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:

• Syllabus and Policies
• Piazza Discussion Board

Recommended Prerequisites

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

Related Courses & Readings

• Applied Comparative Genomics
• Molecular Biology of the Gene (Watson et al)
• Bioinformatics Algorithms: An Active Learning Approach (Compeau and Pevzner)
• Unix and Perl for Biologists (Bradnam et al)

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