Michael F Ochs

Summary

Affiliation: Fox Chase Cancer Center
Country: USA

Publications

  1. ncbi request reprint Incorporation of gene ontology annotations to enhance microarray data analysis
    Michael F Ochs
    Fox Chase Cancer Center, Philadelphia, PA, USA
    Methods Mol Biol 377:243-54. 2007
  2. pmc Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Bossone 714, Drexel University, 3143 Chestnut Street, Philadelphia, PA 19104, USA
    Mol Cancer 5:55. 2006
  3. pmc Three allele combinations associated with multiple sclerosis
    Olga O Favorova
    Department of Molecular Biology and Medical Biotechnology, Russian State Medical University, 15 3d Cherepkovskaya ul, Moscow 121552, Russia
    BMC Med Genet 7:63. 2006
  4. ncbi request reprint Microarrays in cancer: research and applications
    Michael F Ochs
    Department of Information Science and Technology and Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
    Biotechniques . 2003
  5. ncbi request reprint Bayesian decomposition: analyzing microarray data within a biological context
    Michael F Ochs
    Bioinformatics, Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Ann N Y Acad Sci 1020:212-26. 2004
  6. pmc ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor
    Lori Rink
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e54477. 2013
  7. pmc The insulin-like growth factor system as a potential therapeutic target in gastrointestinal stromal tumors
    Martin G Belinsky
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    Cell Cycle 7:2949-55. 2008
  8. pmc Matrix factorization for recovery of biological processes from microarray data
    Andrew V Kossenkov
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Methods Enzymol 467:59-77. 2009
  9. ncbi request reprint Estimating gene function with least squares nonnegative matrix factorization
    Guoli Wang
    Fox Chase Cancer Center, Philadelphia, PA, USA
    Methods Mol Biol 408:35-47. 2007
  10. pmc Determination of strongly overlapping signaling activity from microarray data
    Ghislain Bidaut
    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    BMC Bioinformatics 7:99. 2006

Collaborators

Detail Information

Publications21

  1. ncbi request reprint Incorporation of gene ontology annotations to enhance microarray data analysis
    Michael F Ochs
    Fox Chase Cancer Center, Philadelphia, PA, USA
    Methods Mol Biol 377:243-54. 2007
    ..Here we provide a method to utilize biological annotations in the form of gene ontologies to interpret the results of individual or multiple pattern recognition analyses of a microarray experiment...
  2. pmc Pathway-specific differences between tumor cell lines and normal and tumor tissue cells
    Adam Ertel
    Center for Integrated Bioinformatics, School of Biomedical Engineering, Science and Health Systems, Bossone 714, Drexel University, 3143 Chestnut Street, Philadelphia, PA 19104, USA
    Mol Cancer 5:55. 2006
    ..The aim of the study was to identify significant alterations in pathway usage in cell lines in comparison with normal and tumor tissue...
  3. pmc Three allele combinations associated with multiple sclerosis
    Olga O Favorova
    Department of Molecular Biology and Medical Biotechnology, Russian State Medical University, 15 3d Cherepkovskaya ul, Moscow 121552, Russia
    BMC Med Genet 7:63. 2006
    ..As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS...
  4. ncbi request reprint Microarrays in cancer: research and applications
    Michael F Ochs
    Department of Information Science and Technology and Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
    Biotechniques . 2003
  5. ncbi request reprint Bayesian decomposition: analyzing microarray data within a biological context
    Michael F Ochs
    Bioinformatics, Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Ann N Y Acad Sci 1020:212-26. 2004
    ..By removing routine metabolic signatures and linking specific signatures to signaling pathway activity, BD makes it possible to link changes in microarray results to signaling pathways...
  6. pmc ZNF-mediated resistance to imatinib mesylate in gastrointestinal stromal tumor
    Lori Rink
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 8:e54477. 2013
    ..Knockdown of the 14 IM-sensitizing genes (10 ZNFs) universally led to downregulation of six genes, including TGFb3, periostin, and NEDD9. These studies implicate a role of KRAB-ZNFs in modulating response to TKIs in GIST...
  7. pmc The insulin-like growth factor system as a potential therapeutic target in gastrointestinal stromal tumors
    Martin G Belinsky
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
    Cell Cycle 7:2949-55. 2008
    ..We also discuss how the IGF pathway may provide additional molecular targets for the treatment of GISTs that respond poorly to IM therapy...
  8. pmc Matrix factorization for recovery of biological processes from microarray data
    Andrew V Kossenkov
    The Wistar Institute, Philadelphia, Pennsylvania, USA
    Methods Enzymol 467:59-77. 2009
    ..Differences in the strength of the signatures between the samples suggest that BD will be most useful for systems modeling and BFRM for biomarker discovery...
  9. ncbi request reprint Estimating gene function with least squares nonnegative matrix factorization
    Guoli Wang
    Fox Chase Cancer Center, Philadelphia, PA, USA
    Methods Mol Biol 408:35-47. 2007
    ..Herein, application of this method to microarray data is demonstrated in order to predict gene function...
  10. pmc Determination of strongly overlapping signaling activity from microarray data
    Ghislain Bidaut
    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    BMC Bioinformatics 7:99. 2006
    ....
  11. ncbi request reprint Determining transcription factor activity from microarray data using Bayesian Markov chain Monte Carlo sampling
    Andrew V Kossenkov
    The Wistar Institute, Philadelphia, PA, USA
    Stud Health Technol Inform 129:1250-4. 2007
    ..The new algorithm provides an approach for estimating the levels of transcription factor activity from microarray data, and therefore provides insights into biological response...
  12. ncbi request reprint WaveRead: automatic measurement of relative gene expression levels from microarrays using wavelet analysis
    Ghislain Bidaut
    Bioinformatics, Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111 2497, USA
    J Biomed Inform 39:379-88. 2006
    ....
  13. ncbi request reprint ClutrFree: cluster tree visualization and interpretation
    Ghislain Bidaut
    Division of Population Science, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 20:2869-71. 2004
    ..AVAILABILITY: The ClutrFree Java source code and compiled bytecode are available as a package under the GNU General Public License at http://bioinformatics.fccc.edu..
  14. pmc Matrix factorisation methods applied in microarray data analysis
    Andrew V Kossenkov
    The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
    Int J Data Min Bioinform 4:72-90. 2010
    ..We focus on these methods rather than traditional clustering methods applied to microarray data, which assign one gene to one cluster...
  15. ncbi request reprint ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database
    Andrew Kossenkov
    Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation
    Bioinformatics 19:675-6. 2003
    ..The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page...
  16. pmc LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates
    Guoli Wang
    Division of Population Science, Fox Chase Cancer Center, Philadelphia, PA, USA
    BMC Bioinformatics 7:175. 2006
    ..Previous work has shown that such uncertainties can be extremely valuable for pattern recognition...
  17. pmc Gene expression signatures and response to imatinib mesylate in gastrointestinal stromal tumor
    Lori Rink
    Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
    Mol Cancer Ther 8:2172-82. 2009
    ....
  18. pmc Global reactivation of epigenetically silenced genes in prostate cancer
    Ilsiya Ibragimova
    Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
    Cancer Prev Res (Phila) 3:1084-92. 2010
    ..Further study of the hypermethylome will provide insight into the biology of the disease and facilitate translational studies in prostate cancer...
  19. ncbi request reprint Bayesian decomposition analysis of bacterial phylogenomic profiles
    Ghislain Bidaut
    Division of Population Science, Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
    Am J Pharmacogenomics 5:63-70. 2005
    ..At the same time, the effectiveness of the existing antibacterials is rapidly decreasing due to the spread of multidrug-resistant pathogens...
  20. ncbi request reprint FGDP: functional genomics data pipeline for automated, multiple microarray data analyses
    Jeffrey D Grant
    Bioinformatics, Department of Information Science and Technology, Division of Basic Science, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
    Bioinformatics 20:282-3. 2004
    ..The functional genomics data pipeline provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed and provides a web server and interface for presenting results...
  21. pmc A Markov chain Monte Carlo technique for identification of combinations of allelic variants underlying complex diseases in humans
    Alexander V Favorov
    Bioinformatics Laboratory, GosNIIGenetika, Fersmana St 3 1 31, Moscow 117545, Russia
    Genetics 171:2113-21. 2005
    ..For the simulated data, the algorithm identified all the phenotype-associated allele combinations coded into the data and, for the MS data, it replicated the previously known findings...