BIOE 498/598 Computational Cancer Biology – Fall course

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 (

Credit: 3 undergraduate hours, 4 graduate hours


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.


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