Proposal of a full-day workshop on
Methods and Applications of Systems Biology
Yidong Chen1, Yufei Huang2, Ji Zhang3
1. Greehey Children’s Cancer Research Institute, Dept. of Epidemiology and Biostatistics,
University of Texas Health Science Center at San Antonio,
8403 Floyd Curl drive San Antonio, TX 78229; email: cheny8@uthscsa.edu
2. Dept. of Electrical and Computer Engineering, University of Texas at San Antonio
One UTSA Circle, San Antonio, Texas, 78249-0669; email: yhuang@utsa.edu
3. State Key Laboratory of Medical Genomics, Ruijin Hospital,
Shanghai Jiao Tong University School of Medicine,
197 Ruijin Er Rd., Shanghai 200025; email: jizhang@sibs.ac.cn
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 one-day workshop will address the computational issues in systems biology and
innovative applications of systems biology in studying biological processes, identitying
therapeutic markers, and personalized 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
Contributions to the conference and research field in large:
The theme of this workshop, systems biology, is one of the most actively research area
in bioinformatics and computational biology. This workshop also 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. Our ultimate goal is to bring together some of
the leading researchers in the field and provide a forum for the computational community
to inform and discuss computational and engineering issues as well as the future of
systems biology and medicine.
Plans for advising the workshop
A website will be constructed for the workshop. We also maintain an email list of more
than 300 people in the field. The call for paper (CFP) and related information will be
distributed by the website and email. We will take an active approach to direct contact
and invite some of the leading researchers in the field.