Publications

Journals

• Lori Dalton, Virginia Ballarin and Marcel Brun, "Clustering Algorithms: On Learning, Validation, Performance, and Applications to Genomics", Current Genomics, Volume 10, Number 6, September 2009 , pp. 430-445(16)
• Edward R. Dougherty, Marcel Brun, Jeffrey M. Trent, Michael L. Bittner, "Conditioning-Based Modeling of Contextual Genomic Regulation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 310-320, Apr.-June 2009, doi:10.1109/TCBB.2007.70247
• Marcel Brun, Qian Xu, Edward R. Dougherty, "Which is better: hold-out or full-sample classifier design?" EURASIP Journal on Bioinformatics and Systems Biology, Volume 2008 (2008), Article ID 297945, 8 pages
• Meschino G. J., Espin Andrade R. A., Ballarin V. L., A framework for tissue discrimination in magnetic resonance brain images based on predicates analysis and compensatory fuzzy logic. Intern. J. of Intelligent Computing in Medical Sciences and Image Processing (2008). Vol. 2 (3): pp. 1-16.
• Dmitriy Ovcharenko, Kevin Kelnar, Charles Johnson, Nan Leng, and David Brown. 2007 Genome scale microRNA and siRNA screens identify small RNA modulators of TRAIL-induced death receptor apoptosis pathway. Cancer Research Cancer Research 67: 10782-10788
• Phillip Stafford, Marcel Brun, Edward R. Dougherty, "Three methods for optimization of cross-laboratory and cross-platform microarray expression data", Nucleic Acids Res. 2007 May; 35(10): e72.
• Marcel Brun, Seungchan Kim, Woonjung Choi, and Edward R. Dougherty, "Comparison of network models via steady-state trajectories", EURASIP Journal on Bioinformatics and Systems Biology, 2007, Article ID 82702, 11 pages.
• Charles D Johnson ; Yoganand Balagurunathan, Edward R. Dougherty, Cynthia A Afshari, Qiang He, K. S. Ramos. Insight into redox regulated gene networks in vascular cells 2007. Bioinformation 1(10)
• Vasker Bhattacherjee, Partha Mukhopadhyay, Saurabh Singh, Charles Johnson, John T. Philipose, Courtney P. Warner, Robert M. Greene, M. Michele Pisano (2007) Neural crest and mesoderm lineage-dependent gene expression in orofacial development Differentiation 75 (5), 463-477.
• Scandurra A. G., Meschino G. J., Passoni L. I., Dai Pra A. L., Introzzi A. R., Clara F. M. Optimization of arterial age prediction models based in pulse wave. J. of Physics: Conference Series (2007). Vol. 90
• Santalla H., Meschino G. J., Ballarin V. L., Effects on MR images compression in tissue classification quality. J. of Physics: Conference Series (2007). Vol. 90
• Gonzalez M. A., Meschino G. J., Ballarin V. L., Automatic fuzzy inference system development for marker based watershed segmentation J. of Physics: Conference Series (2007). Vol. 90
• Charles Johnson, Aurora Esquela-Kerscher, Giovanni Stefani, Mike Byrom, Kevin Kelnar, Dmitriy Ovcharenko, Mike Wilson, Xiaowei Wang, Jeffrey Shelton, Jaclyn Shingara, Lena Chin, David Brown and Frank J. Slack. The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res. 2007 Aug 15;67 (16):7713-22 17699775
• Jianping Hua, David W. Craig, Marcel Brun, Jennifer Webster, Victoria Zismann, Waibhav Tembe, Keta Joshipura, Matthew J. Huentelman, Edward R. Dougherty, and Dietrich A. Stephan, "SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays", Bioinformatics 23(1): pp. 57-63, 2007
• John V. Pearson, Matthew J. Huentelman, Rebecca F. Halperin, Waibhav D. Tembe, Stacey Melquist, Nils Homer, Marcel Brun, Szabolcs Szelinger, Keith D. Coon, Victoria L. Zismann, Jennifer A. Webster, Thomas Beach, Sigrid B. Sando, Jan O. Aasly, Reinhard Heun, Frank Jessen, Heike Kolsch, Magdalini Tsolaki, Makrina Daniilidou, Eric M. Reiman, Andreas Papassotiropoulos, Michael L. Hutton, Dietrich A. Stephan, and David W. Craig, "Identification of the genetic basis for complex disorders using pooling-based genome-wide SNP association studies", Am J Hum Genet. 2007 January; 80(1): 126-139.
• Richard Shippy, Paul Wolber, Wendell D. Jones, Roderick V. Jensen, Stephanie Fulmer-Smentek, Charles D. Johnson, P. Scott Pine, Cecilie Boysen, Xu Guo, Eugene Chudin, Yongming Andrew Sun, James C. Willey, Jean Thierry-Mieg, Danielle Thierry-Mieg, Robert A. Setterquist, Mike Wilson, Anne Bergstrom Lucas, Natalia Novoradovskaya, Adam Papallo, Yaron Turpaz, Shawn C. Baker, Janet A Warrington, Leming Shi, and Damir Herman. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol. 2006 Sep;24(9):1123-31.
• Leming Shi, Laura H. Reid, Richard Shippy, Shawn C. Baker, Patrick J. Collins, Francoise de Longueville, Ernest S. Kawasaki, Kathleen Y. Lee, Yuling Luo, Yongming Andrew Sun, Janet A. Warrington, James C. Willey, Robert A. Setterquist, Gavin M. Fischer, David J. Dix, Yvonne P. Dragan, Federico M. Goodsaid, Damir Herman, Roderick V. Jensen, Charles D. Johnson, Wendell D. Jones, Edward K. Lobenhofer, Raj K. Puri, Uwe Scherf, Jean Thierry-Mieg, Weida Tong, Charles Wang, Mike Wilson,, Lu Zhang,, William Slikker, Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep 8;24(9):1151-1161
• Brun Marcel, Sima Chao, Hua Jianping, Lowey James, Carroll Brent, Suh Edward, Dougherty Edward R., "Model-based evaluation of clustering validation measures", Pattern Recognition, 40 (3), pp Pages: 807-824, 2006
• Edward R. Dougherty, Marcel Brun, "On the Number of Close-to-Optimal Feature Sets", Cancer Informatics 2006:2 pp. 189-196, 2006
• Partridge CR, Johnson CD, Ramos KS. In vitro models to evaluate acute and chronic injury to the heart and vascular systems. Toxicol In Vitro. 2005 Aug;19(5):631-44. Review. PMID: 15893448
• Partridge CR, Williams ES, Barhoumi R, Tadesse MG, Johnson CD, Lu KP, Meininger GA, Wilson E, Ramos KS. Novel genomic targets in oxidant-induced vascular injury. J Mol Cell Cardiol. 2005 Jun;38(6):983-96. Epub 2005 Apr 19. PMID: 15910882
• Thackaberry EA, Jiang Z, Johnson CD, Ramos KS, Walker MK. Toxicogenomic Profile of 2,3,7,8-Tetrachlorodibenzo-p-dioxin in the Murine Fetal Heart: Modulation of Cell Cycle and Extracellular Matrix Genes. Toxicol Sci. 2005 PMID: 16120747
• Dougherty E, Brun M.., "A Probabilistic Theory of Clustering", Pattern Recognition , 37 , pp.917-925 , 2004
• Johnson CD, Balagurunathan Y, Tadesse MG, Falahatpisheh MH, Brun M, Walker MK, Dougherty ER, Ramos KS. Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environ Health Perspect. 2004 Mar;112(4):403-12. PMID: 15033587
• G. J. Meschino, E. Moler, Semi-automated segmentation of bone marrow biopsies by texture features and mathematical morphology. Analytical and Quantitative Cytology and Histology 2004 (ISSN 0884?6812) 26 (1): 31-38
• Johnson CD, Balagurunathan Y, Lu KP, Tadesse M, Falahatpisheh MH, Carroll RJ, Dougherty ER, Afshari CA, Ramos KS. Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol Genomics. 2003 May 13;13(3):263-75. PMID: 12657712
• Hashimoto R. F., Dougherty E. R., Brun M., Zhou Z., Bittner M. L., Trent J. M., "Efficient Selection of Feature Sets Possessing High Coefficients of Determination Based on Incremental Determinations", Signal Processing, Vol. 83 (4), pp. 695-712, April 2003
• E. Moler, E. Blotta, J. I. Pastore, G. J. Meschino, Ballarin V. L., Enhancement techniques in fingerprints as a tool in dactyloscopy J. of Comp. Sci. and Tech. (JCST) 2003 (ISSN 1666?6038) 3 (2): 52-55
• Johnson CD, Balagurunathan Y, Lu KP, Tadesse M, Falahatpisheh MH, Carroll RJ, Dougherty ER, Afshari CA, Ramos KS. Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol Genomics. 2003 13;13(3):263-75. PMID: 12657712
• Dougherty E., Barrera J., Brun M., Kim S., Cesar R.M., Chen Y., Bittner M., Trent J.M., "Inference from clustering with application to gene-expression microarray", Journal of Computational Biology, 9 (1), 2002, pp. 105-126
• Garcia MR, Amstalden M, Williams SW, Johnson CD, Nizielski SE, Keisler DH, and Williams GL. Leptin and pubertal development in heifers: relationship of ob gene expression to circulating leptin as measured by heterologous radioimmunoassay. 1999. Biol. Reprod. 60 (Suppl. 1): 253.

Book Chapters

• Davison, T. S., Johnson, C. D., and Andruss, B. F. (2006). Analyzing Micro-RNA Expression Using Microarrays. Methods Enzymol. 411, 14-34.
• Roberto Hirata Jr., Marcel Brun, Junior Barrera, and Edward R. Dougherty, “Aperture filters: theory, application, and multiresolution analysis,” Advances In Nonlinear Signal And Image Processing, eds. Sephen Marshall and Giovanni L. Sicuranza, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, 2006.
• Brun M., Johnson C.D., and Ramos K.S.. Clustering: revealing intrinsic dependencies in microarray data, Genomic Signal Processing: Perspectives, Genomic Signal Processing and Statistics, eds. E. R. Dougherty, I. Shmulevich, J. Chen, and Z. J. Wang, EURASIP Book Series on Signal Processing and Communication, Hindawi Publishing Corporation, 2005.

Patent - Inventor

• Mir-10 regulated genes and pathways as targets for therapeutic intervention 20090192114
• Mir-16 regulated genes and pathways as targets for therapeutic intervention 20090175827
• Mir-34 regulated genes and pathways as targets for therapeutic intervention 20090227533

Additionally, listed as an inventor on over 15 other patent applications.

Ambion TechNotes

• Charles Johnson, Robert Setterquist, Sharmili Moturi, Charmaine San Jose, Penn Whitley Increase Signal and Detect More Genes on Affymetrix™ Arrays Ambion, Inc. TechNote 12(4) page 28-29
• Robert Setterquist, Mike Wilson, Charles Johnson, Shika Agarwal, Sharmili Moturi. Synthesize High Yields of Biotinylated aRNA. Ambion TechNote 12(3) page17-18
• Penn Whitley, Sharmili Moturi, Jose Santiago, Charles Johnson, Robert Setterquist Improved Microarray Sensitivity using Whole Blood RNA Samples Ambion, Inc. TechNote 12(3) page 20-22

Abstracts

• Marcel Brun, Qian Xu, Edward R. Dougherty, "A Criterion for Choosing between Full-sample and Hold-out Classifier Design", IEEE International Workshop on Genomic Signal Processing and Statistics, 2008. GENSiPS 2008. Phoenix, AZ, USA, 8-10-June 2008
• Jason Wiggins, Dmitriy Ovcharenko, Kevin Kelnar, Jaclyn Shingara, Charles D. Johnson, David Brown, and Andreas G. Bader. 2007. microRNAs in the Treatment of Cancer
• A.E. Szafranska, M. Doleshal, B. Cannon, L. Elizondo, J. Ehardt, M. Wilson, B. Choudhury, C.D. Johnson and S. Hunicke-Smith. 2007. Exploration of microRNA Expression Profiling in Fixed Archived Tissues: Lung Cancer Pilot Study
• Yufang Yin, Yufei Huang, Viji Shanmugam, Marcel Brun, Jianping Hua, Edward Dougherty, "A Bayesian approach for uncovering gene network motifs", Fifth IEEE International Workshop on Genomic Signal Processing and Statistics, June 10-12, 2007, Tuusula, Finland (GENSIPS 2007)
• Jin Xu, Timothy S. Davison and Charles D. Johnson. 2006 RANOVA: A New Method of Detecting Differentially Expressed Genes through Probe Level Data from Oligonucleotide Arrays. International Biometric Society of Eastern North American Region.
• Darin M. Taverna, Marcel Brun, Edward R. Dougherty, Yidong Chen, "Quality-based distance measures and applications to clustering", 2nd IEEE/NLM International Workshop on Life Science Systems and Applications, Bethesda, Maryland, 2006 (LSSA 2006)
• Tae-Hoon Chung, Marcel Brun, Seungchan Kim, "Quantization of Global Gene Expression Data", Proceedings of the 5th International Conference on Machine Learning and Applications, pages 187-192, Washington, DC, USA, 2006 (ICMLA 06)
• Johnson C.D., Li Y., Wilson M., Davison, T.S., 2006. PowerAssist™: A Microarray QC Tool. Discovery to Diagnostics.
• Whitley, P., Moturi, S., Santiago J., Agarwal, S., San Jose, C., Johnson, C.D., Wilson M., Setterquist R., 2005. A service for gene expression profiling form Globin-depleted whole blood RNA, Microarray's in Medicine.
• Marcel Brun and Edward R. Dougherty, "Clustering algorithms do not learn, but they can be learned", Proc. SPIE Int. Soc. Opt. Eng. 5916, 59160T (2005)
• Chapman, L.R., Johnson, C.D., Falahatpisheh, M.H., Ramos, K.S. 2004. High Mobility Group A1a gene Behaves as a Stress-Regulated Transcription Factor in Vascular Smooth Muscle Cells. Annual Meeting of Society of Toxicology.
• Johnson, C.D., Thomas, T.L., Ramos, K.S. 2004 A genomic model of benzo(a)pyrene induced atherogenesis. Annual Meeting of Society of Toxicology.
• Falahatpisheh, M.H., Johnson, C.D., Ramos, K.S. 2004. Transcriptional profiles following ligand-activated Ahr signaling in the developing kidney: A role for Wt1 and IGF signaling. Annual Meeting of Society of Toxicology.
• Falahatpisheh, M.H., Johnson, C.D., Ramos, K.S. 2004. Transcriptional profiles following ligand-activated Ahr signaling in the developing kidney: A role for Wt1 and IGF signaling. Annual Meeting of Society of Biochemistry.
• Johnson C.D., Balagurunathan, Y.,Tadesse, M.,Falahatpisheh, M.H., Dougherty, E.R, Walker, M.K. Ramos K.S. 2003. From "omics" to insight: the use of a novel computational approach to study gene-gene interactions. TOXICOL SCI 72 (1): 449 Suppl.
• Walker M. K., C.D. Johnson, M. Tadesse, K.S. Ramos, I.D. Steele, E.A. Thackaberry. 2003. Dioxin induces growth arrest and reduces cell cycle gene expression in the fetal murine heart. TOXICOL SCI 72 (1): 1124 Suppl..
• Ramos, K.S., Johnson, C.D., Falahatpisheh, M.H., Tadesse, M., Thomas, T., Beremand, P., . Lu, K.P, Balagurunathan, Y., Afshari, C.A., Dougherty, E.R.. 2003. Application of clustering methodologies to the analysis of altered cellular phenotypes induced by oxidative stress. TOXICOL SCI 72 (1): 1084 Suppl.
• Partridge, C.R., E.S. Williams, K.P. Lu, S. Chao, C.D. Johnson, R. Mouneimni, G.A. Meininger, E. Wilson, and K.S. Ramos. 2003. Genomic and immunofluorescence analysis of interactive gene networks in oxidant-induced atherogenesis. TOXICOL SCI 72 (1): 459 Suppl. S
• Falahatpisheh, M.H., Johnson, C.D., Tadesse, M.G., Ramos, K.S. 2003. Chemical Disruption of Global Gene Expression during Nephrogenesis: Role of Aryl Hydrocarbon Receptor. TOXICOL SCI 72 (1): 464 Suppl.
• Partridge C.R., Lu K.P., Johnson C.D., Williams E.S., Meininger G.A., Wilson E., Ramos K.S. 2002. Transcriptome analysis of vascular tissue following oxidative injury. Annual Meeting of American Physiological Society.
• Johnson C.D., Lu K.P., Beremand P.D., Thomas T.L., Ramos K.S. 2002. Global gene expression profiles in chemical atherogenesis. Annual Meeting of Society of Toxicology.
• Falahatpisheh, M.H, Johnson, C.D, Ramos K.S. 2002. Global gene expression profiles in disrupted nephrogenesis. Gordon Research Conference
• Partridge, C.R., E.S. Williams, K.P. Lu, S. Chao, C.D. Johnson, R. Mouneimni, G.A. Meininger, E. Wilson, and K.S. Ramos. 2002. Genomic and immunofluorescence analysis of interactive gene networks in oxidant-induced atherogenesis. Annual Meeting of Gulf Coast Society of Toxicology
• Johnson C.D., Lu K. P., Afshari C.A., Balagurunathan Y., Dougherty E.R., Ramos K.S.. 2001. Global response of SMC to oxidative stress. Symposium on Gene Expression and Proteomics in Environmental Health Sciences.
• Brun M., Hirata R., Barrera J., Dougherty E.R., "Hybrid Human-machine Non-linear Filter Design Using Envelopes", Proceedings of the SIBGRAPI 2001, pp. 106-112, October 2001, Florianopolis, Brazil.
• Dougherty E.R., Barrera J., Brun M., Kim S., Marcondes R., Chen Y., Bittner M.L., Trent J.M., "Time series inference from clustering", Proc. SPIE Vol. 4266, p. 222-227, Microarrays: Optical Technologies and Informatics, Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty; Eds., January 2001
• Chen Y., Jiang Y., Dougherty E., Kim S., Yakhini Z., Ben-Dor A., Sampas N., Radamacher M., Simon R., Brun M., Gubitoso M.D., Barrera J., Gooden C., Glatfelter A., Meltzer P., Trent J., Bittner M.L., "Estimating the reliability of inferences based on cDNA microarray ratio data", en Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis, Heidelburg, Germany, October 2000
• Dougherty E., Kim S., Mozelle G., Barrera J., Brun M., "Multiresolution Filter Design", Proc. SPIE Vol. 3961, p. 12-21, Nonlinear Image Processing XI, Edward R. Dougherty; Jaakko T. Astola; Eds., January 2000
• Nizielski S.E., Seo J., Koppanur R., Johnson C.D. 1999. Divergent effects of insulin-like growth factor-I (IGF-I) and growth hormone (GH) on the expression of adipogenic markers in brown vs. white adipose tissue of rats. Annual Meeting of North American Association for the Study of Obesity.
• J. Barrera, E. R. Dougherty and M. Brun, "Hybrid human-machine binary morphological operator design", Proc. SPIE Vol. 3646, p. 162-173, Nonlinear Image Processing X, Edward R. Dougherty; Jaakko T. Astola; Eds., January 1999
• Barrera J., Brun M., "Translation Invariant Transformation of Discrete Random Sets", Proceedings of the SIBGRAPI 98, pp. 450-455, INPA, Rio de Janeiro, October 1998
• Nizielski, S. E. and Johnson C.D. 1997. Expression of a bovine growth hormone (bGH) transgene increases brown adipose tissue (BAT) mass: Involvement of C/EBP-g and PPAR-a. Annual Meeting of North American Association for the Study of Obesity.