Michael F. Ochs

31 papers C 1Misc 6Journal 18Unranked 5
YearRankTypeTitle / Venue / Authors
2018 J jnl
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Bioinform.
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
2017 J jnl
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Bioinform.
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
2015 J jnl
AGA: Interactive pipeline for reproducible genomics analyses.
F1000Research
Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
2015 — conf
The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization.
BIBM
Conor J. Kelton, Waishing Lee, Matthew Rusay, Ondrej Maxian, Elana J. Fertig, Michael F. Ochs
2014 J jnl
Outlier Analysis and Top Scoring Pairfor Integrated Data Analysisand Biomarker Discovery.
IEEE ACM Trans. Comput. Biol. Bioinform.
Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meshinchi, Robert J. Arceci
2013 — conf
Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity.
PRIB
Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meschinchi, Robert J. Arceci
2013 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader
2012 — conf
Identifying context-specific transcription factor targets from prior knowledge and gene expression data.
BIBM
Elana J. Fertig, Alexander V. Favorov, Michael F. Ochs
2012 C conf
Matrix factorization for transcriptional regulatory network inference.
CIBCB
Michael F. Ochs, Elana J. Fertig
2012 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Rachel Karchin, Michael F. Ochs, Joshua M. Stuart, Joel S. Bader
2012 J jnl
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline.
Bioinform.
William Speier, Michael F. Ochs
2011 J jnl
A Comprehensive Statistical Model for Cell Signaling.
IEEE ACM Trans. Comput. Biol. Bioinform.
Erdem Yörük, Michael F. Ochs, Donald Geman, Laurent Younes
2011 — ch.
Cancer Systems Biology.
Handbook of Statistical Bioinformatics
Elana J. Fertig, Ludmila V. Danilova, Michael F. Ochs
2011 Misc conf
Workshop Introduction.
Pacific Symposium on Biocomputing
Michael F. Ochs, Rachel Karchin, Habtom W. Ressom, Robert Gentleman
2010 J jnl
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.
Bioinform.
Elana J. Fertig, Jie Ding, Alexander V. Favorov, Giovanni Parmigiani, Michael F. Ochs
2010 J jnl
Knowledge-based data analysis comes of age.
Briefings Bioinform.
Michael F. Ochs
2010 J jnl
Matrix factorisation methods applied in microarray data analysis.
Int. J. Data Min. Bioinform.
Andrew V. Kossenkov, Michael F. Ochs
2009 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Michael F. Ochs, John Quackenbush, Ramana V. Davuluri, Habtom W. Ressom
2008 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Michael F. Ochs, John Quackenbush, Ramana V. Davuluri
2007 — conf
Determining Transcription Factor Activity from Microarray Data using Bayesian Markov Chain Monte Carlo Sampling.
MedInfo
Andrew V. Kossenkov, Aidan J. Peterson, Michael F. Ochs
2006 J jnl
Determination of strongly overlapping signaling activity from microarray data.
BMC Bioinform.
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
2006 J jnl
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates.
BMC Bioinform.
Guoli Wang, Andrew V. Kossenkov, Michael F. Ochs
2006 Misc conf
Proteomics LIMS: A caBIG™ Project, Year 1.
AMIA
Olga Tchuvatkina, Liat Shimoni, Michael F. Ochs, Thomas D. Moloshok
2006 J jnl
WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis.
J. Biomed. Informatics
Ghislain Bidaut, Frank J. Manion, Christophe Garcia, Michael F. Ochs
2005 J jnl
Bayesian image decomposition applied to relaxographic imaging.
Int. J. Imaging Syst. Technol.
Truman R. Brown, Michael F. Ochs, William D. Rooney, Radka Stoyanova, Xin Li, Charles S. Springer Jr.
2004 J jnl
ClutrFree: cluster tree visualization and interpretation.
Bioinform.
Ghislain Bidaut, Michael F. Ochs
2004 J jnl
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses.
Bioinform.
Jeffrey D. Grant, Luke A. Somers, Yue Zhang, Frank J. Manion, Ghislain Bidaut, Michael F. Ochs
2003 J jnl
ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database.
Bioinform.
Andrew V. Kossenkov, Frank J. Manion, Eugene V. Korotkov, Thomas D. Moloshok, Michael F. Ochs
2003 — conf
Analysis of Phylogenetic Profiles Using Bayesian Decomposition.
CSB
Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F. Ochs
2002 J jnl
Application of Bayesian Decomposition for analysing microarray data.
Bioinform.
Thomas D. Moloshok, R. R. Klevecz, Jeffrey D. Grant, Frank J. Manion, W. F. Speier IV, Michael F. Ochs
2002 J jnl
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster.
Bioinform.
Jeffrey D. Grant, Roland L. Dunbrack Jr., Frank J. Manion, Michael F. Ochs