BME 483/543: Quantitative Systems Biology
Course Material
- Intro
  - Microarray Analysis
  - Micro-RNA Analysis
- Machine Learning in Bioinformatics
  - Machine Learning in Gene Expression Studies
  - Machine Learning in Gene Expression Studies

BME 483/543: Quantitative Systems Biology

Project Deliverables

Course Material

Intro

Dropbox setup
Using file sharing and versioning systems: Github, SVN
Working with webpages in Matlab
File parsing strategies in Matlab. regular expression.

Microarray Analysis

Reading:
- Zvelebil Chapter 15.1, 16 (optional)
- DNA_microarray
- Watch Animation
- Analysis of microarray experiments of gene expression profiling

Lecture Notes: ma.pdf

GEO Demo: geo_demo.mlx, geo_demo.pdf, (bmes_downloadandparsegpl.m and bmes_downloadandparsegse.m available in bmes.ahmet Dropbox folder)
GEO Demo: geo_demo.ipynb

Micro-RNA Analysis

Reading: MicroRNAs: small RNAs with a big role in gene regulation
Lecture Notes: mirna in pain.pdf, mirna target prediction.pptx

Machine Learning in Bioinformatics

Reading:
- Machine learning in bioinformatics

Machine Learning in Gene Expression Studies

Reading:
- Golub_et_al_1999.pdf
- Classifying Microarray Data Using Support Vector Machines
Lecture Notes:
- golub99.acute leukemia.svm.pdf
- svmdemo_golub99.pdf, svmdemo_golub99.mlx
- gene regulation inference.pdf
- Python demo (Not gene expression related): featureselectdemo_diabetes_py.ipynb

Machine Learning in Gene Expression Studies

Reading:
- Golub_et_al_1999.pdf
- Classifying Microarray Data Using Support Vector Machines
Lecture Notes:
- golub99.acute leukemia.svm.pdf
- svmdemo_golub99.pdf, svmdemo_golub99.mlx
- gene regulation inference.pdf
- Python demo (Not gene expression related): featureselectdemo_diabetes_py.ipynb

RNASeq
- nextgen seqalign survey.2010.pdf
- Assignment - RefSeq Experiment in a Yeast Mutant

Genome Assembly
- Genome Assembly

Metagenomics, Microbiome
- Metagenomics
- Microbiome Helper Virtual Box, 16S tutorial, Metagenomics tutorial
- Oracle Virtual Box, ssh, passwordless login
- Initial Assignment: Install Microbiome Helper and run through the Metagenomics Tutorial. Compare your answers to the questions with the answers provided there.
- hwmetagenomics.docx

TODO: Discuss vectorized code: e.g., remove all rows with less than 3 non-nan samples.