Supplementary Materials

G. Bidaut (2006). Estimating gene function in gene deletion mutant, in Methods in Molecular Biology: Microarray Data Analysis, M. Korenberg, Editor, Humana Press, Totowa
http://www.cancerbiostats.onc.jhmi.edu/supportmmbchapter/index.html

Scientific Publications

A. Ertel, A. Verghese, S. W. Byers, M. Ochs, A. Tozeren: “Pathway-specific differences between tumor cell lines and normal and tumor tissue cells”, Mol Cancer, 5, 55, 2006. http://www.molecular-cancer.com/content/5/1/55

J. Spindlen, R. C. Gentleman, P. D. Haaland, M. Langille, N. L. Meur, M. F. Ochs, C. Schmitt, C. A. Smith, A. S. Treistar, R. R. Brinkman: “Data standards for flow cytometry”, Omics, 10, 209, 2006. http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.209

O. O. Favorova, A. V. Favorov, A. N. Boiko, T. V. Andreewski, M. A. Sudomoina, A. D. Alekseenkov, O. G. Kulakova, E. I. Kusev, G. Parmigiani, M. F. Ochs: “Three allele combinations associated with Multiple Sclerosis”, BMC Medical Genetics, 7, 63, 2006. http://www.biomedcentral.com/1471-2350/7/63

G. Wang, A. Kossenkov, M. F. Ochs: LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates, BMC Bioinformatics, 7, 175, 2006. http://www.biomedcentral.com/1471-2105/7/175

G. Bidaut, K. Suhre, J.-M. Claverie, M. F. Ochs: Determination of strongly overlapping signaling activity from microarray data, BMC Bioinformatics, 7, 99, 2006. http://www.biomedcentral.com/1471-2105/7/99

A. V. Favorov, T. V. Andreewski, M. A. Sudomoina, O. O. Favorova, G. Parmigiani, M. F. Ochs: “A Markov Chain Monte Carlo technique for identification of combinations of allelic variants underlying complex diseases”, Genetics, 171, 2123, 2005. http://www.genetics.org/cgi/content/full/171/4/2113

T. R. Brown, M. F. Ochs, W. D. Rooney, R. S. Stoyanova, X. Li, C. S. Springer, Jr.: “Bayesian Image Decomposition applied to relaxographic imaging”, International Journal of Imaging Systems and Technology, 15, 209, 2005.

A. J. Peterson, A. V. Kossenkov, M. F. Ochs: “Linking gene expression patterns and transcriptional regulation in Plasmodium falciparum”, in J. Shoemaker and S. Lin, Editors, Methods of Microarray Data Analysis V, In Press.

G. Bidaut, K. Suhre, J-M. Claverie, M. F. Ochs: “Bayesian Decomposition analysis of bacterial phylogenomic profiles”, American Journal of Pharmacology, 5, 63, 2005.

A. V. Kossenkov, G. Bidaut, and M. F. Ochs: “Genes associated with prognosis in adenocarcinomas across studies at multiple institutions”, in J. Shoemaker and S. Lin, Editors, Methods of Microarray Data Analysis IV, 239 – 253, Kluwer Academic, Boston, 2005.

T. D. Moloshok, D. J. Datta, A. V. Kossenkov, M. F. Ochs: “Bayesian Decomposition classification of the project normal data set”, in K. Johnson and S. Lin, Editors, Methods of Microarray Data Analysis III, 211 – 232, Kluwer Academic, Boston, 2003.

A. Frolov, S. Chahwan, M. Ochs, J. P. Arnoletti, Z.-Z.Pan, O. Favorova, J. A. Fletcher, M. von Mehren, B. L. Eisenberg, and A. K. Godwin: "Response markers and the molecular mechanisms of action of Gleevec in gastrointestinal stromal tumors (GISTs)," Molecular Cancer Therapeutics, 2, 699, 2003. http://mct.aacrjournals.org/cgi/content/full/2/8/699

G. Bidaut, J.D. Grant, T.D. Moloshok, F. J. Manion, M. F. Ochs: “Bayesian Decomposition analysis of gene expression in yeast deletion mutants”, in K. Johnson and S. Lin, Editors, Methods of Microarray Data Analysis II, 105 - 122, Kluwer Academic, Boston, 2002.

T. D. Moloshok, R. R. Klevecz, J. D. Grant, F. J. Manion, W. F. Speier IV, M. F. Ochs: "Application of Bayesian Decomposition for analyzing microarray data", Bioinformatics, 18, 566, 2002. http://bioinformatics.oxfordjournals.org/cgi/reprint/18/4/566

H.W. Kestler III, Y. Li, Y.M. Naidu, C.F. Butler, M.F. Ochs, G. Jaenel, N.W. King, M.D. Daniel, R.C. Desrosiers. "Comparison of simian immunodeficiency virus isolates", Nature, 331, 619, 1988. http://www.nature.com/nature/journal/v331/n6157/abs/331619a0.html

Software Tools and Systems

G. Bidaut, F. J. Manion, C. Garcia, C., M. F. Ochs: “WaveRead: automatic measurement of relative gene expression levels from microarrays using wavelet analysis”, J Biomedical Informatics, 39, 379, 2006.

M. F. Ochs, E. M. Goralczyk, J. D. Grant, F. J. Manion, A. Yeung, S. Seeholzer, G. Mathew, R. R. Hardy, J. R. Beck: “A unified laboratory information management system for research data”, MedInfo, 1784, 2004.

G. Bidaut and M. F. Ochs: “ClutrFree: Cluster tree visualization and interpretation”, Bioinformatics, 20, 2869, 2004. http://bioinformatics.oxfordjournals.org/cgi/reprint/20/16/2869

J. D. Grant, L. A. Somers, Y. Zhang, F. J. Manion, G. Bidaut, and M. F. Ochs: “FGDP: functional genomics data pipeline for automated, multiple microarray data analyses”, Bioinformatics, 20, 282, 2004. http://bioinformatics.oxfordjournals.org/cgi/reprint/20/2/282

A.V . Kossenkov, F.J. Manion, E. Korotkov, T.D. Moloshok, M.F. Ochs: “ASAP: Automated Sequence Annotation Pipeline for web-based updating of sequence information with a local dynamic database”, Bioinformatics, 19, 675, 2003. http://bioinformatics.oxfordjournals.org/cgi/reprint/19/5/675

J.D. Grant, R. L. Dunbrack, F. J. Manion, M. F. Ochs: "BeoBLAST: A Package for Distributed BLAST and PSI-BLAST on a Beowulf Cluster", Bioinformatics, 18, 765, 2002. http://bioinformatics.oxfordjournals.org/cgi/reprint/18/5/765

J. D. Grant, D. Broccoli, M. Muquit, F. J. Manion, J. Tisdall, M. F. Ochs: "Telometric: a tool providing simplified, reproducible measurements of telomeric DNA from constant field agarose gels", BioTechniques, 31, 1314, 2001.

REVIEWS AND CHAPTERS

A. V. Kossenkov, G. Bidaut, M. F. Ochs: “Estimating cellular signaling from transcription data”, in K. A. Do, P. Mueller, M. Vannucci, Editors, Bayesian Inference for Gene Expression and Proteomics, Cambridge University Press, 2006.

M. F. Ochs, A. J. Peterson, A. V. Kossenkov, G. Bidaut: “Incorporation of gene ontology to enhance microarray data analysis”, in M. Korenberg, Editor, Methods in Molecular Biology: Microarray Data Analysis, Humana Press, Totowa, In Press.

M. F. Ochs, T. D Moloshok, G. Bidaut, G. Toby: “Bayesian Decomposition: Analyzing microarray data within a biological context”, Annals of the New York Academy of Sciences, 1020, 212, 2004.

M.F. Ochs and E.A. Golemis: “The biology behind gene expression: a basic tutorial”, in K. Johnson and S. Lin, Editors, Methods of Microarray Data Analysis III, p. 9 - 24, Kluwer Academic, Boston, 2003.

M.F. Ochs: "Bayesian Decomposition", in G. Parmigiani, E. Garrett, R. Irizarry and S. Zeger, Editors, The Analysis of Gene Expression Data: Methods and Software, Springer Verlag: New York, 2003.

M.F. Ochs and A.K. Godwin: “Microarrays in cancer: Research and applications”, BioTechniques, 34, S4, 2003.

M.F. Ochs and G. Bidaut: "Microarray Data Normalization", in S. Shah and G. Kamerova, Editors, Microarray Image Analysis - Nuts and Bolts, DNA Press, LLC: London, 2002.

E. A. Golemis, M.F. Ochs, E. N. Pugacheva: "Signal transduction driving technology driving signal transduction: Factors in the design of targeted therapies", Journal of Cellular Biochemistry, Supplement, 37, 4, 2001.