Computational and Systems Immunology

Resources to remember

Lecture 1 - 6/27: Francesco Vallania, Stanford

Reading 1: Shenn-Orr and Gaujoux. Computational deconvolution: extracting cell type-specific information from heterogeneous samples. Current Opinion in Immunology (2013).

Reading 2: Newman et al. Robust enumeration of cell subsets from tissue expression profiles. Nature Methods (2015).

Lecture 2 - 7/11: Pratip Chattopadhyay, New York University

Reading: Chattopadhyay et al. Single-cell technologies for monitoring immune systems. Nature Immunology (2014).

Lecture 3 - 7/18: Richard Bourgon, Genentech

Reading: Haverty et al. Reproducible pharmacogenomic profiling of cancer cell line panels. Nature (2016).

Lecture 4 - 7/25: James Heath, California Institute of Technology

Reading 1: Wei et al. Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma. Cancer Cell (2016).

Reading 2: Peng et al. Sensitive, non-destructive detection and analysis of neoantigen-specific T cell populations from tumors and blood. Preprint under review (2017).

Lecture 5 - 8/1: Joachim Schultze, University of Bonn

Reading: Xue et al. Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation. Immunity (2014).

Lecture 6 - 8/8: John Tsang, National Institute of Allergy and Infectious Disease

Reading 1: Tsang. Utilizing population variation, vaccination, and systems biology to study human immunology. Trends in Immunology (2015).

Reading 2: Martins et al. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Systems (2017).

Reading 3: Lu et al. Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations. Immunity (2016).

Reading 4: Sparks et al. Expanding the Immunology Toolbox: Embracing Public-Data Reuse and Crowdsourcing. Immunity (2016).

Lecture 7 - 8/15: Serghei Mangul, University of California, Los Angeles

Reading 1: Mangul et al. Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing. Preprint (2017).

Reading 2: Mangul et al. Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Preprint (2017).