Michael F. Ochs

发表

Genomics Data Analysis Pipelines

Michael F. Ochs, M. Ochs, 2010 .

Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity

Michael F. Ochs, Michael Considine, Soheil Meschinchi, 2013, PRIB.

Session Introduction

Ramana V. Davuluri, Michael F. Ochs, J. Quackenbush, 2009, Pacific Symposium on Biocomputing.

Bayesian Decomposition Classification of the Project Normal Data Set

Michael F. Ochs, Thomas D. Moloshok, D. Datta, 2004 .

Enter the matrix: Interpreting unsupervised feature learning with matrix decomposition to discover hidden knowledge in high-throughput omics data

Aedín C. Culhane, Casey S. Greene, Raman Arora, 2017, bioRxiv.

Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery

Michael F. Ochs, Soheil Meschinchi, Jason E. Farrar, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

Jie Ding, Michael F. Ochs, Giovanni Parmigiani, 2010, Bioinform..

Abstract LB-317: Interactive pipeline for reproducible genomics analyses

Michael F. Ochs, Yingying Wei, Michael Considine, 2014 .

A Comprehensive Statistical Model for Cell Signaling

Donald Geman, Erdem Yörük, Laurent Younes, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster

Roland L. Dunbrack, Frank J. Manion, Michael F. Ochs, 2002, Bioinform..

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization

Michael F. Ochs, Elana J. Fertig, Ondrej Maxian, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Enter the matrix: factorization uncovers knowledge from omics Names/Affiliations

Aedín C. Culhane, Casey S. Greene, Raman Arora, 2018 .

Bayesian image decomposition applied to relaxographic imaging

Xin Li, Michael F. Ochs, Truman R. Brown, 2005, Int. J. Imaging Syst. Technol..

Matrix factorisation methods applied in microarray data analysis

Michael F. Ochs, Andrew V. Kossenkov, M. Ochs, 2010, Int. J. Data Min. Bioinform..

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

Frank J. Manion, Michael F. Ochs, Eugene V. Korotkov, 2003, Bioinform..

FGDP: functional genomics data pipeline for automated, multiple microarray data analyses

Yue Zhang, Frank J. Manion, Michael F. Ochs, 2004, Bioinform..

Proteomics LIMS: A caBIG™ Project, Year 1

Olga Tchuvatkina, Michael F. Ochs, Thomas D. Moloshok, 2006, AMIA.

ClutrFree: cluster tree visualization and interpretation

Michael F. Ochs, Ghislain Bidaut, M. Ochs, 2004, Bioinform..

Determination of strongly overlapping signaling activity from microarray data

Jean-Michel Claverie, Michael F. Ochs, Ghislain Bidaut, 2006, BMC Bioinformatics.

Matrix factorization for transcriptional regulatory network inference

Michael F. Ochs, Elana J. Fertig, E. Fertig, 2012, 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

Michael F. Ochs, Michael Considine, Emily Flam, 2016, bioRxiv.

Updating annotations with the distributed annotation system and the automated sequence annotation pipeline

Michael F. Ochs, William Speier, W. Speier, 2012, Bioinform..

Analysis of phylogenetic profiles using Bayesian decomposition

Jean-Michel Claverie, Michael F. Ochs, Ghislain Bidaut, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

A Bayesian Markov chain Monte Carlo solution of the bilinear problem

Michael F. Ochs, Truman R. Brown, Radka Stoyanova, 2001 .

LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates

Guoli Wang, Michael F. Ochs, Andrew V. Kossenkov, 2006, BMC Bioinformatics.

Biomedical Informatics for Cancer Research: Introduction

Ramana V. Davuluri, Michael F. Ochs, John T. Casagrande, 2010 .

Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer

Donald Geman, Michael F. Ochs, Bahman Afsari, 2016, bioRxiv.

2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012, Philadelphia, PA, USA, October 4-7, 2012

Xiaohua Hu, Yunming Ye, Majid Sarrafzadeh, 2012, IEEE International Conference on Bioinformatics and Biomedicine.

PatternMarkers and Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS) for data-driven detection of novel biomarkers via whole transcriptome Non-negative matrix factorization (NMF)

Michael F. Ochs, Wai-shing Lee, Michael Considine, 2016 .

Application of Bayesian Decomposition for analysing microarray data

Frank J. Manion, Michael F. Ochs, Thomas D. Moloshok, 2002, Bioinform..

Biomedical Informatics for Cancer Research: Springer

Ramana V. Davuluri, Michael F. Ochs, John T. Casagrande, 2010 .

Knowledge-based data analysis comes of age

Michael F. Ochs, M. Ochs, 2010, Briefings Bioinform..

Determining Transcription Factor Activity from Microarray Data using Bayesian Markov Chain Monte Carlo Sampling

Michael F. Ochs, Andrew V. Kossenkov, Aidan J. Peterson, 2007, MedInfo.

WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis

Christophe Garcia, Frank J. Manion, Michael F. Ochs, 2006, J. Biomed. Informatics.

Cancer Systems Biology

Michael F. Ochs, Elana J. Fertig, Ludmila V. Danilova, 2011, Handbook of Statistical Bioinformatics.

CoGAPS: Stochastic Nonnegative Matrix Factorization by Bayesian Markov Chain Monte Carlo

Michael F. Ochs, Elana J. Fertig, Alexander V. Favorov, 2015 .

Gene Function Analysis

Michael F. Ochs, M. Ochs, 2007, Methods in Molecular Biology™.

Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma

Michael F. Ochs, Elana J. Fertig, Daria A. Gaykalova, 2014, PloS one.

Genes Associated with Prognosis in Adenocarcinoma Across Studies at Multiple Institutions

Michael F. Ochs, Andrew V. Kossenkov, Ghislain Bidaut, 2005 .

Activation of the NOTCH pathway in head and neck cancer.

Michael F. Ochs, Ashish Choudhary, Yan Liu, 2014, Cancer research.

Biomedical Informatics for Cancer Research

Ramana V. Davuluri, Michael F. Ochs, R. Davuluri, 2014 .

Implications of Systemic Dysfunction for the Etiology of Malignancy

Michael F. Ochs, Sarah S. Knox, S. Knox, 2013, Gene regulation and systems biology.

Bayesian Decomposition Analysis of Gene Expression in Yeast Deletion Mutants

Frank J. Manion, Michael F. Ochs, Thomas D. Moloshok, 2002 .

Microarrays in cancer: Research and applications: Introduction

Michael F. Ochs, Andrew K. Godwin, 2003 .

Linking Gene Expression Patterns and Transcriptional Regulation in Plasmodium falciparum

Michael F. Ochs, Andrew V. Kossenkov, M. Ochs, 2007 .

Bayesian Inference for Gene Expression and Proteomics: Estimating Cellular Signaling from Transcription Data

Michael F. Ochs, Andrew V. Kossenkov, Ghislain Bidaut, 2006 .

Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development

Michael F. Ochs, Elana J. Fertig, Alexander V. Favorov, 2011, Front. Gene..

A Markov Chain Monte Carlo Technique for Identification of Combinations of Allelic Variants Underlying Complex Diseases

Michael F. Ochs, Giovanni Parmigiani, Alexander V. Favorov, 2005 .

Serum microRNA Biomarkers for Detection of Non-Small Cell Lung Cancer

Michael F. Ochs, Ashish Choudhary, Joseph A. Califano, 2012, PloS one.

A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)

Louise C. Showe, John R. Gilbertson, Michael F. Ochs, 2007, Cancer informatics.