CancerInSilico simulates bulk and single-cell gene expression data from mathematical models to enable benchmarking of time course analysis methods with known ground truth.

PLoS Computational Biology · Apr 19, 2019Peer-reviewedSystems Biology

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.

Genevieve Stein-O’Brien, Luciane Tsukamoto Kagohara, Sijia Li, Manjusha Thakar, Ruchira S. Ranaweera, Hiroyuki Ozawa, Haixia Cheng, Michael Considine, Sandra Schmitz, Alexander V. Favorov, Ludmila Danilova, Joseph A. Califano, Evgeny Izumchenko, Daria A. Gaykalova, Christine H. Chung, Elana Judith Fertig

The paper uses integrated time course omics analysis to distinguish immediate therapeutic response from acquired resistance in head and neck cancer.

Genome Medicine · May 23, 2018Peer-reviewedSystems Biology

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

Bahman Afsari, Theresa W. Guo, Michael Considine, Liliana Florea, Luciane Tsukamoto Kagohara, Genevieve Stein-O’Brien, Dylan Z. Kelley, Emily L. Flam, Kristina Diana A. Zambo, Patrick K. Ha, Donald Geman, Michael F. Ochs, Joseph A. Califano, Daria A. Gaykalova, Alexander V. Favorov, Elana Judith Fertig

SEVA identifies differential heterogeneity in gene isoform usage between cancer subtypes using RNA-seq data.

Bioinformatics · Jan 11, 2018Peer-reviewedGenomics

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

Genevieve Stein-O’Brien, Jacob Carey, Wai Shing Lee, Michael Considine, Alexander V. Favorov, Emily L. Flam, Theresa W. Guo, Sijia Li, Luigi Marchionni, Thomas D. Sherman, Shawn Sivy, Daria A. Gaykalova, Ronald D.G. McKay, Michael F. Ochs, Carlo Colantuoni, Elana Judith Fertig

The paper introduces PatternMarkers and GWCoGAPS to identify data-driven biomarkers from whole-genome data using NMF, demonstrating their application on GTex data.

Bioinformatics · Jan 30, 2017Peer-reviewedBioinformatics