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Novartis Genentech
Ontario Institute for Cancer Research
Roswell Park Cancer Institute
University of Toronto

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Theme by orderedlist

BioC 2018: Where Software and Biology Connect

When: July 25 (Developer Day) 26 and 27, 2018
Where: Victoria University, University of Toronto, Toronto, Canada
Twitter: #bioc2018


Ba-Alawi W*, Haibe-Kains B. Enhancing Drug Sensitivity Prediction using Logical Models. Keywords: GeneExpression, Pharmacogenomics, StatisticalMethod, BiomarkerDiscovery.

Burton D*, McCall M. Incorporating Uncertainty in a Ternary Gene Regulatory Network Model. Keywords: CellBiology, GraphAndNetwork, Software.

Daniela Cassol* and Thomas Girke. systemPipeR: NGS Workflow Environment with Command-Line Interface. Keywords: Generic Workflow Environment, NGS Data Analysis, Command-line Interface, Visualization, Reporting Infrastructure.

Cheng PF*, Dummer R, Robinson M, Morgan M, Levesque MP. TCGAbrowser. Keywords: Software, WorkflowStep, Visualization.

Clark O*, Safikhani Z, Smirnov P, and Haibe-Kains B. Gene isoforms as expression-based biomarkers predictive of drug response in vitro. Keywords: PharmacoGx, Biomarkers, Isoforms, Splicing, Drug Response.

Daniel Giguere*, Jean Macklaim, Greg Gloor. omicplotR: A Shiny app for exploring omic datasets as compositions software. Keywords: RNASeq, Metagenomics, Visualization, GUI.

Diya Das*, Levi Gadye, Michael A. Sanchez, Kelly Street, Ariane Baudhuin, Allon Wagner, Michael B. Cole, Yoon Gi Choi, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit, Davide Risso, John Ngai and Russell B. Fletcher. Unraveling Tissue Regeneration With Single-Cell RNA-Sequencing. Keywords: Normalization, Clustering, RNASeq, SingleCell, Software.

Drnevich J*, Tseng M*, Dalling J, Heath K, and Ferrer A. Transcriptome assembly problems found using Bioconductor packages. Keywords: Transcription, RNASeq, Clustering, Visualization.

Ho C*, Kofia V, Smirnov P, Ba-alawi W, Safikhani Z, Haibe-Kains B. PharmacoDB: an integrative web application for mining multiple pharmacogenomic datasets. Keywords: pharmacogenetics, pharmacogenomics, visualization.

Chiaowen Joyce Hsiao*, PoYuan Tung, John Blischak, Jonathan Burnett, Kenneth Barr, Yoav Gilad and Matthew Stephens. The identification and assessment of cell cycle signatures in single-cell gene expression data. Keywords: SingleCell, RNASeq, Transcriptomics, GeneRegulation, Classification.

Chiaowen Joyce Hsiao*, PoYuan Tung, John Blischak, Jonathan Burnett, Kenneth Barr, Yoav Gilad and Matthew Stephens. Identification and assessment of cell cycle signatures in single-cell gene expression data. Keywords: SingleCell, RNASeq, Transcriptomics, GeneRegulation, Classification.

Chang Cao, Davide Chicco*, Michael M. Hoffman. The MCC-F1 curve: a performance evaluation technique for binary classification. Keywords: Matthews Correlation Coefficient, Confusion Matrix, F1 Score, Accuracy, Applied Statistics.

Innes BT* and Bader GD. scClustViz - Single-cell RNAseq Cluster Assessment and Interactive Visualisation. Keywords: Visualization, SingleCell, Transcriptomics, GUI.

Benjamin K Johnson*, Asif Zubair, Timothy J Triche Jr. ATACseeker: a toolkit for ATAC- and scATAC-seq analysis. Keywords: ATACSeq, QualityControl, SingleCell, DifferentialPeakCalling, Visualization.

Bo Li*, Wail Ba-Alawi, Benjamin Haibe-Kains. R-LOBICO: an R package for building logical models. Keywords: Software, Classification, Pharmacogenomics.

Tamara Mahbubani*, Chantal Ho, Wail Ba-Alawi, Petr Smirnov, Benjamin Haibe-Kains, Arvind Singh Mer. BioHeat: an R Package for Interactive Heat Map Visualization. Keywords: Visualization, Pathways, Software, MultipleComparison.

Ann Meyer*, Michelle D Brazas, and B.F.F. Ouellette. Tracking Workshop Development and Online User Access. Keywords: Education.

Zhun Miao*, Ke Deng, Xiaowo Wang, Xuegong Zhang. DEsingle for detecting three types of differential expression in single-cell RNA-seq data. Keywords: DifferentialExpression, GeneExpression, RNASeq, SingleCell, Transcriptomics.

Nagraj VP, Magee M, and Sheffield NC*. LOLAweb: A containerized web application for interactive genomic locus overlap enrichment analysis. Keywords: ChIPSeq, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GenomeAnnotation.

Vandana Sandhu*, Knut Jorgen Labori, Ayelet Borgida, Ilinca Lungu, John Bartlett, Sara Hafezi-Bakhtiari, Rob Denroche, Gun Ho Jang, Danielle Pasternack, Faridah Mbaabali, Matthew Watson, Julie Wilson, Elin H. Kure, Steven Gallinger, Benjamin Haibe-Kains. Meta-analysis of transcriptomic profiles identifies prognostic model for pancreatic ductal adenocarcinoma patients. Keywords: Meta-analysis, One Sample Classifier, Top Scoring Pairs, Overall Survival Predictive Model.

Heewon Seo* and Benjamin Haibe-Kains. Pharmacogenomics of Gemcitabine in Pancreatic Cancer Cell Lines. Keywords: Pharmacogenomics, Gemcitabine, Pancreatic Cancer, Cell Lines.

Shorser S*, Reactome Team, Wu G, Hermajob H, D’Eustachio P and Stein L. The Reactome Knowledgebase.

Mer, Arvind Singh*, Brew Ben Ortmann, Janosch Goldenberg Anna Haibe-Kains Benjamin. Xeva: an R package for patient derived xenograft data management and analysis. Keywords: Pharmacogenomics, Biomarker, Xenografts, Drug Response.

Smirnov P*, Kofia V, Zhu K, Safikhani K, Ho C, Pugh T, Haibe-Kains B. Leveraging Preclinical Pharmacogenomics Studies to Inform Precision Medicine Research. Keywords: Pharmacogenomics, Visualization, GeneExpression, Regression, Software.

Smith I*, Haibe-Kains B. Identifying Biomarkers For Drug Sensitivity in Cancer With DNA Methylation Data. Keywords: Pharmacogenomics, DifferentialMethylation, DNAMethylation, DimensionReduction, CancerData.

Sohail N*, Johnson B, Zubair A, Triche T. MTseeker: mitochondrial variant analysis tools for Bioconductor. Keywords: MitochondrialVariation, VariantAnnotation, FunctionalPrediction, DataRepresentation, Visualization.

Luyi Tian, Shian Su*, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Shalin H Naik, Matthew E Ritchie. Tools for preprocessing and benchmarking single cell RNA-sequencing data. Keywords: SingleCell, Preprocessing, Sequencing, QualityControl.

Seyed Ali Madani Tonekaboni*, Parisa Mazrooei, Victor Kofia, Benjamin Haibe-Kains, Mathieu Lupien. CREAM as an open source R package for calling clusters of genomic regions. Keywords: Cis-Regulatory Element, Clustering, CORE, Super-enhancer.