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This book is the first of its kind to provide a large collection of bioinformatics problems with accompanying solutions. Notably, the problem set includes all of the problems offered in Biological Sequence Analysis (BSA), by Durbin et al., widely adopted as a required text for bioinformatics courses at leading universities worldwide. Although many of the problems included in BSA as exercises for its readers have been repeatedly used for homework and tests, no detailed solutions for the problems were available. Bioinformatics instructors had therefore frequently expressed a need for fully worked solutions and a larger set of problems for use on courses. This book provides just that: following the same structure as BSA and significantly extending the set of workable problems it will facilitate a better understanding of the contents of the chapters in BSA and will help its readers develop problem solving skills that are vitally important for conducting successful research in the growing field of bioinformatics. All of the material has been class-tested by the authors at Georgia Tech, where the first ever M.Sc. degree program in Bioinformatics was held. MARK BORODOVSKY is the Regents' Professor of Biology and Biomedical Engineering and Director of the Center for Bioinformatics and Computational Biology at Georgia Institute of Technology in Atlanta. He is the founder of the Georgia Tech M.Sc. and Ph.D. degree programs in Bioinformatics. His research interests are in bioinformatics and systems biology. He has taught Bioinformatics courses since 1994. SVETLANA EKISHEVA is a Research Scientist at the School of Biology, Georgia Institute of Technology, Atlanta. Her research interests are inbioinformatics, applied statistics and stochastic processes. Her expertise includes teaching probability theory and statistics at universities in Russia and in the USA.
The binding of antibiotics and drugs to DNA is a fast developing area of research with important applications in medicine, particularly the treatment of cancer. Sequence-specific DNA Binding Agents uniquely discusses key aspects of this topic, providing a novel perspective on the subject. Written by experts in the field, this book discusses diverse modes of binding of antibiotics and drugs to DNA, emphasising matters that are important or promising for cancer treatment. Chapters discuss established agents like actinomycin D but also look at novel drugs with strong potential in chemotherapy such as new topoisomerase inhibitors, telomerase inhibitors, peptide nucleic acids and triple helix-forming oligonucleotides. There are also sections discussing methodological advances including computational methods, slow kinetics, melting curve analysis and approaches to medicinal chemistry. Finally there is a section on RNA structure and its potential as a drug target. The book is ideal for researchers in industry and academia who require a comprehensive source of reference to this rapidly expanding subject.
Microarray analysis is a highly efficient tool for assessing the expression of a large number of genes simultaneously, and offers a new means to classify cancer and other diseases. Gene expression profiling can also be used to predict clinical outcome and response to specific therapeutic agents. This survey spans recent applications of microarrays in clinical medicine, covering malignant disease including acute leukaemias, lymphoid malignancies and breast cancer, together with diabetes and heart disease. Investigators in oncology, pharmacology and related clinical sciences, as well as basic scientists, will value this review of a promising new diagnostic and prognostic technology.
Fungal comparative genomics started in 2000 by the genome sequencing of several yeast species. Since then, over 30 fungal genome sequences have become available. This set represents a huge evolutionary divergence, but also contains closely related genomes. This volume describes how to use this set of genomes to trace events in genome evolution, to extract information about highly conserved and less conserved sequence elements, and to develop novel methods in genomics.
Microarray Technology Through Applications provides the reader with an understanding, from an applications perspective, of the diverse range of concepts required to master the experimental and data analysis aspects of microarray technology. The first chapter is a concise introduction to the technology and provides the theoretical background required to understand the subsequent sections. The following chapters are a series of case studies representative of the most general and important applications of microarray technology, including CGH, analysis of gene expression, SNP arrays and protein arrays. The case studies are written by experts in the field and describe prototypic projects, indicating how to generalize the approach to similar studies. There are detailed step-by-step protocols describing the specific experimental and data analysis protocols mentioned in the case study section. There is also information on printing glass DNA microarray slides and data interpretation. Colour figures and data sets are provided on the website at http://www.garlandscience.com/9780415378536
This book introduces a discrete optimisation technique in four applications: classic Traveller Salesperson Problem (TSP), Multilocus Genetic Mapping, Multilocus Consensus Genetic Mapping, and Physical Mapping. Each of the four sections contains the problem formulation, description of the algorithm, and experimental results. The foregoing problems are solved on the basis of Guided Evolution Strategy (GES) algorithm. The algorithm was implemented in MultiPoint package (http://multiqtl.com). The developed analytical tools were applied in many genome mapping projects.
Alternative splicing occurs in most human genes and contributes to protein diversity by producing multiple mRNAs from each gene. In this book, the authors present new developments in alternative splicing research. Topics discussed include alternative splicing alterations in Alzheimer's disease; plant RNA-binding proteins implicate mRNA processing in abscisic acid (ABA) responses; comprehensive analyses of alternative exons in neuronally differentiated P19 cells; an epigenetic view on alternative splicing; identification of genuine alternative splicing variants for rare or long-sized transcripts; alternative RNA splicing and regulation of nitric oxide signalling; alternative splicing by analysing human mRNA diversity using data of FLJ human cDNAs; alternative splicing in human immune systems and auto-immune diseases; and poly (ADP-Ribosyl)ation regulation in alternative splicing.
Viral diseases have an important impact on public health world-wide. New genomic technologies are providing infectious disease scientists with a unique ability to study at the genetic level those viruses that cause disease and the interactions they have with infected hosts. In this book, the authors present new research in viral genomes. Topics include improvements in HSV-1 derived amplicon vectors for gene transfer; viral genome research in papillomavirus; the synthetic synthesis of viral genomes; and a novel bioinformatic method to analyse over 10,000 influenza virus strains simultaneously.
Are you considering to test your own DNA? Do you want to learn more about your health and ancestry? Understand your DNA - A Guide is about what you can use genetics for. For a few hundred dollars, you can now scan your own genes. Millions of people all over the world have already done so. Everyone wants to see what they can get to know about themselves, and the market growing rapidly. But what does it require from you? And what can you really use a DNA test for? Understand your DNA - A Guide helps you put the plots and charts of consumer genetics into perspective and enables you to figure out what's up and down in the media headlines. The book is also a key input for today's debate about what we as a society can and want to do with medical genetics. Genetics will play a growing role in the future. Understand your DNA - A Guide is an easy-to-read and necessary guide to that future. The book is provided with a foreword by Professor Sham Pak-Chung of Hong Kong University.While there are many books about genetics, they typically take the perspective of a scientist wanting to understand the molecular levels. At the same time, direct-to-consumer genetics is a booming market, with millions of people already tested. Very little has been published that will guide them for real, because the need here is more focused on medical and practical understanding, than focussed on molecules.This book therefore aims to hit that vacant spot in the market. It's a walk-through of all concepts that are necessary to understand in your own analysis. Meanwhile, it is also limited in scope to only those concepts - thus distinguishing it from broader works.The book is appropriate for the readerships in modern multi-ethnic metropolises because it mixes European and Asian examples, both from the collaboration between the author from Europe and the foreword-writer, Prof. Pak Sham of Hong Kong University. But also, because many of the examples in the book concerns differences and similarities between Asian and European ethnicities, something the author believes is a trend in time.
Polyploidy plays an important role in biological diversity, trait improvement, and plant species survival. Understanding the evolutionary phenomenon of polyploidy is a key challenge for plant and crop scientists. This book is made up of contributions from leading researchers in the field from around the world, providing a truly global review of the subject. Providing broad-ranging coverage, and up-to-date information from some of the world's leading researchers, this book is an invaluable resource for geneticists, plant and crop scientists, and evolutionary biologists.
Chromatin is DNA plus the proteins (and RNA) that package DNA within the cell nucleus. The primary functions of chromatin are: to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene expression and DNA replication. In this book, the authors present topical research in the study of chromatin including the varied functions of aurora kinases A and B in mitosis and carcinogenesis; the chromatin state of pluripotent stem cells; MITF meets chromatin in melanoma; the state of chromatin as an integrative indicator of cell stress; analysing DNA damage and its repair throughout entire genomes; the cloning process, structural characterisation of Revolver transposon and its patented application for chromosome tags; DNA damage and Rad16; and glucocorticoid-induced chromatin remodelling.
A plasmid is a DNA molecule that is separate from, and can replicate independently of, the chromosomal DNA. They are double-stranded and circular in form. Plasmids usually occur naturally in bacteria, but are sometimes found in eukaryotic organisms. In this book, the authors present current research in the genetics, applications and health issues relating to plasmids. Topics include the development of multifunctional plasmids for diverse biotechnological applications; plasmids as indispensable components of multipartite azospirillum genomes; structural and segregational instability in plasmid biology; and conjugal plasmid transfer and phage inhibition kinetics.
The technique of DNA Sequencing lies at the heart of modern molecular biology. Since current methods were first introduced, sequence databases have grown exponentially, and are now an indispensable research tool. This up-to-date, practical guide is unique in covering all aspects of the methodology of DNA sequencing, as well as sequence analysis. It describes the basic methods (both manual and automated) and the more advanced techniques (for example, those based on PCR) before moving on to key applications. The final section focuses on the analysis of sequence data; it details the software available, and explains how the Internet can be used for accessing software and major databases. By explaining the options available and their merits, DNA Sequencing allows newcomers to the field to decide which method is the most suitable for their application. For experienced sequencers the book is a useful reference source for details of the less common techniques and as a means of updating knowledge.
Integration and Visualization of Gene Selection and Gene Regulatory Networks for Cancer Genome helps readers identify and select the specific genes causing oncogenes. The book also addresses the validation of the selected genes using various classification techniques and performance metrics, making it a valuable source for cancer researchers, bioinformaticians, and researchers from diverse fields interested in applying systems biology approaches to their studies.
Stem cells are cells found in all multi cellular organisms. They are characterised by the ability to renew themselves through mitotic cell division and differentiate into a diverse range of specialised cell types. This book presents and discusses current research in the study of stem cell research, including cancer and prostate stem cells; neural stem cells and taurine; interactions between transplanted neural stem cells and host tissue; retrovirus vector silencing in stem cells and moral and scientific consideration in embryonic stem cell research.
The past few years have witnessed a revolution in our ability to obtain DNA from ancient humans. This important new data has added to our knowledge from archaeology and anthropology, helped resolve long-existing controversies, challenged long-held views, and thrown up remarkable surprises. The emerging picture is one of many waves of ancient human migrations, so that all populations living today are mixes of ancient ones, and often carry a genetic component from archaic humans. David Reich, whose team has been at the forefront of these discoveries, explains what genetics is telling us about ourselves and our complex and often surprising ancestry. Gone are old ideas of any kind of racial apurity.' Instead, we are finding a rich variety of mixtures. Reich describes the cutting-edge findings from the past few years, and also considers the sensitivities involved in tracing ancestry, with science sometimes jostling with politics and tradition. He brings an important wider message: that we should recognize that every one of us is the result of a long history of migration and intermixing of ancient peoples, which we carry as ghosts in our DNA. What will we discover next?
Several problems in modern genome mapping analysis belong to the field of discrete optimisation on a set of all possible orders. In this book, formulations, mathematical models and algorithms for genetic/genomic mapping problem that can be formulated in TSP-like terms are proposed. Since the 1960s, Operational Research techniques have extensively been developed to support organisations in their Manpower Planning challenge -- a fundamental aspect of Human Resource Management in organisations. This book reviews the techniques and alternative approaches that have been introduced in Manpower Planning (e.g., simulation techniques), and in general, the Markov Chain Theory. Furthermore, the authors of this book propose a new class of strategies for giving the optimal inventory replenishments for each retailer. In addition, the authors demonstrate how to increase the usage of iterative methods in all possible fields by accelerating such solvers using Reconfigurable Hardware. An optimisation method for material layout of incompressible rubber components is presented as well. Other chapters in this book use a generic approach to study minimisation problems on a complete metric space, provide a novel design method in the case of an output feedback suboptimal control problem, derive Levy process-based models of jump diffusion-type for banking operations involving securitisation, capital and profitability, and investigate the optimality of the loan securitisation process that has had a prominent role to play in the sub-prime mortgage crisis (SMC).
Telomerase is a ribonucleoprotein enzyme that catalyses the cellular synthesis of telomeric DNA during cellular division, resulting in maintenance of telomere length and increased proliferative potential. Several studies suggest that the telomerase may play an important role in the diagnosis and prognosis of cancer because its expression strongly correlates with the potential tumour progression. Ninety percent of human cancers on different organs have shown high telomerasa activity. This book reviews research in the field of telomerase including functions of telomerase independent of its interaction with telomeres on gene expression and chromatin structure; histone deacetylase inhibition as an anticancer telomerase-targeting strategy and others.
Organic europium complexes are of considerable interest due to their sharp narrow emission spectrum and potentially high emission quantum efficiency, originated from 2D0-7F2 electronic transitions of the central ions. Therefore, organic europium complexes have well applications in organic light-emitting diodes. Furthermore, organic europium complexes also show well electrical switching characteristics in diodes, potential applications as memory devices in information storage. This book reviews the achieved progresses in organic europium complexes and their applications in organic light-emitting diodes and memory devices.
New methods used for the detection of DNA hybridisation process, including electrochemical, optical scattering, surface plasmon resonance, nanogravimetric, and fluorimetric are described and their application in assays assessing DNA damage is discussed in this book. The analyses of damage and alterations for the DNA in solution as well as for the DNA immobilised on core-shell gold nanoparticles and solid electrodes are presented. These methods enable evaluating the degree of DNA damage caused by toxicants and can be applied to studies of the interactions of atrazine and other herbicides and pesticides with DNA.
Gene duplication has long been believed to have played a major role in the rise of biological novelty through evolution of new function and gene expression patterns. The first book to examine gene duplication across all levels of biological organization, "Evolution after Gene Duplication" presents a comprehensive picture of the mechanistic process by which gene duplication may have played a role in generating biodiversity.
Key Features: Explores comparative genomics, genome evolution studies and analysis of multi-gene families such as "Hox," globins, olfactory receptors and MHC (immune system)A complete post-genome treatment of the topic originally covered by Ohno's 1970 classic, this volume extends coverage to include the fate of associated regulatory pathwaysTaps the significant increase in multi-gene family data that has resulted from comparative genomicsComprehensive coverage that includes opposing theoretical viewpoints, comparative genomics data, theoretical and empirical evidence and the role of bioinformatics in the study of gene duplication
This up-to-date overview of theory and mathematical models along with practical examples is suitable for scientists across various levels of biology as well as instructors and graduate students.
Genome stability of every species depends on complex interaction of predefined and environmentally induced genetic and epigenetic states. Predefined states consist of chromatin structure and cell metabolic processes such as DNA repair, radical scavenging and cell signalling, whereas induced states depend on interactions with the environment. Organisms are able to respond to a changing environment by various alterations in their somatic cells as well as in their germline and progeny. In this book, we will describe various phenomena associated with the maintenance of genome stability. These include genetic and epigenetic responses to various stresses in exposed cells and organisms, bystander and, bystander-like effects, transgenerational changes in genome stability and stress tolerance in bacteria, plants and animals.
On September 11, 2001, 2,792 people were killed in terrorist attacks on the World Trade Center (WTC) in New York City. The number of victims, the condition of their remains, and the duration of the recovery effort made the identification of the victims the most difficult ever undertaken by the forensic community in this country. In response to this need, the National Institute of Justice (NIJ), the research, development, and evaluation agency of the U.S. Department of Justice, brought together a group of experts to provide advice and support throughout the identification effort. Called the Kinship and Data Analysis Panel (KADAP), the group made recommendations on new forensic technologies, tools, policies, and procedures to help identify those who perished in the WTC attack. This book contains the KADAP's "lessons learned," particularly regarding DNA protocols, laboratory techniques, and statistical approaches, in the DNA identification of WTC victims. It is written primarily for the Nation's forensic laboratory directors and other officials who may be responsible for organising and managing the DNA identification response to a mass fatality incident. This book discusses the incorporation of DNA identification into a mass fatality disaster plan, including how to: Establish laboratory policies and procedures, including the creation of sample collection documents. Assess the magnitude of an identification effort, and identify and acquire resources to respond.
"What underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences?" In approaching this question a number of probability models are introduced and anyalyzed.Throughout the book, the theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results.
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