Michael F. Ochs

Publication Activity (10 Years)

Years Active: 2002-2018
Publications (10 Years): 2

Top Topics

Inter Annotator Agreement

Saccharomyces Cerevisiae

Gene Expression

Matrix Factorisation

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Pacific Symposium on Biocomputing

Publications

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, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana J. Fertig
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. Bioinform. 34 (11) (2018)
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, Ronald McKay, Michael F. Ochs, Carlo Colantuoni, Elana J. Fertig
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinform. 33 (12) (2017)
Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
AGA: Interactive pipeline for reproducible genomics analyses. F1000Research 4 (2015)
Conor J. Kelton, Waishing Lee, Matthew Rusay, Ondrej Maxian, Elana J. Fertig, Michael F. Ochs
The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization. BIBM (2015)
Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meshinchi, Robert J. Arceci
Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (3) (2014)
Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meschinchi, Robert J. Arceci
Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity. PRIB (2013)
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
Session Introduction. Pacific Symposium on Biocomputing (2013)
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader
Session Introduction. Pacific Symposium on Biocomputing (2012)
William Speier, Michael F. Ochs
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline. Bioinform. 28 (21) (2012)
Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs
Identifying context-specific transcription factor targets from prior knowledge and gene expression data. BIBM (2012)
Michael F. Ochs, Elana J. Fertig
Matrix factorization for transcriptional regulatory network inference. CIBCB (2012)
Erdem Yörük, Michael F. Ochs, Donald Geman, Laurent Younes
A Comprehensive Statistical Model for Cell Signaling. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Michael F. Ochs, Rachel Karchin, Habtom W. Ressom, Robert Gentleman
Workshop Introduction. Pacific Symposium on Biocomputing (2011)
Michael F. Ochs
Knowledge-based data analysis comes of age. Briefings Bioinform. 11 (1) (2010)
Elana J. Fertig, Jie Ding, Alexander V. Favorov, Giovanni Parmigiani, Michael F. Ochs
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinform. 26 (21) (2010)
Andrew V. Kossenkov, Michael F. Ochs
Matrix factorisation methods applied in microarray data analysis. Int. J. Data Min. Bioinform. 4 (1) (2010)
Michael F. Ochs, John Quackenbush, Ramana Davuluri, Habtom W. Ressom
Session Introduction. Pacific Symposium on Biocomputing (2009)
Michael F. Ochs, John Quackenbush, Ramana Davuluri
Session Introduction. Pacific Symposium on Biocomputing (2008)
Andrew V. Kossenkov, Aidan J. Peterson, Michael F. Ochs
Determining Transcription Factor Activity from Microarray Data using Bayesian Markov Chain Monte Carlo Sampling. MedInfo (2007)
Guoli Wang, Andrew V. Kossenkov, Michael F. Ochs
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates. BMC Bioinform. 7 (2006)
Olga Tchuvatkina, Liat Shimoni, Michael F. Ochs, Thomas D. Moloshok
Proteomics LIMS: A caBIG™ Project, Year 1. AMIA (2006)
Ghislain Bidaut, Frank J. Manion, Christophe Garcia, Michael F. Ochs
WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis. J. Biomed. Informatics 39 (4) (2006)
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
Determination of strongly overlapping signaling activity from microarray data. BMC Bioinform. 7 (2006)
Truman R. Brown, Michael F. Ochs, William D. Rooney, Radka Stoyanova, Xin Li, Charles S. Springer Jr.
Bayesian image decomposition applied to relaxographic imaging. Int. J. Imaging Syst. Technol. 15 (1) (2005)
Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, Michael F. Ochs
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses. Bioinform. 20 (2) (2004)
Ghislain Bidaut, Michael F. Ochs
ClutrFree: cluster tree visualization and interpretation. Bioinform. 20 (16) (2004)
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
Analysis of Phylogenetic Profiles Using Bayesian Decomposition. CSB (2003)
Andrew V. Kossenkov, Frank J. Manion, Eugene V. Korotkov, Thomas D. Moloshok, Michael F. Ochs
ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database. Bioinform. 19 (5) (2003)
Thomas D. Moloshok, R. R. Klevecz, Jeffrey D. Grant, Frank J. Manion, W. F. Speier IV, Michael F. Ochs
Application of Bayesian Decomposition for analysing microarray data. Bioinform. 18 (4) (2002)
Jeffrey D. Grant, Roland L. Dunbrack Jr., Frank J. Manion, Michael F. Ochs
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster. Bioinform. 18 (5) (2002)