EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research
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README.md

README.md

EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research

Class Hours: Monday + Wednesday @ 3p - 3:50p in Malone 107
Office Hours: Wednesday @ 4-5p in Malone 323 and by appointment

The goal of this course is to prepare undergraduates to understand and perform state-of-the-art biomedical research. This will be accomplished through three main components: (1) classroom-style lectures on cross cutting techniques for biomedical research focusing on data visualization, statistical inference, and scientific computing; (2) research presentations from distinguished faculty on their active research projects; and (3) a major research project to be performed under the mentorship of a JHU professor. Students will present their research during an in-class symposium at the end of the semester. Grading will be based on homework exercises, a written research proposal, an interim research report, an oral research presentation, and a final research report.

Course Resources:

Recommended Prerequisites

  • Online introduction to Unix/Linux. Students are strongly recommended to complete one of the following online tutorials before class begins.
  • Access to a Linux Machine, or Install VirtualBox (Unfortuantely, even Mac will not work correctly for some programs)

Related Courses & Readings

Preliminary Schedule

# Date Lecture Readings & Resources Assignment
1. Th 8/31 Introduction * Biological data sciences in genome research (Schatz, 2015, Genome Research)
* Big Data: Astronomical or Genomical? (Stephens et al, 2015, PLOS Biology)
Sign Up for Piazza
Mon 9/4 🔸 Labor Day Break!
2. Wed 9/6 Lecture 1: Intro to Pvalues * The contribution of de novo coding mutations to autism spectrum disorder (Iossifov et al, 2014, Nature)
3. Mon 9/11 Faculty Presentation 1: Alan Yuille Compositional Cognition, Vision, and Learning
4. Wed 9/13 Lecture 2: Intro to the Binomial Distribution Coin flipping notebook
5. Mon 9/18 Lecture 3: Intro to the Exponential Distribution Probability Notebooks Exercise 1
6. Wed 9/20 Faculty Presentation 2: TJ Ha Single-molecule analysis of complex biological systems.
7. Mon 9/25 Lecture 4: The human genome * The Sequence of the Human Genome (Venter et al, 2001, Science)
* Initial sequencing and analysis of the human genome (IHGSP, 2001, Nature)
Exercise 1 Due; Research Proposal Assigned
8. Wed 9/27 Faculty Presentation 3: Ulrich Mueller Auditory Perception and Development of Neocortical Circuits
9. Mon 10/2 Lecture 5: Rachel Green Understanding the ribosome Research Proposal Due
10. Wed 10/4 Faculty Presentation 4: Steven Salzberg Computational Biology and Genomics
11. Mon 10/9 Faculty Presentation 5: Alexis Battle Understanding the impact of human genetic variation on complex traits
12. Wed 10/11 Lecture 6: Genome Sequencing * Coming of age: ten years of next-generation sequencing technologies (Goodwin et al, 2016, Nature Reviews Genetics)
* High‐throughput sequencing for biology and medicine (Soon et al, 2013, Molecular Systems Biology)
13. Mon 10/16 Lecture 7: Genome Assembly * De novo genome assembly: what every biologist should know (Baker, 2012, Nature Methods) In class exercise
14. Wed 10/18 Faculty Presentation 6: Carl Wu Chromatin structure and the regulation of gene expression
15. Mon 10/23 Lecture 8: Variant Calling * PolyBayes: A general approach to single-nucleotide polymorphism discovery (Marth et al, 1999, Nature Genetics)
* GATK: A framework for variation discovery and genotyping using next-generation DNA sequencing data (Depristo et al, 2011, Nature Genetics)
16. Wed 10/25 Lecture 9: Human Evolution * An integrated map of genetic variation from 1,092 human genomes (1000 Genomes Consortium, 2012, Nature)
* Analysis of protein-coding genetic variation in 60,706 humans (Let et al, 2016, Nature)
Exercise 2
17. Mon 10/30 Lecture 10: Disease Genomics * Genome-Wide Association Studies (Bush & Moore, 2012, PLOS Comp Bio)
18. Wed 11/1 Graduate Student Panel
19. Mon 11/6 Faculty Presentation 7: Jennifer Doudna CRISPR Biology
20. Wed 11/8 Faculty Presentation 8: Ben Langmead Efficient, Scalable, and Interpretable analysis of high throughput biological data Interm Research Report Assignment
21. Mon 11/13 Faculty Presentation 9: Andy Feinberg Epigenetics in development and disease
22. Wed 11/15 Faculty Presentation 10: Rong Li Cellular asymmetry, division and evolution Interm Research Report Due
Mon 11/20 🔸 Thanksgiving Break!
Wed 11/22 🔸 Thanksgiving Break!
23. Mon 11/27 Lecture 11: Genomic Futures
24. Wed 11/29 Research Presentations I Research Presentation
25. Mon 12/4 Research Presenations II Research Presentation
26. Wed 12/6 Reseach Presentations III Research Presentation
Wed 12/20 Research Report Due Research Report Due