Bioinformatics Of Genome Evolution From Ancestral To Modern Metabolism Phylogenomics And Comparative Genomics To Understand Microbial Evolution

Author : Marco Fondi
Publisher : Firenze University Press
Page : 82 pages
File Size : 49,5 Mb
Release : 2011
Category : Medical
ISBN : 9788866550433

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Bioinformatics of Genome Evolution: from Ancestral to Modern Metabolism Phylogenomics and Comparative Genomics to Understand Microbial Evolution by Marco Fondi Pdf

Bioinformatics, that is the interdisciplinary field that blends computer science and biostatistics with biological and biomedical sciences, is expected to gain a central role in next feature. Indeed, it has now affected several fields of biology, providing crucial hints for the understanding of biological systems and also allowing a more accurate design of wet lab experiments. In this work, the analysis of sequence data has be used in different fields, such as evolution (e.g. the assembly and evolution of metabolism), infections control (e.g. the horizontal flow of antibiotic resistance), ecology (bacterial bioremediation).

Author : Marco Fondi
Publisher : Unknown
Page : 128 pages
File Size : 55,5 Mb
Release : 2009
Category : Electronic
ISBN : OCLC:955681701

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Bioinformatics of Genome Evolution by Marco Fondi Pdf

Author : Cedric Chauve,Nadia El-Mabrouk,Eric Tannier
Publisher : Springer
Page : 0 pages
File Size : 41,8 Mb
Release : 2016-09-27
Category : Computers
ISBN : 1447170164

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Models and Algorithms for Genome Evolution by Cedric Chauve,Nadia El-Mabrouk,Eric Tannier Pdf

This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Author : Maria Di Rosa
Publisher : Firenze University Press
Page : 224 pages
File Size : 54,6 Mb
Release : 2022
Category : Science
ISBN : 9788855184199

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Tectono-metamorphic evolution of the continental units along the edge between Alpine and Hercynian Corsica by Maria Di Rosa Pdf

In this work the central area of Corsica island was studied in order to reconstruct the tectono-metamorphic history of the continental and oceanic high pressure units that occupy the structurally deeper levels of the tectonic stacking of Alpine Corsica and their stratigraphic and structural relationship with the European margin (Hercynian Corsica). The study includes the geological mapping, the mesoscale and microscale structural analysis, the acquisition of chemical analyzes and micromaps with the microprobe, thermobarometric estimation through specific methodologies for metapelites, U-Th-Pb dating of zircons and allanites. The results obtained allows to reconstruct the geodynamic model of this sector of the Alpine belt from the Permian to the Burdigalian.

Author : David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini
Publisher : Springer Science & Business Media
Page : 272 pages
File Size : 45,5 Mb
Release : 2009-02-26
Category : Science
ISBN : 9781848002548

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Computing for Comparative Microbial Genomics by David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini Pdf

Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

Author : Dalila De Vita
Publisher : Firenze University Press
Page : 68 pages
File Size : 49,6 Mb
Release : 2022
Category : Medical
ISBN : 9788855183437

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Functional validation of genetic variants identified by next generation sequencing in malformations of cortical development by Dalila De Vita Pdf

Malformations of cortical development (MCDs) result from a disruption in the process of the human brain cortex formation: currently, there are no pharmacological treatments for diffuse MCDs. Next-generation sequencing has accelerated the identification of MCDs causing genes: in some cases, functional studies are needed to clarify the role of genetic variants. The aim of this PhD project has been to apply a multidisciplinary approach to identify causative mutations in patients with MCDs, validate the pathogenic role of the identified mutations, and assess the effectiveness of novel in vitro treatment for mTOR pathway related MCDs.

Author : Laura Colzi
Publisher : Firenze University Press
Page : 232 pages
File Size : 47,5 Mb
Release : 2022
Category : Science
ISBN : 9788855183796

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Isotopic fractionation study towards massive star-forming regions across the Galaxy by Laura Colzi Pdf

One of the most important tools to investigate the chemical history of our Galaxy and our own Solar System is to measure the isotopic fractionation of chemical elements. In the present study new astronomical observations devoted to the study of hydrogen and nitrogen fractionation (D/H and 14N/15N ratios) of molecules, towards massive star-forming regions in different evolutionary phases, have been presented. Moreover, a new detailed theoretical study of carbon fractionation, 12C/13C ratios, has been done. One of the main results was the confirmation that the 14N/15N ratio increases with the galactocentric distance, as predicted by stellar nucleosynthesis Galactic chemical evolution models. This work gives new important inputs on the understanding of local chemical processes that favor the production of molecules with different isotopes in star-forming regions.

Author : Enzo Marino
Publisher : Firenze University Press
Page : 232 pages
File Size : 51,9 Mb
Release : 2010
Category : Coastal engineering
ISBN : 9788866550518

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An Integrated Nonlinear Wind-Waves Model for Offshore Wind Turbines by Enzo Marino Pdf

This thesis presents a numerical model capable of simulating offshore wind turbines exposed to extreme loading conditions. External condition-based extreme responses are reproduced by coupling a fully nonlinear wave kinematic solver with a hydro-aero-elastic simulator. First, a two-dimensional fully nonlinear wave simulator is developed. The transient nonlinear free surface problem is formulated assuming the potential theory and a high-order boundary element method is implemented to discretize Laplace's equation. For temporal evolution a second-order Taylor series expansion is used. The code, after validation with experimental data, is successfully adopted to simulate overturning plunging breakers which give rise to dangerous impact loads when they break against wind turbine substructures. Emphasis is then placed on the random nature of the waves. Indeed, through a domain decomposition technique a global simulation framework embedding the numerical wave simulator into a more general stochastic environment is developed. The proposed model is meant as a contribution to meet the more and more pressing demand for research in the offshore wind energy sector as it permits taking into account dangerous effects on the structural response so as to increase the global structural safety level.

Author : Cristina Polito
Publisher : Firenze University Press
Page : 70 pages
File Size : 54,6 Mb
Release : 2011
Category : Medical
ISBN : 9788866550372

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Molecular Imaging in Parkinson's Disease by Cristina Polito Pdf

The present work explores brain functional changes in drug-naïve Parkinson's disease (PD) patients by means of molecular imaging techniques. Thirty-one consecutive drug-naïve PD patients from the Neurological Clinic of the University of Flor-ence underwent clinical assessment, neuropsychological assessment, MRI, [123I]FP-CIT SPECT, [18F]FDG PET. First, [18F]FDG-PET was employed to identify in drug-naïve PD patients brain metabolic alteration uniquely related to disease process and not modulated by anti-parkinsonian therapeutic intervention. Second, [18F]FDG-PET and [123I]FP-CIT SPECT were employed together to explore the early functional changes in brain function related to dopaminergic depletion in the putamen and in the caudate nucleus.

Author : Mathieu Blanchette,Aïda Ouangraoua
Publisher : Springer
Page : 325 pages
File Size : 43,9 Mb
Release : 2018-10-04
Category : Computers
ISBN : 9783030008345

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Comparative Genomics by Mathieu Blanchette,Aïda Ouangraoua Pdf

This book constitutes the proceedings of the 16th International Conference on Comparative Genomics, RECOMB-CG 2018, held in Magog-Orford, QC, Canada, in October 2018. The 18 full papers presented were carefully reviewed and selected from 29 submissions. The papers cover topics such as: genome rearrangements; genome sequencing; applied comparative genomics; reconciliation and coalescence; and phylogenetics.

Author : Francesca D. Ciccarelli,István Miklós
Publisher : Springer
Page : 249 pages
File Size : 44,7 Mb
Release : 2009-09-30
Category : Science
ISBN : 9783642047442

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Comparative Genomics by Francesca D. Ciccarelli,István Miklós Pdf

As genome-sequencing costs continue their downward spiral, sequencing of closely related organisms has become increasingly a?ordable. The growing amount of genomic data available demands for the constant development of computational tools to be applied in comparative genomics. The RECOMB Workshop on C- parative Genomics (RECOMB-CG) is devoted to bringing together scientists working on all aspects of comparative genomics, from computer scientists, ma- ematicians and statisticians working on novel computational approaches for genome analysis and comparison, to biologists applying these computational tools to study the structure and the evolution of prokaryotic and eukaryotic genomes. This volume contains the 19 papers presented at the 7th Annual RECOMB-CG workshop held during September 27–29, 2009 at the Renyi Institute, in Budapest, Hungary. The papers published in these proceedings were selected for oral p- sentation from 31 submissions from scientists around the world. Each paper was reviewed by at least three members of the Program Committee in a stringent and thoughtful peer-review process.

Author : Ying Xu
Publisher : Imperial College Press
Page : 494 pages
File Size : 51,5 Mb
Release : 2008
Category : Science
ISBN : 9781860949838

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Computational Methods for Understanding Bacterial and Archaeal Genomes by Ying Xu Pdf

Over 500 prokaryotic genomes have been sequenced to date, and thousands more have been planned for the next few years. While these genomic sequence data provide unprecedented opportunities for biologists to study the world of prokaryotes, they also raise extremely challenging issues such as how to decode the rich information encoded in these genomes. This comprehensive volume includes a collection of cohesively written chapters on prokaryotic genomes, their organization and evolution, the information they encode, and the computational approaches needed to derive such information. A comparative view of bacterial and archaeal genomes, and how information is encoded differently in them, is also presented. Combining theoretical discussions and computational techniques, the book serves as a valuable introductory textbook for graduate-level microbial genomics and informatics courses.

Author : Paul G. Higgs,Teresa K. Attwood
Publisher : John Wiley & Sons
Page : 532 pages
File Size : 55,8 Mb
Release : 2013-04-30
Category : Science
ISBN : 9781118697061

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Bioinformatics and Molecular Evolution by Paul G. Higgs,Teresa K. Attwood Pdf

In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses.

Author : Arcady R. Mushegian
Publisher : Elsevier
Page : 280 pages
File Size : 54,6 Mb
Release : 2010-07-20
Category : Science
ISBN : 0080546099

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Foundations of Comparative Genomics by Arcady R. Mushegian Pdf

This book provides an overview of computational analysis of genes and genomes, and of some most notable findings that come out of this work. Foundations of Comparative Genomics presents a historical perspective, beginning with early analysis of individual gene sequences, to present day comparison of gene repertoires encoded by completely sequenced genomes. The author discusses the underlying scientific principles of comparative genomics, argues that completion of many genome sequences started a new era in biology, and provides a personal view on several state-of-the-art issues, such as systems biology and whole-genome phylogenetic reconstructions. This book is an essential reference for researchers and students in computational biology, evolutionary biology, and genetics. Presents an historic overview of genome biology and its achievements Includes topics not covered in other books such as minimal and ancestral genomes Discusses the evolutionary resilience of protein-coding genes and frequent functional convergence at the molecular level Critically reviews horizontal gene transfer and other contentious issues Covers comparative virology as a somewhat overlooked foundation of modern genome science

Author : David A Liberles
Publisher : Oxford University Press on Demand
Page : 267 pages
File Size : 43,7 Mb
Release : 2007-05-31
Category : Science
ISBN : 9780199299188

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Ancestral Sequence Reconstruction by David A Liberles Pdf

Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a range of fields.Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including wholeproteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized toprovide insights and inform future research.This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.