Teaching

  • Deep Learning in Genomics and Biomedicine (CS273B, BIODS 237, BIOMEDIN 273B, GENE 236)
    Recent breakthroughs in high-throughput genomic and biomedical data are transforming biological sciences into "big data" disciplines. In parallel, progress in deep neural networks are revolutionizing fields such as image recognition, natural language processing and, more broadly, AI. This course explores the exciting intersection between these two advances. The course will start with introduction to deep learning and overview the relevant background in genomics and high-throughput biotechnology, focusing on the available data and their relevance. It will then cover the ongoing developments in deep learning (supervised, unsupervised and generative models) with the focus on the applications of these methods to biomedical data, which are beginning to produced dramatic results.  In addition to predictive modeling, the course emphasizes how to visualize and extract interpretable, biological insights from such models. Recent papers from the literature will be presented and discussed. Students will work in groups on a final class project using real world datasets.
  • Big Data for Biologists - Decoding Genomic Function (HUMBIO 51)
    Biology and medicine are becoming increasingly data-intensive fields. This course is designed to introduce students interested in human biology and related fields to methods for working with large biological datasets. There will be in-class activities analyzing real data that have revealed insights about the role of the genome and epigenome in health and disease. For example, we will explore data from large-scale gene expression and chromatin state studies. The course will provide an introduction to the relevant topics in biology and to fundamental computational skills such as editing text files, formatting and storing data, visualizing data and writing data analysis scripts. Students will become familiar with both UNIX and Python. This course is designed at the introductory level. Previous university-level courses in biology and programming experience are not required
  • Genetics and Developmental Biology Training Camp (GENE200, DBIO 200)
    Open to first year Department of Genetics and Developmental Biology students, to others with consent of instructors. Introduction to basic manipulations, both experimental and conceptual, in genetics and developmental biology.

  • GENE 222: Cloud Computing for Biology and Healthcare (BIOMEDIN 222, CS 273C)
    Big Data is radically transforming healthcare. To provide real-time personalized healthcare, we need hardware and software solutions that can efficiently store and process large-scale biomedical datasets. In this class, students will learn the concepts of cloud computing and parallel systems' architecture. This class prepares students to understand how to design parallel programs for computationally intensive medical applications and how to run these applications on computing frameworks such as Cloud Computing and High Performance Computing (HPC) systems. Prerequisites: familiarity with programming in Python and R.

  • Statistical and Machine Learning Methods for Genomics (Sp15-BIO-268-01 / STATS-345-01 / CS-373-01 / GENE-245-01 / BIOMEDIN-245-01)
    Introduction to statistical and computational methods for genomics. Sample topics include: expectation maximization, hidden Markov model, Markov chain Monte Carlo, ensemble learning, probabilistic graphical models, kernel methods and other modern machine learning paradigms. Rationales and techniques illustrated with existing implementations used in population genetics, disease association, and functional regulatory genomics studies. Instruction includes lectures and discussion of readings from primary literature. Homework and projects require implementing some of the algorithms and using existing toolkits for analysis of genomic datasets.

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