New Publication by Arshan Nasir, PhD Student

Arshan Nasir, an Informatics PhD Student,  has published a new article titled “Global Patterns of Protein Domain Gain and Loss in Superkingdoms” in PLOS Computational Biology. This is Arshan’s first publication from his PhD Research.  He is currently spending the Spring 2014 semester conducting research at the Universitié Paris-Sud, Institute Génétique et Microbiolgie as a recipient of the Chateaubriand Fellowship.

Grad Student Spotlight: Kyungho Lee

The work of Kyungho Lee, a graduate student in Informatics, was one of five artists featured during the art show at VizWeek 2012, held in last October in Seattle. VizWeek is the premier forum for computer scientists working in scientific and information visualization. Lee's work deals with the compression and data loss caused by our digital world.  More

Two New Publications by PhD Student Khuram Shahzad

Khuram Shahzad, a current PhD student in the Illinois Informatics Institute, has recently published two new research articles. Bioinformatics and Gene Network Analysis of the Swine Mammary Gland Transcriptome during Late Gestation was published in the July 2013 issue of Bioinformatics and Biology Insights and can be accessed online here.  Shahzad's second article titled Insight from βC1 protein model for implication in cotton leaf curl disease was published in the journal Bioinformation and is also available online.


PhD student Arshan Nasir wins award


Informatics PhD candidate Arshan Nasir and his advisor Professor Gustavo Caetano-Anolles, professor of crop sciences, and their collaborator Kyung Mo Kim of the Korea Research Institute of Bioscience and Biotechnology were rewarded for their publication of their article Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya” from BioMed Central.  The article is available online at  The award will be presented later this month in Boston.

Atlas.ti 7 data analysis program available on campus


ATLAS is excited to announce that we now have Atlas.ti 7 available on all of the computers in our lab located at Lincoln Hall 2043. Atlas.ti is a qualitative data analysis program designed to help researchers manage and analyze non-numerical data such as text, video, audio and graphics in a meaningful and systematic way. Students and faculty engaged in qualitative or mixed-methods research are invited to use the lab or request a consultation at:

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