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Frontiers in Computational and Systems Biology

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Biological and biomedical studies have entered a new era due to the widespread use of mathematical models and computational approaches. What was no more than a theoretician's fantasy 20 years ago has become the blooming field of computational biology. Furthermore, this powerful and stimulating research paradigm in biological studies has in turn led to new developments in mathematics, physics and computer science.

This unique volume surveys state-of-the-art research on statistical methods in molecular and systems biology, with contributions from leading experts in the field. Each chapter discusses theoretical aspects, applications to biological problems, and possible future developments. Understanding the biology at a molecular and system level stands among the most exciting challenges faced by modern science. This text clearly demonstrates how computational and mathematical approaches continue to address this challenge.

Topics and features:

  • Presents the use of thermodynamic models to analyze gene regulatory mechanisms
  • Reviews major algorithms for RNA secondary structure prediction, with a focus on ensemble-based approaches
  • Discusses how developments in the area of oligo arrays has led to a better understanding of the array mechanism and improvements in microarray data analysis
  • Examines the application of models of stochastic processes in nonequilibrium thermodynamics and biological signal transduction
  • Describes phylogenetic footprinting methods for TFBS identification, based on alignments
  • Introduces penalized regression-based methods for constructing genetic interaction or regulatory networks
  • Investigates the specific role played by irreversible Markov processes in modeling cellular biochemical systems
  • Explores the concept of gene modules in a transcriptional regulatory network

With reviews of current hot topics in computational biology and systems biology, supplied by an international selection of top researchers, this is an essential text for researchers and graduate students in computational biology, biology and mathematics.

Author(s): Chieh-Chun Chen, Sheng Zhong (auth.), Jianfeng Feng, Wenjiang Fu, Fengzhu Sun (eds.)
Series: Computational Biology 15
Edition: 1
Publisher: Springer-Verlag London
Year: 2010

Language: English
Pages: 24
Tags: Computational Biology/Bioinformatics; Systems Biology; Statistics and Computing/Statistics Programs; Probability and Statistics in Computer Science

Front Matter....Pages I-XXV
Analysis of Combinatorial Gene Regulation with Thermodynamic Models....Pages 1-17
RNA Secondary Structure Prediction and Gene Regulation by Small RNAs....Pages 19-37
Some Critical Data Quality Control Issues of Oligoarrays....Pages 39-59
Stochastic-Process Approach to Nonequilibrium Thermodynamics and Biological Signal Transduction....Pages 61-81
Granger Causality: Theory and Applications....Pages 83-111
Transcription Factor Binding Site Identification by Phylogenetic Footprinting....Pages 113-131
Learning Network from High-Dimensional Array Data....Pages 133-156
Computational Methods for Predicting Domain–Domain Interactions....Pages 157-173
Irreversible Stochastic Processes, Coupled Diffusions and Systems Biochemistry....Pages 175-201
Probability Modeling and Statistical Inference in Periodic Cancer Screening....Pages 203-218
On Construction of the Smallest One-sided Confidence Intervals and Its Application in Identifying the Minimum Effective Dose....Pages 219-230
Group Variable Selection Methods and Their Applications in Analysis of Genomic Data....Pages 231-248
Modeling Protein-Signaling Networks with Granger Causality Test....Pages 249-257
DNA Copy Number Profiling in Normal and Tumor Genomes....Pages 259-281
Spatial Disease Surveillance: Methods and Applications....Pages 283-300
From QTL Mapping to eQTL Analysis....Pages 301-329
An Evaluation of Gene Module Concepts in the Interpretation of Gene Expression Data....Pages 331-349
Readout of Spike Waves in a Microcolumn....Pages 351-369
False Positive Control for Genome-Wide ChIP-Chip Tiling Arrays....Pages 371-381
Back Matter....Pages 383-401