Organizers:

Yufei Huang  Dept. of Electrical and Computer Engineering, University of Texas at San Antonio and Ghreehy Children’s Cancer Institute, University of Texas Health Science Center (yhuang@utsa.edu)

Yidong Chen  National Cancer Institute, National Institute of Health (Yidong@mail.nih.gov)

Topics:

Systems biology is a groundbreaking research area that seeks to understand interplays of molecules and cells in time and space to determine functioning of a complex biological system. Translation of such knowledge into medicine is and will continue to revolutionize disease diagnosis and prognosis, medical therapy, prevention, drug discovery, and drug design.

In contrast to the experimental-centric approach of the traditional biomedical research, systems biology relies on iterative application of biomedical experiments and knowledge with mathematical modeling and systems control theory. Systems biology investigates temporal and physiological dynamics of gene functions, genetic associations to tissues and cell types, genome-wide polymorphism, among many others.  Such systems approach has also provided us with a new framework to disease understanding, diagnosis, therapy, and prevention. Focus therein is given to understand how mutation and perturbation alter networks of genes and proteins and identify markers and drug targets in the context of gene and protein networks. While many existing models and computational approaches have already proven successful in this research, systems biology research coupled with advances in high throughput biomedical technologies presents a host of new computational challenges especially associated with high dimension, complexity, and dynamics of the systems as well as heterogeneity of ever-growing biomedical data and information.    

This workshop intends to address the development of translational research of systems biology into medicine. We desire to attract high-quality papers addressing recent computational and technological advances in systems biology and systems medicine. Possible topical areas of interest include, but are not limited to the following:

• 1.     Gene-gene interaction, and genetic regulatory networks
• a.     Reverse engineering gene regulatory networks and pathways
• b.    Genetic network modeling and simulation
• c.    Dynamics and control of genetic regulatory networks
• d.    Network model based analysis methods for molecular target identification, gene set enrichment and sample classification

• 2.     Computational issues in global and targeted genomics and proteomics
• a.     Integration of multi-scale and multi-level data and knowledge
• b.     Global identification of targets and regulation of miRNA
• c.     Computational methods for cis- and trans-regulatory element identification via ChIP-chip and ChIP-seq technologies
• d.    Data analysis methods for SNP/genotype data
• e.     System level disease prognosis and diagnosis including biomarker discovery and cell type fingerprints identification
• f.     Clinical Applications of systems biology

• 3.     Computational analysis of single-cell and signal-molecule systems
• a.     Nanotechnology for drug delivery and personalized medicine
• b.    New high throughput technologies and related computational issues including next-generation sequencing and microfluidic chips
• c.     In-vivo and in-vitro imaging and diagnostics

Schedule: Prospective authors should submit a 2- to 4-page extended abstract through workshop paper submission systems. Review, revision, and publication will be according to the following schedule:

•        September 1, 2008: Due date for extended abstract
•        September 20, 2008: Notification of paper acceptance to authors
•        October 1, 2008: Camera-ready of accepted abstracts
•        November 3-5, 2008: Workshops