Laboratory for Computational Systems Biology






Johannes Freudenberg Johannes Freudenberg
Research Associate
freudejm at uc dot edu
318 Kettering



University of Cincinnati, Cincinnati, Ohio, Ph.D (2009) Bioinformatics
Universität Leipzig, Leipzig, Germany, Diplom (2004) Computer Science with minor in Biomedicine

Professional Experience

2008 - present, Research Associate, Department of Environmental Health, University of Cincinnati
2004 - 2007 Graduate Assistant, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
2002 - 2003 Database Programmer, Center for Clinical Trials, Leipzig, Germany
1999 - 2001 Graduate Assistant, Department of Computer Science, Universität Leipzig, Leipzig, Germany



  • Freudenberg JM, Sivaganesan S, Wager M, and Medvedovic M. A semi-parametric Bayesian model for unsupervised differential co-expression analysis. BMC Bioinformatics 11:234. 2010. (Support page).
  • Shinde K, Phatak M, Freudenberg JM, Chen J, Li Q, Vineet JK, Hu Z, Ghosh K, Meller J, and Medvedovic M. Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics 11:27. 2010.
2009 2007
  • Kaiser S, Park YK, Franklin JL, Halberg RB, Yu M, Jessen WJ, Freudenberg J, Chen X, Haigis K, Jegga AG, Kong S, Sakthivel B, Xu H, Reichling T, Azhar M, Boivin GP, Roberts RB, Bissahoyo AC, Gonzales F, Bloom GC, Eschrich S, Carter SL, Aronow JE, Kleimeyer J, Kleimeyer M, Ramaswamy V, Settle SH, Boone B, Levy S, Graff JM, Doetschman T, Groden J, Dove WF, Threadgill DW, Yeatman TJ, Coffey RJ Jr, and Aronow BJ. Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer. Genome Biology 8(7): R131. 2007.

  • Ray M, Dharmarajan S, Freudenberg J, Zhang W, and Patterson GA. Expression profiling of human donor lungs to understand primary graft dysfunction after lung transplantation. American Journal of Transplantation 7(10):2396-2405. 2007.


  • Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Research 33(18):5914-23. 2005