الصفحة 1
الصفحة 1
Molecular evolutionary models in drug discovery
Explores the application of evolutionary molecular models in drug discovery in which secondary metabolites play a fundamental role. Secondary metabolites are not produced in isolation, they are the result of the interaction of genes, metabolism and the environment. The book examines the role of secondary metabolites as leads in drug discovery and on the development of a rational bioprospecting model for new medicines based on the evolution of secondary metabolism. These evolutionary models are part of biological systems and are the most reliable expression of the functioning of living beings.
Introduction to Computational Biology : An Evolutionary Approach
Molecular biology has changed dramatically over the past two decades. Until the early 1990s genes were studied one at a time by small teams of researchers; today entire genomes are sequenced by internationally collaborating laboratories. In the bygone gene-centered era the accumulation of data was the rate-limiting step in research. Now that step is often data interpretation. This is increasingly dependent on computational methods and as a consequence, computational biology has emerged in the past decade as a new subdiscipline of biology. This introduction to computational biology is centered on the analysis of molecular sequence data. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models. In the second part evolutionary time takes center stage and phylogenetic reconstruction, the analysis of sequence variation, and the dynamics of genes in populations are explained in detail. In addition, the book contains a computer program with a graphical user interface that allows the reader to experiment with a number of key concepts developed by the authors.
Immunoinformatics
Immunoinformatics is an emerging subdiscipline of bioinformatics. It utilizes mathematics, information science, computer engineering, genomics, proteomics and immunological methods to bridge immunology and informatics. Similar to bioionformatics which became a driving force in genome research, immunoinformatics enables data-driven research strategies and systems approaches that aim at understanding the networks regulating the immune system. Considering the breath of topic, Immunoinformatics was composed to provide a cross-section of research ranging from data integration, epitope predictions to systems level applications. In ten chapters experts in the field introduce and discuss research strategies for immunologists and bioinformaticians who wish to endeavour existing and new approaches to gain insight into the workings of the immune system.
Evolutionary Genomics : Statistical and Computational Methods
This book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results.
Comparative genomics ; Vol.15 : Using Fungi as Models
Fungal comparative genomics started in 2000 by the genome sequencing of several yeast species other than the canonical Saccharomyces cerevisiae. Since then, over 30 fungal genome sequences have become available. This set represents a total evolutionary divergence comparable to that between vertebrates and arthropods, but also contains closely related genomes. This volume describes how we can use this set of genomes to trace large and small-scale events in genome evolution, to extract information about highly conserved and less conserved sequence elements, and to develop novel methods in genomics that will have an impact on genomics at large.
Chemolithoautotrophic Bacteria : Biochemistry and Environmental Biology
Covers in detail advances in the biochemistry and physiology of several chemolithoautotrophic bacteria as well as their relationship to certain environments. Included are recent findings regarding the oxidation mechanisms of ammonia, nitrite, sulfur compounds, and ferrous iron by special bacteria. The characteristics of many cytochromes are described to further advance the understanding of bacterial oxidation systems of inorganic compounds. Applications of bacteria, such as in sewage treatment and in biohydometallurgy, among others, are detailed, and bacteria considered closest to the origins of life are discussed in the final chapter.
Bioinformatics and the cell : Modern computational approaches in genomics, proteomics and transcriptomics
"Xuhua Xia’s Bioinformatics and the Cell is a welcome addition to the bourgeoning field of bioinformatics text books. Xia stakes out a too-often neglected middle ground in bioinformatics by presenting a work that emphasizes methods’ biological utility without eschewing algorithmic formalism. Readers will find a well-rounded presentation of bioinformatics techniques employed in genomics, transcriptomics and proteomics – unified throughout by the common theme of molecular evolution."
Bacteriocins : Ecology and Evolution
Microbes produce an extraordinary array of defense systems. These include bacteriocins, a class of antimicrobial molecules with narrow killing spectra, produced by bacteria. The book describes the diversity and ecological role of bacteriocins of Gram-positive and Gram-negative bacteria, presenting a new classification scheme for the former and a state-of-the-art look at the role of bacteriocins in bacterial communication. It discusses the molecular evolution of colicins and colicin-like bacteriocins, and provides a contemporary overview of archaeocins, bacteriocin-like antimicrobials produced by archaebacteria. Furthermore, various modeling (in silico) studies elucidate the role of bacteriocins in microbial community dynamics and fitness, delving into rock-paper-scissors competition and the counter-intuitive survival of the weakest. The book makes compelling reading for a multi-faceted scientific audience, including those working in the fields of biodiversity and biotechnology, notably in the human and animal health domain.
Analysis of phylogenetics and evolution with R
This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments.
