Computational and Systems Immunology

Resources to remember

Lecture 1 - 6/26: Meromit Singer, Dana-Farber Cancer Institute

Reading 1: Singer et al. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell (2016).

Reading 2: Wang et al. Molecular Dissection of CD8+ T-Cell Dysfunction. Trends in Immunology (2017).

Lecture 2 - 7/10: Leeat Keren, Stanford University

Reading 1: Angelo et al. Multiplexed ion beam imaging of human breast tumors. Nature Medicine (2014).

Reading 2: Van Valen et al. Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments. PLOS Computational Biology (2016).

Lecture 3 - 7/17: Burkhard Becher, University of Zurich

Reading 1: Mrdjen et al. High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease. Immunity (2018).

Reading 2: Krieg et al. High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nature Medicine (2017).

Reading 3: Spath et al. Dysregulation of the Cytokine GM-CSF Induces Spontaneous Phagocyte Invasion and Immunopathology in the Central Nervous System. Immunity (2017).

Lecture 4 - 7/24: Peggie Cheung, Stanford University

Reading 1: Cheung et al. Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell (2018).

Lecture 5 - 7/31: Kole Roybal, University of California, San Francisco

Reading 1: Roybal et al. Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. Annul. Rev. Immunol. (2017).

Reading 2: Morsut et al. Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. Cell (2016).

Reading 3: Roybal et al. Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. Cell (2016).

Reading 4: Roybal et al. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell (2016).

Lecture 6 - 8/7: Houston Gilbert, Genentech

Reading 1: Prowell et al. Seamless Oncology-Drug Development. New England Journal of Medicine (2016).

Reading 2: Kang et al. Pembrolizumab KEYNOTE-001: an adaptive study leading to accelerated approval for two indications and a companion diagnostic. Annals of Oncology (2017).

Reading 3: Langer et al. Carboplatin and pemetrexed with or without pembrolizumab for advanced, non-squamous non-small-cell lung cancer: a randomised, phase 2 cohort of the open-label KEYNOTE-021 study. The Lancet Oncology (2016).

Lecture 7 - 8/14: Vesteinn Thorsson, Institute for Systems Biology

Reading 1: Saltz et al. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Reports (2018).

Reading 2: Thorsson et al. The Immune Landscape of Cancer Immunity (2018).