Bioinformatics
Chapters
Clues from 3-dimensional Structure Analysis and Molecular Modelling: New Insights Into Cytochrome P450 Mechanisms and Functions
Karin Schleinkofer and Thomas Dandekar
Cytochrome P450 is a focus of attention as it comprises one of the largest superfamilies of enzyme proteins. Metabolization of many drugs is affected by cytochrome P450. It is an attractive drug target, e.g., cytochrome P450s of Mycobacterium tuberculosis are promising targets in the fight agains...
Correlations between Quantitative Measures of Genome Evolution, Expression and Function
Yuri I. Wolf, Liran Carmel and Eugene V. Koonin
In addition to multiple, complete genome sequences, genome-wide data on biological prop properties of genes, such as knockout effect, expression levels, protein-protein interactions, and others, are rapidly accumulating. Numerous attempts were made by many groups to examine connections between th...
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*
One of the emerging technologies in computational biology is text-mining which in cludes natural language processing. This technology enables extraction of parts of relevant biological knowledge from a large volume of scientific documents in an automated fashion. We present several systems which ...
Limitations and Potential for the Identification of Ecologically Important Genes
Christian Schlotterer
A recent series of publications demonstrated that identification of genomic regions subjected to positive selection (hitchhiking mapping) is possible and could be applied in an ecological context. This review focuses on the use of microsatellite markers in genome scans for the identification of b...
Literature and Genome Data Mining for Prioritizing Disease-associated Genes
Carolina Perez-Iratxeta, Peer Bork and Miguel A. Andrade
The first step in understanding the molecular biology of an inherited disease is to identify which gene or genes are carrying variants. This process starts with locating the mutations in a chromosomal band, as narrow as possible, and follows with the manual analysis of all the genes mapping in th...
Literature and Genome Data Mining for Prioritizing Disease-Associated Genes
Carolina Perez-Iratxeta, Peer Bork and Miguel A. Andrade
The first step in understanding the molecular biology of an inherited disease is to identify which gene or genes are carrying variants. This process starts with locating the mutations in a chromosomal band, as narrow as possible, and follows with the manual analysis of all the genes mapping in thi...
Model-Based Inference of Transcriptional Regulatory Mechanisms from DNA Microarray Data
Harmen J. Bussemaker
The development of DNA microarray technology has made it possible to monitor the mRNA abundance of all genes simultaneously (the transcriptome) for a variety of cellular conditions. In addition, microarray-based genomewide measurements of promoter occupancy (the occupome) are now available for an...
Mystery, Astrology or Service Technology?
Frank Eisenhaber*
Mathematical interpretation and integration of experimental data for the goal of biological theory development has had little, if none, impact on previous progress in life sciences compared with the sophistication of experimental approaches themselves. The genesis of recent spectacular breakthrou...
Prediction of Protein Function Two Basic Concepts and One Practical Recipe
Frank Eisenhaber
The analysis of uncharacterized biomolecular sequences obtained as a result of genetic screens, expression profile studies, etc. is a standard task in a life science research environment. The understanding of protein function is typically the main difficulty. This chapter intends to give practica...
Reliable and Specific Protein Function Prediction by Combining Homology with Genomic(s) Context
Martijn A. Huynen, Berend Snel and Toni Gabaldón
Completely sequenced genomes and other types of genomics data provide us with new information to predict protein function. While classical, homology-based function prediction provides information about a proteins’ molecular function (what does the protein do at a molecular scale?), the analysis ...
The Predictive Power of Molecular Network Modelling: Case Studies of Predictions with Subsequent Experimental Verification
Stefan Schuster*, Edda Klipp and Marko Marhl
Since the 1960s, the mathematical modelling of intracellular systems, such as metabolic pathways, signal transduction cascades and transport processes, is an ever-increasing field of research. The results of most modelling studies in this field are in good qualitative or even quantitative agreeme...
Theory of Early Molecular Evolution: Predictions and Confirmations
Edward N. Trifonov
A new theory of early molecular evolution is described, proceeding from original speculations to specific predictions and their confirmations. This classical cycle is then repeated generating the earliest picture of evolving Life. First, a consensus temporal order (“chronology”) of appearance of ...
Understanding the Functional Importance of Human Single Nucleotide Polymorphisms
Saurabh Asthana and Shamil Sunyaev
Single nucleotide polymorphisms (SNPs) are the major source of human genetic varia tion, and the functional subset of SNPs, predominantly in protein coding regions, con tributes to phenotypic variation. However, much of the variation in coding regions may not produce any functional effects. There...
