Methods in Quantitative Biology Fall 2019
 
 
The Sackler 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 2019

Course Directors:
David Fenyö (David@FenyoLab.org)
Mark Grivainis (Mark.Grivainis@nyulangone.org)

Teaching Assistant:
Cooper Devlin (jcooperdevlin@gmail.com)

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 (20%)
Lectures

Lecture 1 Introduction & Best Practices (September 3, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
Lecturer: Fenyo (Slides)


Lecture 2 Biomedical Data: Clinical Data (September 5, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
Lecturer: Iturrate (Slides)

Reading List
  • Coorevits . et al., Electronic health records: new opportunities for clinical research. (2013) Journal of Internal Medicine


    Lecture 3 HPC (September 10, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Siavosh-haghighi (Slides)


    Lecture 4 Biomedical Data: Lab II - Clinical Data (September 12, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 1 (HPC & Biomedical Data)
    Lecturer: Grivainis (Slides)


    Lecture 5 Biomedical Data: NYU Data Catalog (September 19, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Contaxis (Slides)


    Lecture 6 Biomedical Data: Institutional Review Board (September 26, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: More (Slides)


    Lecture 7 Biomedical Data: Lab I - Molecular Data (October 1, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Devlin (Slides)

    Reading List
  • Karczewski and Snyder. Integrative omics for health and disease. (2018) Nature Reviews


    Lecture 8 Statistics (October 3, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 2 (IRB & NYU DataCatalog)
    Lecturer: Fenyo

    Reading List
  • Statistics for Biologists


    Lecture 9 Statistics (October 10, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 3 (Stats Part 1)
    Lecturer: Fenyo


    Lecture 10 Signal Processing (October 22, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 4 (Stats Part 2)
    Lecturer: Fenyo (Slides)


    Lecture 11 Signal Processing - Lab (October 24, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Devlin (Slides)

    Reading List
  • Assignment: Add comments to the signal processing code provided describing what is being done in the code.
  • Sun X, Wang X, et al.: "Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression", Proc Natl Acad Sci U S A. 2018 May 25. pii: 201722565


    Lecture 12 Signal Processing - Discussion (October 29, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 5 (Signal Processing)
    Lecturer: Fenyo & Devlin

    Reading List
  • R. Thomas et al.: Features that define the best ChIP-seq peak calling algorithms, Briefings in Bioinformatics, 18 (2017) 441-450


    Lecture 13 Modeling/Simulation (October 31, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Fenyo (Slides)


    Lecture 14 Modeling/Simulation - Discussion (November 5, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 6 (Modeling and Simulation)
    Lecturer: Fenyo & Devlin

    Reading List
  • Discussion Paper: Gao et al., Prevention and Control of Zika as Mosquito-Borne and Sexually Transmitted Disease: A Mathematical Modeling Analysis.(2016) Scientific Reports


    Lecture 15 Data Visualization - Discussion (November 7, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Ruggles

    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 16 Data Visualization - ggplot2 Lab (November 12, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Devlin

    Reading List
  • Assignment: TBD


    Lecture 17 Data Visualization - Illustrator Lab (November 14, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Lecturer: Devlin

    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 18 Data Visualization - Interactive (November 19, 2019 Science Building, 435 East 30th St, 7th Floor, Room 720 5:30-7pm)
    Quiz 7 (Data Visualization)
    Lecturer: Grivainis (Slides)
    Tutorial Instructor: Grivainis (Bokeh-Example.ipynb )

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

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