giacomo Finocchiaro
    The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
    Nucleic Acids Res 35:1488-500. 2007
  3. pmc Identification and analysis of co-occurrence networks with NetCutter
    Heiko Muller
    Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    PLoS ONE 3:e3178. 2008
  4. ncbi request reprint Molecular signature of retinoic acid treatment in acute promyelocytic leukemia
    Natalia Meani
    Institute of Molecular Oncology of the Italian Foundation for Cancer Research, Via Adamello 16, 20139 Milan, Italy
    Oncogene 24:3358-68. 2005
  5. pmc Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control
    Giacomo Finocchiaro
    European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy
    BMC Bioinformatics 6:S14. 2005
  6. ncbi request reprint Lap2alpha expression is controlled by E2F and deregulated in various human tumors
    Paola Parise
    The FIRC Institute of Molecular Oncology Foundation, Milan, Italy
    Cell Cycle 5:1331-41. 2006
  7. ncbi request reprint Identification of target genes of the p16INK4A-pRB-E2F pathway
    Richard Vernell
    Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
    J Biol Chem 278:46124-37. 2003
  8. ncbi request reprint GenePicker: replicate analysis of Affymetrix gene expression microarrays
    Giacomo Finocchiaro
    Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    Bioinformatics 20:3670-2. 2004
  9. ncbi request reprint DEK Expression is controlled by E2F and deregulated in diverse tumor types
    Maria Stella Carro
    The FIRC Institute of Molecular Oncology Foundation, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    Cell Cycle 5:1202-7. 2006
  10. pmc A large fraction of extragenic RNA pol II transcription sites overlap enhancers
    Francesca De Santa
    Department of Experimental Oncology, European Institute of Oncology Campus IFOM IEO, Milan, Italy
    PLoS Biol 8:e1000384. 2010

Collaborators

Detail Information

Publications13

  1. pmc Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME
    Giacomo Finocchiaro
    The FIRC Institute of Molecular Oncology Foundation, Milan, Italy
    Nucleic Acids Res 35:2343-55. 2007
    ..The genes constituting different communities are characterized by common genomic features and strongly enriched cis-regulatory modules in their upstream regulatory regions that are consistent with pathway assignment of those genes...
  2. pmc Localizing hotspots of antisense transcription
    Giacomo Finocchiaro
    The FIRC Institute of Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy
    Nucleic Acids Res 35:1488-500. 2007
    ..Interestingly, a similar size distribution of 5'UTRs and first exons is observed for genes silenced by CpG island methylation in human cancer...
  3. pmc Identification and analysis of co-occurrence networks with NetCutter
    Heiko Muller
    Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    PLoS ONE 3:e3178. 2008
    ..The methodologies and statistical models used to evaluate the significance of association between co-occurring entities are quite diverse, however...
  4. ncbi request reprint Molecular signature of retinoic acid treatment in acute promyelocytic leukemia
    Natalia Meani
    Institute of Molecular Oncology of the Italian Foundation for Cancer Research, Via Adamello 16, 20139 Milan, Italy
    Oncogene 24:3358-68. 2005
    ....
  5. pmc Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control
    Giacomo Finocchiaro
    European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy
    BMC Bioinformatics 6:S14. 2005
    ..Here we propose using a repository of published gene lists for the identification of interesting datasets to be subjected to more detailed numerical analysis...
  6. ncbi request reprint Lap2alpha expression is controlled by E2F and deregulated in various human tumors
    Paola Parise
    The FIRC Institute of Molecular Oncology Foundation, Milan, Italy
    Cell Cycle 5:1331-41. 2006
    ..In agreement with its regulation by E2F, LAP2alpha over expression in primary tumors was found to be correlated with tumor proliferation rate...
  7. ncbi request reprint Identification of target genes of the p16INK4A-pRB-E2F pathway
    Richard Vernell
    Department of Experimental Oncology, European Institute of Oncology, 20141 Milan, Italy
    J Biol Chem 278:46124-37. 2003
    ....
  8. ncbi request reprint GenePicker: replicate analysis of Affymetrix gene expression microarrays
    Giacomo Finocchiaro
    Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    Bioinformatics 20:3670-2. 2004
    ..AVAILABILITY: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html. SUPPLEMENTARY INFORMATION: http://www.ifom-firc.it/RESEARCH/Appl_Bioinfo/tools.html...
  9. ncbi request reprint DEK Expression is controlled by E2F and deregulated in diverse tumor types
    Maria Stella Carro
    The FIRC Institute of Molecular Oncology Foundation, Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    Cell Cycle 5:1202-7. 2006
    ..Expression levels of DEK in human tumors have been investigated by tissue micro array analysis. We find that DEK is overexpressed in many solid tumors such as colon cancer, larynx cancer, bladder cancer, and melanoma...
  10. pmc A large fraction of extragenic RNA pol II transcription sites overlap enhancers
    Francesca De Santa
    Department of Experimental Oncology, European Institute of Oncology Campus IFOM IEO, Milan, Italy
    PLoS Biol 8:e1000384. 2010
    ..Discrimination between lncRNAs generated by canonical RNA genes and products of transcribed enhancers will provide a framework for experimental approaches to lncRNAs and help complete the annotation of mammalian genomes...
  11. ncbi request reprint Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases
    Alessandro Guffanti
    FIRC Institute of Molecular Oncology, Milan, Italy
    Appl Bioinformatics 2:245-9. 2003
    ..We also report some comparative evidence about the importance of biological database synchronisation and cross-references in the process of generating annotation tables for DNA chips...
  12. pmc Acute myeloid leukemia fusion proteins deregulate genes involved in stem cell maintenance and DNA repair
    Myriam Alcalay
    Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
    J Clin Invest 112:1751-61. 2003
    ..We propose that expansion of the stem cell compartment and induction of a mutator phenotype are relevant features underlying the leukemic potential of AML-associated fusion proteins...