Methods in Quantitative Biology (BMSC-GA 4449) and Methodological Foundations of BMI (BMIN-GA 1001) Fall 2020
David Fenyö (David@FenyoLab.org)
Mark Grivainis (Mark.Grivainis@nyulangone.org)
Cooper Devlin (email@example.com)
Grant Hussey (Grant.Hussey@nyulangone.org)
This course provides an overview of foundational knowledge and essential methods relevant for all areas of biomedical informatics. Students will explore recurring themes and application domains most frequently used in the field. The course will be technical and rigorous, and it will include a number of computer science topics. The course content has been selected by the curriculum committee, and the topics will change over time. The majority of the coursework will be programming assignments and readings.
The student will learn and understand the most commonly used methodologies in the field of biomedical informatics.
Working knowledge of R and Python is required:
- Programming Assignments (40%).
- Discussions (40%)
- Participation and Quizzes (20%)
Lecture 1 Introduction (September 10, 2020, 5:30-7pm)
Lecturer: Devlin, Fenyo, Grivainis & Hussey
Lecture 2 Biomedical Data: NYU Data Catalog (September 15, 2020, 5:30-7pm)
Lecture 3 Biomedical Data: Molecular Data Lab I (September 17, 2020, 5:30-7pm)
Karczewski and Snyder. Integrative omics for health and disease. (2018) Nature Reviews
Lecture 4 Biomedical Data: Molecular Data Lab II (September 22, 2020, 5:30-7pm)
Lecture 5 Biomedical Data: Clinical Data (September 24, 2020, 5:30-7pm)
Coorevits et al., Electronic health records: new opportunities for clinical research. (2013) Journal of Internal Medicine
Lecture 6 Biomedical Data: Institutional Review Board (September 29, 2020, 5:30-7pm)
Lecture 7 Statistics I: Overview (October 1, 2020, 5:30-7pm)
Statistics for Biologists
Lecture 8 Statistics II (October 6, 2020, 5:30-7pm)
Lecture 9 Statistics III (October 8, 2020, 5:30-7pm)
Lecture 10 Statistics IV (October 13, 2020, 5:30-7pm)
Lecture 11 Biomedical Data: Clinical Data Lab (October 15, 2020, 5:30-7pm)
Lecture 12 Modeling/Simulation - COVID-19 Transmission (October 20, 2020, 5:30-7pm)
Lecturer: Hussey & Cooper
Lecture 13 Modeling/Simulation - COVID-19 Transmission (October 22, 2020, 5:30-7pm)
Lecturer: Hussey & Cooper
Lecture 14 Modeling/Simulation - Bacterial Interactions I (October 27, 2020, 5:30-7pm)
Reading: Kelsic ED, Zhao J, Vetsigian K, Kishony R: Counteraction of antibiotic production and degradation stabilizes microbial communities, Nature. 2015 May 28;521(7553):516-9.
Lecture 15 Modeling/Simulation - Bacterial Interactions II (October 29, 2020, 5:30-7pm)
Lecture 16 Signal Processing: 1D (November 3, 2020, 5:30-7pm)
Lecture 17 Signal Processing - 2D (November 5, 2020, 5:30-7pm)
Lecture 18 Signal Processing - NLP (November 10, 2020, 5:30-7pm)
Quiz 5 (Signal Processing)
Lecture 19 Data Visualization - Discussion (November 12, 2020, 5:30-7pm)
Nature Methods Points of View
Assignment: Based on best-practices described by the reading, find a figure from a publication that you feel is particularly good. Each student will present 2 minutes on why their figure is the best choice and students will vote on their top pick.
Lecture 20 Data Visualization - Illustrator Lab (November 17, 2020, 5:30-7pm)
Assignment: Given this figure, improve the formatting and layout of the figure and add a schematic drawing of the associated cellular pathway.
Lecture 21 Data Visualization - Interactive (November 19, 2020, 5:30-7pm)
Lecture 22 Topics in data analysis (November 24, 2020, 5:30-7pm)