Johannes M Freudenberg

Summary

Affiliation: University of Cincinnati
Country: USA

Publications

  1. pmc Genomics Portals: integrative web-platform for mining genomics data
    Kaustubh Shinde
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati OH 45267 0056, USA
    BMC Genomics 11:27. 2010
  2. pmc CLEAN: CLustering Enrichment ANalysis
    Johannes M Freudenberg
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av, ML 56, Cincinnati OH 45267 0056, USA
    BMC Bioinformatics 10:234. 2009
  3. pmc Generalized random set framework for functional enrichment analysis using primary genomics datasets
    Johannes M Freudenberg
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
    Bioinformatics 27:70-7. 2011
  4. pmc Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules
    Jing Chen
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
    PLoS Comput Biol 9:e1003198. 2013
  5. pmc WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results
    Vineet K Joshi
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av, ML 56, Cincinnati OH 45267 0056, USA
    Source Code Biol Med 6:3. 2011
  6. pmc A semi-parametric Bayesian model for unsupervised differential co-expression analysis
    Johannes M Freudenberg
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati OH 45267 0056, USA
    BMC Bioinformatics 11:234. 2010
  7. pmc Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia
    Neville N C Tam
    Department of Environmental Health, University of Cincinnati Medical Center, Kettering Laboratory, Suite 128, 3223 Eden Avenue, Cincinnati, Ohio 45267 0056, USA
    Mol Endocrinol 24:2207-17. 2010

Collaborators

Detail Information

Publications7

  1. pmc Genomics Portals: integrative web-platform for mining genomics data
    Kaustubh Shinde
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati OH 45267 0056, USA
    BMC Genomics 11:27. 2010
    ..Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems...
  2. pmc CLEAN: CLustering Enrichment ANalysis
    Johannes M Freudenberg
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av, ML 56, Cincinnati OH 45267 0056, USA
    BMC Bioinformatics 10:234. 2009
    ....
  3. pmc Generalized random set framework for functional enrichment analysis using primary genomics datasets
    Johannes M Freudenberg
    Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
    Bioinformatics 27:70-7. 2011
    ..This can lead to loss of statistical power and can introduce biases affecting the interpretation of experimental results...
  4. pmc Genome-wide signatures of transcription factor activity: connecting transcription factors, disease, and small molecules
    Jing Chen
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
    PLoS Comput Biol 9:e1003198. 2013
    ..The package also contains all data used in the analysis including 494 TREG binding profiles based on ENCODE ChIP-seq data. The treg package can be downloaded at http://GenomicsPortals.org. ..
  5. pmc WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results
    Vineet K Joshi
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Av, ML 56, Cincinnati OH 45267 0056, USA
    Source Code Biol Med 6:3. 2011
    ..For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at http://ClusterAnalysis.org/...
  6. pmc A semi-parametric Bayesian model for unsupervised differential co-expression analysis
    Johannes M Freudenberg
    Laboratory for Statistical Genomics and Systems Biology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati OH 45267 0056, USA
    BMC Bioinformatics 11:234. 2010
    ..Given pre-defined sets of biological samples, such analysis aims at identifying genes that are co-expressed in one, but not in the other set of samples...
  7. pmc Research resource: estrogen-driven prolactin-mediated gene-expression networks in hormone-induced prostatic intraepithelial neoplasia
    Neville N C Tam
    Department of Environmental Health, University of Cincinnati Medical Center, Kettering Laboratory, Suite 128, 3223 Eden Avenue, Cincinnati, Ohio 45267 0056, USA
    Mol Endocrinol 24:2207-17. 2010
    ....