Lectures
- 1/14/2020 (Tue): Lecture 1 - Course introduction, policies, prospective topics & course project (Slides)
- 1/16/2020 (Thu): Lecture 2 - Genome Assembly Overview (Slides)
- 1/21/2020 (Tue): Lecture 3 - Genome Assembly Overview (Slides)
- 1/23/2020 (Thu): Lecture 4 - Genome Aseembly Details (Slides), Presenter 1 (David A)
- 1/28/2020 (Tue): Lecture 5 - Genome Assembly Lab - Data Preprocessing (Slides)
- 1/30/2020 (Thu): Lecture 6 - Genome Assembly Lab (Slides), Presenter 2 (Yassin)
- 2/4/2020 (Tue): Lecture 7 - Genome Assembly Lab (Slides - Cont)
- 2/6/2020 (Thu): Lecture 8 - Genome Assembly Lab (Slides)), Presenter 3 (Huan)
- 2/11/2020 (Tue): Lecture 9 - RNA-Seq Overview (Slides)
- 2/13/2020 (Thu): Lecture 10 - RNA-Seq: Aligner, Output (SAM) and Visualization (Slides), Presenter 4 (John)
- 2/18/2020 (Tue): Lecture 11 - RNA-Seq: GTF/GFF and Splice Aligner (Slides)
- 2/20/2020 (Thu): Lecture 12 - RNA-Seq: GTF/GFF and Splice Aligner (Slides), Presenter 5 (Andrew)
- 2/25/2020 (Tue): Lecture 13 - Splice Aligner Lab (Slides)
- 2/27/2020 (Thu): Lecture 14 - Expression Quantification (Slides), Presenter 6 (David D)
- 3/3/2020 (Tue): Lecture 15 - Quantificaiton and Differential Expression Analysis (Slides)
- 3/5/2020 (Thu): Lecture 16 - Oxford MinION Lab
- 3/10/2020 (Tue): No Class (Spring Break)
- 3/12/2020 (Thu): No Class (Spring Break)
- 3/17/2020 (Tue): No Class (Suspension of classes by COVID-19)
- 3/19/2020 (Thu): No Class (Suspension of classes by COVID-19)
- 3/24/2020 (Tue): Online Lecture 17 - Differential Expression Analysis (Slides), Presenter 7 (Stephen)
- 3/26/2020 (Thu): Online Lecture 18 - RNA-Seq Analysis Summary (Slides), Presenter 8 (Feiya)
- 3/31/2020 (Tue): Online Lecture - Single Cell RNA-Seq (Guest Lecturer: Scott Lewis, Slides, Lab R-Script, Lab Data)
- 4/2/2020 (Thu): Online Lecture - Metagenomics Overview (Slides), Presenter 9 (Peter)
- 4/7/2020 (Tue): Online Lecture - Metagenomics Tools (Slides)
- 4/9/2020 (Thu): No Class (Easter Break)
- 4/14/2020 (Tue): Online Lecture - Metagenomics Lab, Presenter 10 (Cory) (Slides)
- 4/16/2020 (Thu): Online Lecture - Variant Calling, Presenter 11 (Wanxiang) (Slides)
- 4/21/2020 (Tue): Online Lecture - Modeling and Simulation 1 (Slides), Presenter 12 (Yujing – Canceled)
- 4/23/2020 (Thu): Online Lecture - Modeling and Simulation 2 (Slides, Lab: COPASI file), Presenter 13 (Christina)
- 4/28/2020 (Tue): Online Lecture - Modeling and Simulation 3 (Slides), Finalize Lectures (other important topics in Bioinformatics)
- 4/30/2020 (Thu): Online Lecture - Final Project Group Presentations
Literature Review Paper
- Grading rubric for literature review presentation
- Paper1: A guide to sequence your favorite plant genomes
- Review Due: 11:00 am, Thu, Jan 23, 2020
- Presenter: David A
- Paper2: Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
- Review Due: 11:00 am, Thu, Jan 30, 2020
- Presenter: Yassin
- Paper3: Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin
- Paper4: A survey of best practices for RNA-seq data analysis
- Review Due: 11:00 am, Thu, Feb 13, 2020
- Presenter: John
- Paper5: Transcriptomics technologies
- Review Due: 11:00 am, Thu, Feb 20, 2020
- Presenter: Andrew
- Paper6: Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains
- Review Due: 11:00 am, Thu, Feb 27, 2020
- Presenter: David D
- Paper7: Current best practices in single‐cell RNA‐seq analysis: a tutorial
- Review Due: 11:00 am, Tue, Mar 24, 2020
- Presenter: Stephen
- Paper8: Single-cell transcriptional analyses of spasmolytic polypeptide-expressing metaplasia arising from acute drug injury and chronic inflammation in the stomach
- Review Due: 11:00 am, Thu, Mar 26, 2020
- Presenter: Feiya
- Paper9: Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
- Review Due: 11:00 am, Thu, Apr 2, 2020
- Presenter: Peter
- Paper10: Massive metagenomic data analysis using abundance-based machine learning
- Review Due: 11:00 am, Tue, Apr 7, 2020
- Presenter: Cory
- Paper11: Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
- Paper12: Modeling and Simulation Tools: From Systems Biology to Systems Medicine
- Review Due: 11:00 am, Tue, Apr 21, 2020
- Presenter: Yujing
- Paper13: A stochastic model of size control in the budding yeast cell cycle
- Review Due: 11:00 am, Thu, Apr 23, 2020
- Presenter: Christina
Assignments
- Due: 1/24/2020 (Fri) 11pm – Programing HW #1 (10pt): Rosalind Problem 1 @ SLU BCB5250
- Due: 2/3/2020 (Mon) 11pm – Programing HW #2 (10pt): Rosalind Problem 2-3 @ SLU BCB5250
- Due: 2/9/2020 (Sun) 11pm – Lab HW #1 (Genome Assembly) (50pt)
- Due: 2/10/2020 (Mon) 11pm – Programing HW #3 (10pt): Rosalind Problem 4-5 @ SLU BCB5250
- Due: 2/17/2020 (Mon) 11pm – Programing HW #4 (10pt): Rosalind Problem 6-7 @ SLU BCB5250
- Due: 2/24/2020 (Mon) 11pm – Programing HW #5 (10pt): Rosalind Problem 8-9 @ SLU BCB5250
- Due: 3/23/2020 (Mon) 11pm – Programing HW #6 (10pt): Rosalind Problem 10-12 @ SLU BCB5250
- Due: 4/6/2020 (Mon) 11pm – Programing HW #7 (10pt): Rosalind Problem 13-14 @ SLU BCB5250
- Due: 4/13/2020 (Mon) 11pm – Programing HW #8 (10pt): Rosalind Problem 15-17 @ SLU BCB5250
- Due: 4/28/2020 (Tue) 11:59pm – Lab HW #2 (RNA-Seq) (50pt)
- Due: 4/28/2020 (Tue) 11:59pm – Lab HW #3 (Metagenomics) (50pt)
- Due: 4/28/2020 (Tue) 11:59pm – HW #4 (Copasi) (50pt)
Term Project
Oxford MinION Lab