Elana J. Fertig

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.

Application of local ensemble transform Kalman filter: Perfect model experiments with NASA FVGCM model

Hong Li, Istvan Szunyogh, Eric J. Kostelich, 2006 .

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

Yong Tang, Michael Considine, Elana J. Fertig, 2018 .

Synthesizer: Expediting synthesis studies from context-free data with natural language processing

Jordan Gumm, Benjamin Fertig, Sameer Chavan, 2016 .

projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering

Gaurav Sharma, Carlo Colantuoni, Elana J. Fertig, 2019, bioRxiv.

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

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

Assimilating non-local observations with a local ensemble Kalman filter

Istvan Szunyogh, Edward Ott, Brian R. Hunt, 2007 .

switchBox: an R package for k-Top Scoring Pairs classifier development

Donald Geman, Bahman Afsari, Luigi Marchionni, 2015, Bioinform..

Decomposing cell identity for transfer learning across cellular measurements, platforms, tissues, and species

Carlo Colantuoni, Elana J. Fertig, Genevieve Stein-O'Brien, 2018, bioRxiv.

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 .

GAPS/CoGAPS Users Manual

Elana J. Fertig, 2011 .

StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data

Elena D. Stavrovskaya, Andrey A. Mironov, Sarah J. Wheelan, 2017, bioRxiv.

Cancer Systems Biology

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

StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data

Elena D. Stavrovskaya, Andrey A. Mironov, Sarah J. Wheelan, 2017, bioRxiv.

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

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

CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures

Elana J. Fertig, Tiger Gao, Thomas D. Sherman, 2020, BMC bioinformatics.

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.

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.

Bahman Afsari, Michael Considine, Emily Flam, 2017, Cancer research.

Improved analyses and forecasts with AIRS temperature retrievals using the local ensemble transform Kalman filter

Istvan Szunyogh, Eric J. Kostelich, Junjie Liu, 2011 .

Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes

Aleksander S. Popel, Elana J. Fertig, Niranjan B. Pandey, 2015, Scientific Reports.

Assimilating Nonlocal Observations using a Local Ensemble Kalman Filter

Istvan Szunyogh, Edward Ott, Brian R. Hunt, 2007 .

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..

Evaluation of a Strategy for the Assimilation of Satellite Radiance Observations with the Local Ensemble Transform Kalman Filter

Istvan Szunyogh, Eric J. Kostelich, Elana J. Fertig, 2011 .