Methods in Quantitative Biology Fall 2021
 
 
The Vilcek Institute of Graduate Biomedical Sciences at NYU School of Medicine
 
Methods in Quantitative Biology (BMSC-GA 4449) and Methodological Foundations of BMI (BMIN-GA 1001) Fall 2021

Course Directors:
David Fenyö (David@FenyoLab.org)

Teaching Assistant:
Grant Hussey (Grant.Hussey@nyulangone.org)
Brianna Berrios (Brianna.Berrios@nyulangone.org)

Course Overview

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.

Learning objectives

The student will learn and understand the most commonly used methodologies in the field of biomedical informatics.

Programming Languages

Working knowledge of R and Python is required:

Course Assessment
  • Programming Assignments (40%).
  • Discussions (40%)
  • Participation and Quizzes (20%)
Lectures

Lecture 1 Introduction (September 9, 2021, 3-4:30pm, SB 103)
Lecturer: Fenyo, Berrios & Hussey

Lecture 2 Biomedical Data: NYU Data Catalog (September 14, 2021, 3:45-5:15pm, TRB 120)
Lecturer: Contaxis
Reading List
  • Gregory K, Khalsa SJ, Michener WK, Psomopoulos FE, de Waard A, Wu M. Eleven quick tips for finding research data. Ouellette F, editor. PLoS Comput Biol. 2018 Apr 12;14(4):e1006038.

    Lecture 3 Biomedical Data: Clinical Data (September 16, 2021, 3-4:30pm, Zoom Only)
    Lecturer: Iturrate
    Reading List
  • Coorevits et al., Electronic health records: new opportunities for clinical research. (2013) Journal of Internal Medicine
  • Basch E, Schrag D. The Evolving Uses of "Real-World" Data: JAMA. 321 (2019) 1359-1360.
  • Callahan A, Shah NH, Chen JH: Research and Reporting Considerations for Observational Studies Using Electronic Health Record Data. Ann Intern Med. 172 (2020) S79-S84.

    Lecture 4 Biomedical Data: Clinical Data Lab (September 21, 2021, 3:45-5:15pm, Zoom Only)
    Lecturer: Grivainis

    Lecture 5 Signal Processing: 1D Signals (September 23, 2021, 3-4:30pm, SB G19)
    Lecturer: Fenyo

    Lecture 6 Signal Processing: Image Analysis (September 28, 2021, 3:45-5:15pm, SB G19)
    Lecturer: Keegan

    Lecture 7 Biomedical Data: Molecular Data Lab (September 30, 2021, 3-4:30pm, SB G19)
    Lecturer: Berrios
    Reading List
  • Karczewski and Snyder. Integrative omics for health and disease. (2018) Nature Reviews

    Lecture 8 Signal Processing: Image Analysis (October 5, 2021, 3:45-5:15pm, Zoom Only)
    Lecturer: Keegan

    Lecture 9 Statistics I: Introduction (October 7, 2021, 3-4:30pm, SB G19)
    Lecturer: Hussey

    Reading List
  • Statistics for Biologists

    Lecture 10 Statistics II: Simple linear regression and other techniques (October 12, 2021, 3:45-5:15pm, SB 103)
    Lecturer: Hussey

    Lecture 11 Statistics III: Bayesian statistics (October 14, 2021, 3-4:30pm, SB G19)
    Lecturer: Hussey

    Lecture 12 Modeling/Simulation - COVID-19 Transmission (October 19, 2021, 3:45-5:15pm, SB G19)
    Lecturer: Hussey

    Lecture 13 Modeling/Simulation - COVID-19 Transmission (October 21, 2021, 3-4:30pm, SB G19)
    Lecturer: Hussey

    Lecture 14 Modeling/Simulation - Bacterial Interactions I (October 26, 2021, 3:45-5:15pm, SB G19)
    Lecturer: Fenyo
    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 28, 2021, 3-4:30pm, SB G19)
    Lecturer: Berrios/Fenyo

    No class on November 2

    Lecture 16 Data Visualization - Discussion (November 4, 2021, 3-4:30pm, SB G19)
    Lecturer: Fenyo

    Reading List
  • 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 17 Data Visualization - Interactive (November 9, 2021, 3:45-5:15pm, Zoom Only)
    Lecturer: Grivainis

    Lecture 18 Institutional Review Board (November 11, 2021, 3-4:30pm, SB G19)
    Lecturer: More

    Lecture 19 Data Visualization - Illustrator Lab (November 16, 2021, 3:45-5:15pm, SB G19)
    Lecturer: Hussey
    Reading List
  • Assignment: Given this figure, improve the formatting and layout of the figure and add a schematic drawing of the associated cellular pathway.

    Lecture 20 Topics in data analysis (November 18, 2021, 3-4:30pm, SB G19)
    Lecturer: Yanai


    Break November 19 - December 1

    Lecture 21 Data Visualization (December 2, 2021, 3-4:30pm, Zoom Only)
    Lecturer: Kristen Dancell-Manning

    Lecture 22 Final project presentations (December 7, 2021, 3:45-5:15pm, SB G19)

    Lecture 23 Final project presentations (December 9, 2021, 3-4:30pm, SB G19)

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

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