Frank Eisenhaber
Bioinformatics Group
Institute of Molecular Pathology
Vienna, Austria

About this Book

In this anthology, leading researchers present critical reviews of methods and high-impact applications in computational biology that lead to results that also non-bioinformaticians must know to design efficient experimental research plans. Discovering Biomolecular Mechanisms with Computational Biology also summarizes non-trivial theoretical predictions for regulatory and metabolic networks that have received experimental confirmation.

Discovering Biomolecular Mechanisms with Computational Biology is essential reading for life science researchers and higher-level students that work on biomolecular mechanisms and wish to understand the impact of computational biology for their success.

Table of Contents

Introduction Bioinformatics: Mystery, Astrology or Service Technology?
Frank Eisenhaber

SECTION I: DERIVING BIOLOGICAL FUNCTION OF GENOME INFORMATION
WITH BIOMOLECULAR SEQUENCE AND STRUCTURE ANALYSIS

1. Reliable and Specific Protein Function Prediction by Combining Homology with Genomic(s) Context
Martijn A. Huynen, Berend Snel and Toni Gabaldón

2. Clues from Three-Dimensional Structure Analysis and Molecular Modelling:
New Insights into Cytochrome P450 Mechanisms and Functions
Karin Schleinkofer and Thomas Dandekar

3. Prediction of Protein Function: Two Basic Concepts and One Practical Recipe
Frank Eisenhaber

SECTION II: COMPLEMENTING BIOMOLECULAR SEQUENCE ANALYSIS
WITH TEXT MINING IN SCIENTIFIC ARTICLES

4. Extracting Information for Meaningful Function Inference through Text-Mining
Hong Pan, Li Zuo, Rajaraman Kanagasabai, Zhuo Zhang, Vidhu Choudhary, Bijayalaxmi Mohanty, Sin Lam Tan, S.P.T. Krishnan, Pardha Sarathi Veladandi, Archana Meka, Weng Keong Choy, Sanjay Swarup and Vladimir B. Bajic

5. Literature and Genome Data Mining for Prioritizing Disease-Associated Genes
Carolina Perez-Iratxeta, Peer Bork and Miguel A. Andrade

SECTION III: MECHANISTIC PREDICTIONS FROM THE ANALYSIS
OF BIOMOLECULAR NETWORKS

6. Model-Based Inference of Transcriptional Regulatory Mechanisms from DNA Microarray Data
Harmen J. Bussemaker

7. The Predictive Power of Molecular Network Modelling: Case Studies of Predictions with Subsequent Experimental Verification
Stefan Schuster, Edda Klipp and Marko Marhl

SECTION IV: MECHANISTIC PREDICTIONS FROM THE ANALYSIS
OF BIOMOLECULAR SEQUENCE POPULATIONS: CONSIDERING EVOLUTION
FOR FUNCTION PREDICTION

8. Theory of Early Molecular Evolution: Predictions and Confirmations
Edward N. Trifonov

9. Hitchhiking Mapping: Limitations and Potential for the Identification of Ecologically Important Genes
Christian Schlötterer

10. Understanding the Functional Importance of Human Single Nucleotide Polymorphisms
Saurabh Asthana and Shamil Sunyaev

11. Correlations between Quantitative Measures of Genome Evolution, Expression and Function
Yuri I. Wolf, Liran Carmel and Eugene V. Koonin