Of interest to informatics students, particularly those interested in bioinformatics.
BIOE 498 / 598 – Computational Cancer Biology (Fall 2012)
CRN: 56892
Tue and Thu 2PM-3:20PM
Instructor: Jian Ma (jianma@illinois.edu)
Credit: 3 undergraduate hours, 4 graduate hours
Description
We will explore basic biology of cancer. We will discuss mathematical modeling of the process of
carcinogenesis as somatic evolution of cells. We will also focus on current research topics in cancer
biology using data from next-generation sequencing (NGS) technologies. Related tools and resources
will be examined. A selection of the latest research papers in this emerging field will be discussed.
Algorithmic and modeling methods will be stressed, but biological results and their significance will
also be addressed. The class will provide hands-on experience of using computational tools to solve
questions related to cancer genomics.
Topics
A Brief Tour of the Human Genome
Basics of Cancer Genetics
Algorithms for Sequence Alignment
Methods for Transcriptome Analysis based on RNA-seq
Identifying Aberrant Genes in Cancer
Methods for Discovering Driver Mutations in Cancer
Models of Cancer Genome Evolution and Metastasis
Models of Chromosomal Abnormalities in Cancer
Cancer Epigenomes
Models for Cancer Somatic Evolutions
One-hit and Two-hit Stochastic Models of Cancer Initiation
Competition Dynamics and Cancer Evolution
Genome-wide Association Studies of Cancer
Computer Lab Sessions
Discussion Sessions