BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. - Jeffrey D. Grant; Roland L. Dunbrack Jr.; Frank J. Manion; Michael F. Ochs (Bioinform., 2002)

Application of Bayesian Decomposition for analysing microarray data. - Thomas D. Moloshok; R. R. Klevecz; Jeffrey D. Grant; Frank J. Manion; W. F. Speier IV; Michael F. Ochs (Bioinform., 2002)

Analysis of Phylogenetic Profiles Using Bayesian Decomposition. - Ghislain Bidaut; Karsten Suhre; Jean-Michel Claverie; Michael F. Ochs (CSB, 2003)

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. - Andrew V. Kossenkov; Frank J. Manion; Eugene V. Korotkov; Thomas D. Moloshok; Michael F. Ochs (Bioinform., 2003)

ClutrFree: cluster tree visualization and interpretation. - Ghislain Bidaut; Michael F. Ochs (Bioinform., 2004)

FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. - Jeffrey D. Grant; Luke A. Somers; Yue Zhang; Frank J. Manion; Ghislain Bidaut; Michael F. Ochs (Bioinform., 2004)

Bayesian image decomposition applied to relaxographic imaging. - Truman R. Brown; Michael F. Ochs; William D. Rooney; Radka Stoyanova; Xin Li; Charles S. Springer Jr. (Int. J. Imaging Syst. Technol., 2005)

Proteomics LIMS: A caBIG™ Project, Year 1. - Olga Tchuvatkina; Liat Shimoni; Michael F. Ochs; Thomas D. Moloshok (AMIA, 2006)

Determination of strongly overlapping signaling activity from microarray data. - Ghislain Bidaut; Karsten Suhre; Jean-Michel Claverie; Michael F. Ochs (BMC Bioinform., 2006)

LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates. - Guoli Wang; Andrew V. Kossenkov; Michael F. Ochs (BMC Bioinform., 2006)

WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. - Ghislain Bidaut; Frank J. Manion; Christophe Garcia; Michael F. Ochs (J. Biomed. Informatics, 2006)

Determining Transcription Factor Activity from Microarray Data using Bayesian Markov Chain Monte Carlo Sampling. - Andrew V. Kossenkov; Aidan J. Peterson; Michael F. Ochs (MedInfo, 2007)

Session Introduction. - Michael F. Ochs; John Quackenbush; Ramana Davuluri (Pacific Symposium on Biocomputing, 2008)

Session Introduction. - Michael F. Ochs; John Quackenbush; Ramana Davuluri; Habtom W. Ressom (Pacific Symposium on Biocomputing, 2009)

Knowledge-based data analysis comes of age. - Michael F. Ochs (Briefings Bioinform., 2010)

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. - Elana J. Fertig; Jie Ding; Alexander V. Favorov; Giovanni Parmigiani; Michael F. Ochs (Bioinform., 2010)

Matrix factorisation methods applied in microarray data analysis. - Andrew V. Kossenkov; Michael F. Ochs (Int. J. Data Min. Bioinform., 2010)

Cancer Systems Biology. - Elana J. Fertig; Ludmila V. Danilova; Michael F. Ochs (Handbook of Statistical Bioinformatics, 2011)

Workshop Introduction. - Michael F. Ochs; Rachel Karchin; Habtom W. Ressom; Robert Gentleman (Pacific Symposium on Biocomputing, 2011)

A Comprehensive Statistical Model for Cell Signaling. - Erdem Yörük; Michael F. Ochs; Donald Geman; Laurent Younes (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Identifying context-specific transcription factor targets from prior knowledge and gene expression data. - Elana J. Fertig; Alexander V. Favorov; Michael F. Ochs (BIBM, 2012)

Matrix factorization for transcriptional regulatory network inference. - Michael F. Ochs; Elana J. Fertig (CIBCB, 2012)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Joel S. Bader (Pacific Symposium on Biocomputing, 2012)

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. - William Speier; Michael F. Ochs (Bioinform., 2012)

Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity. - Michael F. Ochs; Jason E. Farrar; Michael Considine; Yingying Wei; Soheil Meschinchi; Robert J. Arceci (PRIB, 2013)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Trey Ideker; Joel S. Bader (Pacific Symposium on Biocomputing, 2013)

Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery. - Michael F. Ochs; Jason E. Farrar; Michael Considine; Yingying Wei; Soheil Meshinchi; Robert J. Arceci (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. - Conor J. Kelton; Waishing Lee; Matthew Rusay; Ondrej Maxian; Elana J. Fertig; Michael F. Ochs (BIBM, 2015)

AGA: Interactive pipeline for reproducible genomics analyses. - Michael Considine; Hilary S. Parker; Yingying Wei; Xaio Xia; Leslie Cope; Michael F. Ochs; Elana J. Fertig (F1000Research, 2015)

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. - Genevieve L. Stein-O'Brien; Jacob L. Carey; Waishing Lee; Michael Considine; Alexander V. Favorov; Emily Flam; Theresa Guo; Sijia Li; Luigi Marchionni; Thomas Sherman; Shawn Sivy; Daria A. Gaykalova; et al. (Bioinform., 2017)

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. - Bahman Afsari; Theresa Guo; Michael Considine; Liliana Florea; Luciane T. Kagohara; Genevieve L. Stein-O'Brien; Dylan Kelley; Emily Flam; Kristina D. Zambo; Patrick K. Ha; Donald Geman; Michael F. Ochs; et al. (Bioinform., 2018)