From genes to networks: in systematic points of view
We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology.
Volume 5 Supplement 3
Edited by Ke Zhang, Yunlong Liu, Hamid R Arabnia
BIOCOMP 2010 - The 2010 International Conference on Bioinformatics and Computational Biology.
Las Vegas, NV, USA12-15 July 2010
We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology.
For RNA-seq data, the aggregated counts of the short reads from the same gene is used to approximate the gene expression level. The count data can be modelled as samples from Poisson distributions with possibl...
A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating br...
State Space Model (SSM) is a relatively new approach to inferring gene regulatory networks. It requires less computational time than Dynamic Bayesian Networks (DBN). There are two types of variables in the lin...
Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs...
Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been u...
Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breas...
Bone cells can sense physical forces and convert mechanical stimulation conditions into biochemical signals that lead to expression of mechanically sensitive genes and proteins. However, it is still poorly und...
To understand transcriptional regulatory networks (TRNs), especially the coordinated dynamic regulation between transcription factors (TFs) and their corresponding target genes during development, computationa...
The availability of temporal measurements on biological experiments has significantly promoted research areas in systems biology. To gain insight into the interaction and regulation of biological systems, math...
Various gene-expression signatures for breast cancer are available for the prediction of clinical outcome. However due to small overlap between different signatures, it is challenging to integrate existing dis...
Currently, several systems have been proposed to classify viruses and indicate the relationships between different ones, though each system has its limitations because of the complexity of viral origins and th...
Numerous genetic and genomic datasets related to complex diseases have been made available during the last decade. It is now a great challenge to assess such heterogeneous datasets to prioritize disease genes ...
The primary objectives of this paper are: 1.) to apply Statistical Learning Theory (SLT), specifically Partial Least Squares (PLS) and Kernelized PLS (K-PLS), to the universal "feature-rich/case-poor" (also kn...
To understand how infectious agents disseminate throughout a population it is essential to capture the social model in a realistic manner. This paper presents a novel approach to modeling the propagation of th...