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Course Materials for EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research

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

Class Hours: Monday + Wednesday @ 3p - 3:50p in Hodson 311
Schatz Office Hours: Monday @ 4-5p in Malone 323 and by appointment
CA: Melanie Kirsche - Office Hours Wednesday @ 9-10 AM in Malone 216 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


# Date Lecture Readings & Resources Assignment
1. Th 8/29 Lecture 1. 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 9/2 🔸 Labor Day Break!
2. Wed 9/4 Lecture 2. 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)
Assignment 1
3. Mon 9/9 Lecture 3. Genome Assembly * De novo genome assembly: what every biologist should know (Baker, 2012, Nature Methods)
4. Wed 9/11 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)
Assignment 2
5. Mon 9/16 Lecture 5. Whole Genome Alignment * Versatile and open software for comparing large genomes (Kurtz et al, 2004) Genome Biology
6. Wed 9/18 Lecture 6. Read Mapping * How to map billions of short reads onto genomes (Trapnell and Salzberg, 2009, Nature Biotech)
* Bowtie: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (Langmead et al, 2009, Genome Biology)
* BWA-MEM: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (Li, 2013, arXiv)
7. Mon 9/23 Lecture 7. Variant Identification * SAM/BAM/Samtools: The Sequence Alignment/Map format and SAMtools (Li et al, 2009, Bioinformatics)
* IGV: Integrative genomics viewer (Robinson et al, 2011, Nature Biotech)
* 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)
* Scalpel: Accurate de novo and transmitted indel detection in exome-capture data using microassembly (Narzisi et al, 2014, Nature Methods)
Assignment 3
8. Wed 9/25 Lecture 8. 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)
* A Draft Sequence of the Neandertal Genome (Green et al. 2010, Science)
* Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals (Vernot et al. 2016. Science)
9. Mon 9/30 Lecture 9. Human Genetic Diseases * Genome-Wide Association Studies (Bush & Moore, 2012, PLOS Comp Bio)
* The contribution of de novo coding mutations to autism spectrum disorder (Iossifov et al, 2014, Nature)
10. Wed 10/2 Research Lab 1: How to Give a Talk Meet in Maryland 217!!! Project Pitch
11. Mon 10/7 Faculty Presentation 1 Alexis Battle
12. Wed 10/9 Faculty Presentation 2 Steven Salzberg
13. Mon 10/14 Lecture 10. RNA-seq * RNA-Seq: a revolutionary tool for transcriptomics (Wang et al, 2009. Nature Reviews Genetics)
* Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Trapnell et al, 2012, Nature Protocols)
* Salmon provides fast and bias-aware quantification of transcript expression (Patro et al, 2017, Nature Methods)
* Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications (Krueger and Andrews, 2011, Bioinformatics)
14. Wed 10/16 Lecture 11. Gene Finding & HMMs * Glimmer: Microbial gene identification using interpolated Markov models
* MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
* What is a hidden Markov model?
Written abstract
15. Mon 10/21 Lecture 12. Gene Regulation * ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions (Furey, 2012, Nature Reviews Genetics)
* PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls (Rozowsky et al. 2009. Nature Biotech)
* Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome (Lieberman-Aiden et al, 2009, Science)
16. Wed 10/23 Research Lab 2: Proposal Presentations Project details
17. Mon 10/28 Regulatory States, ENCODE, GTEx, RoadMap * An integrated encyclopedia of DNA elements in the human genome (The ENCODE Project Consortium, Nature, 2012)
* Genetic effects on gene expression across human tissues (GTEx Consortium, Nature, 2017)
* Integrative analysis of 111 reference human epigenomes (Roadmap Epigenome Consortium, Nature, 2015)
* ChromHMM: automating chromatin-state discovery and characterization (Ernst & Kellis, 2012, Nature Methods)
* Segway: Unsupervised pattern discovery in human chromatin structure through genomic segmentation (Hoffman et al, 2012, Nature Methods)
18. Wed 10/30 Research Lab 3: Data Requirements
19. Mon 11/4 Lecture 13. Cancer Genomics * The Hallmarks of Cancer (Hanahan & Weinberg, 2000, Cell)
* Evolution of Cancer Genomes (Yates & Campbell, 2012, Nature Reviews Genetics)
* Comprehensive molecular portraits of human breast tumours (TCGA, 2012, Nature)
20. Wed 11/6 Machine Learning Primer Preliminary Report
21. Mon 11/11 Lecture 14. Metagenomics * Kraken: ultrafast metagenomic sequence classification using exact alignments (Wood and Salzberg, 2014, Genome Biology)
* Chapter 12: Human Microbiome Analysis (Morgan and Huttenhower)
22. Wed 11/13 Lecture 15. Plant Genomics * Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato (Soyk et al. 2019 Nature Plants
* RaGOO: Fast and accurate reference-guided scaffolding of draft genomes (Alonge et al. 2019. Genome Biology)
23. Mon 11/18 Grad Student Forum
24. Wed 11/20 Research Lab 4: Presentation Preparation
Mon 11/25 🔸 Thanksgiving Break!
Wed 11/27 🔸 Thanksgiving Break!
25. Mon 11/18 Lecture 16. Genomic Futures * "Snyderome" Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (Chen et al, 2012, Cell)
* Identifying Personal Genomes by Surname Inference (Gymrek et al, 2013, Science)
26. Wed 12/4 Research Presentations Research Presentation
Wed 12/18 Research Report Due Research Report Due


Course Materials for EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research






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