Statistical And Evolutionary Analysis Of Biological Networks

Author : Michael P. H. Stumpf,Carsten Wiuf
Publisher : World Scientific
Page : 179 pages
File Size : 41,9 Mb
Release : 2010
Category : Mathematics
ISBN : 9781848164345

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Statistical and Evolutionary Analysis of Biological Networks by Michael P. H. Stumpf,Carsten Wiuf Pdf

Networks provide a very useful way to describe a wide range of different data types in biology, physics and elsewhere. Apart from providing a convenient tool to visualize highly dependent data, networks allow stringent mathematical and statistical analysis. In recent years, much progress has been achieved to interpret various types of biological network data such as transcriptomic, metabolomic and protein interaction data as well as epidemiological data. Of particular interest is to understand the organization, complexity and dynamics of biological networks and how these are influenced by network evolution and functionality. This book reviews and explores statistical, mathematical and evolutionary theory and tools in the understanding of biological networks. The book is divided into comprehensive and self-contained chapters, each of which focuses on an important biological network type, explains concepts and theory and illustrates how these can be used to obtain insight into biologically relevant processes and questions. There are chapters covering metabolic, transcriptomic, protein interaction and epidemiological networks as well as chapters that deal with theoretical and conceptual material. The authors, who contribute to the book, are active, highly regarded and well-known in the network community. Sample Chapter(s). Chapter 1: A Network Analysis Primer (350 KB). Contents: A Network Analysis Primer (M P H Stumpf & C Wiuf); Evolutionary Analysis of Protein Interaction Networks (C Wiuf & O Ratmann); Motifs in Biological Networks (F Schreiber & H SchwAbbermeyer); Bayesian Analysis of Biological Networks: Clusters, Motifs, Cross-Species Correlations (J Berg & M Lnssig); Network Concepts and Epidemiological Models (R R Kao & I Z Kiss); Evolutionary Origin and Consequences of Design Properties of Metabolic Networks (T Pfeiffer & S Bonhoeffer); Protein Interactions from an Evolutionary Perspective (F Pazos & A Valencia); Statistical Null Models for Biological Network Analysis (W P Kelly et al.). Readership: Academics, researchers, postgraduates and advanced undergraduates in bioinformatics. Biologists, mathematicians/statisticians, physicists and computer scientists.

Author : Björn H. Junker,Falk Schreiber
Publisher : Wiley-Interscience
Page : 392 pages
File Size : 44,8 Mb
Release : 2008-03-14
Category : Computers
ISBN : 9780470253465

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Analysis of Biological Networks by Björn H. Junker,Falk Schreiber Pdf

An introduction to biological networks and methods for their analysis Analysis of Biological Networks is the first book of its kind to provide readers with a comprehensive introduction to the structural analysis of biological networks at the interface of biology and computer science. The book begins with a brief overview of biological networks and graph theory/graph algorithms and goes on to explore: global network properties, network centralities, network motifs, network clustering, Petri nets, signal transduction and gene regulation networks, protein interaction networks, metabolic networks, phylogenetic networks, ecological networks, and correlation networks. Analysis of Biological Networks is a self-contained introduction to this important research topic, assumes no expert knowledge in computer science or biology, and is accessible to professionals and students alike. Each chapter concludes with a summary of main points and with exercises for readers to test their understanding of the material presented. Additionally, an FTP site with links to author-provided data for the book is available for deeper study. This book is suitable as a resource for researchers in computer science, biology, bioinformatics, advanced biochemistry, and the life sciences, and also serves as an ideal reference text for graduate-level courses in bioinformatics and biological research.

Author : Matthias Dehmer,Frank Emmert-Streib,Armin Graber,Armindo Salvador
Publisher : John Wiley & Sons
Page : 441 pages
File Size : 53,8 Mb
Release : 2011-04-08
Category : Medical
ISBN : 9783527638086

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Applied Statistics for Network Biology by Matthias Dehmer,Frank Emmert-Streib,Armin Graber,Armindo Salvador Pdf

The book introduces to the reader a number of cutting edge statistical methods which can e used for the analysis of genomic, proteomic and metabolomic data sets. In particular in the field of systems biology, researchers are trying to analyze as many data as possible in a given biological system (such as a cell or an organ). The appropriate statistical evaluation of these large scale data is critical for the correct interpretation and different experimental approaches require different approaches for the statistical analysis of these data. This book is written by biostatisticians and mathematicians but aimed as a valuable guide for the experimental researcher as well computational biologists who often lack an appropriate background in statistical analysis.

Author : Rasmus Nielsen
Publisher : Springer Science & Business Media
Page : 503 pages
File Size : 42,8 Mb
Release : 2006-05-06
Category : Science
ISBN : 9780387277332

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Statistical Methods in Molecular Evolution by Rasmus Nielsen Pdf

In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. This book provides an overview of the statistical theory and methods used in studies of molecular evolution. It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. The chapters are written by the leaders of field and they will take the reader from basic introductory material to the state-of-the-art statistical methods. This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. The chapters of the book assume no advanced mathematical skills beyond basic calculus, although familiarity with basic probability theory will help the reader. Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. Rasmus Nielsen received his Ph.D. form the University of California at Berkeley in 1998 and after a postdoc at Harvard University, he assumed a faculty position in Statistical Genomics at Cornell University. He is currently an Ole Rømer Fellow at the University of Copenhagen and holds a Sloan Research Fellowship. His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. From the reviews: "...Overall this is a very useful book in an area of increasing importance." Journal of the Royal Statistical Society "I find Statistical Methods in Molecular Evolution very interesting and useful. It delves into problems that were considered very difficult just several years ago...the book is likely to stimulate the interest of statisticians that are unaware of this exciting field of applications. It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods." Marek Kimmel for the Journal of the American Statistical Association, September 2006 "Who should read this book? We suggest that anyone who deals with molecular data (who does not?) and anyone who asks evolutionary questions (who should not?) ought to consult the relevant chapters in this book." Dan Graur and Dror Berel for Biometrics, September 2006 "Coalescence theory facilitates the merger of population genetics theory with phylogenetic approaches, but still, there are mostly two camps: phylogeneticists and population geneticists. Only a few people are moving freely between them. Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. Although Nielsen did not contribute a chapter to his book, his work permeates all its chapters. This book gives an overview of his interests and current achievements in molecular evolution. In short, this book should be on your bookshelf." Peter Beerli for Evolution, 60(2), 2006

Author : Francois Kepes
Publisher : World Scientific
Page : 531 pages
File Size : 46,9 Mb
Release : 2007
Category : Medical
ISBN : 9789812772367

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Biological Networks by Francois Kepes Pdf

This volume presents a timely and comprehensive overview of biological networks at all organization levels in the spirit of the complex systems approach. It discusses the transversal issues and fundamental principles as well as the overall structure, dynamics, and modeling of a wide array of biological networks at the molecular, cellular, and population levels. Anchored in both empirical data and a strong theoretical background, the book therefore lends valuable credence to the complex systems approach. Sample Chapter(s). Chapter 1: Scale-Free Networks in Biology (821 KB). Contents: Scale-Free Networks in Biology (E Almaas et al.); Modularity in Biological Networks (R V Sol(r) et al.); Inference of Biological Regulatory Networks: Machine Learning Approaches (F d''Alch(r)-Buc); Transcriptional Networks (F K(r)p s); Protein Interaction Networks (K Tan & T Ideker); Metabolic Networks (D A Fell); Heterogeneous Molecular Networks (V Schnchter); Evolution of Regulatory Networks (A Veron et al.); Complexity in Neuronal Networks (Y Fr(r)gnac et al.); Networks of the Immune System (R E Callard & J Stark); A History of the Study of Ecological Networks (L-F Bersier); Dynamic Network Models of Ecological Diversity, Complexity, and Nonlinear Persistence (R J Williams & N D Martinez); Infection Transmission through Networks (J S Koopman). Readership: Graduate students and industry experts in systems biology and complex systems; biologists; chemists; physicists; mathematicians; computer scientists

Author : S. N. Dorogovtsev,J.F.F. Mendes
Publisher : Oxford University Press
Page : 282 pages
File Size : 54,6 Mb
Release : 2013-11
Category : Business & Economics
ISBN : 9780199686711

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Evolution of Networks by S. N. Dorogovtsev,J.F.F. Mendes Pdf

We live in a world of networks, where everything is amazingly close to everything else. The notion of 'network' turns out to be central to our times: the Internet and WWW are changing our lives; our physical existence is based on various biological networks; we are involved in all-enveloping networks of economic and social relations. Only in the 1990s did physicists begin to explore real networks, both natural and artificial, as evolving systems with intriguingly complex and effective architectures. Progress has been so immediate and astounding that we actually face a new science based on a new set of concepts, and, one may even say, on a new philosophy: the natural philosophy of a small world. Old ideas from mathematics, statistical physics, biology, computer science, and so on take on quite new forms in applications to real evolving networks. - What is common to all networks? - What are the general principles of the organization and evolution of networks? - How do the laws of nature work in communication, biological, and social networks? - What are networks? This book, written by physicists, answers these questions and presents a general insight into the world of networks.

Author : Mark R. T. Dale,Marie-Josée Fortin
Publisher : Cambridge University Press
Page : 233 pages
File Size : 41,7 Mb
Release : 2021-04-15
Category : Language Arts & Disciplines
ISBN : 9781108491846

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Quantitative Analysis of Ecological Networks by Mark R. T. Dale,Marie-Josée Fortin Pdf

Displays the broad range of quantitative approaches to analysing ecological networks, providing clear examples and guidance for researchers.

Author : Anonim
Publisher : Elsevier
Page : 526 pages
File Size : 52,7 Mb
Release : 2011-09-22
Category : Science
ISBN : 0080550592

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Complex Systems by Anonim Pdf

There has been recently some interdisciplinary convergence on a number of precise topics which can be considered as prototypes of complex systems. This convergence is best appreciated at the level of the techniques needed to deal with these systems, which include: 1) A domain of research around a multiple point where statistical physics, information theory, algorithmic computer science, and more theoretical (probabilistic) computer science meet: this covers some aspects of error correcting codes, stochastic optimization algorithms, typical case complexity and phase transitions, constraint satisfaction problems. 2) The study of collective behavior of interacting agents, its impact on understanding some types of economical and financial problems, their link to population and epidemics dynamics, game theory, social, biological and computer networks and evolution. The present book is the written version of the lectures given during the Les Houches summer school session on "Complex Systems", devoted to these emerging interdisciplinary fields. The lectures consist both in a number of long methodological courses (probability theory, statistical physics of disordered systems, information theory, network structure and evolution, agent-based economics and numerical methods) and more specific, 'problem oriented' courses. Lecturers are all leading experts in their field; they have summarized recent results in a clear and authoritative manner. The "Les Houches lecture notes" have a long tradition of excellence and are often found to be useful for a number of years after they were written. The book is of interest to students and researchers with various backgrounds: probability theory, computer science, information theory, physics, finance, biology, etc. · Topical and comprehensive survey of the emerging, interdisciplinary field of "Complex Systems", covered by recognized world experts · "Les Houches lectures notes": a long tradition of excellence and long-lasting impact · Of interest to a broad audience (mathematics, physics, biology, informatics, finance, geology, etc.) · Some applications may have concrete impact · Selected topics in complex systems: forefront of research in the field

Author : Xun Gu
Publisher : OUP Oxford
Page : 272 pages
File Size : 45,6 Mb
Release : 2010-11-04
Category : Science
ISBN : 9780199213269

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Statistical Theory and Methods for Evolutionary Genomics by Xun Gu Pdf

Summarises the statistical framework of evolutionary genomics, and illustrates how statistical modelling and testing can enhance our understanding of functional genomic evolution.

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 48,7 Mb
Release : 2024-05-17
Category : Electronic
ISBN : 9789814475396

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Biological Networks by Anonim Pdf

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 386 pages
File Size : 55,9 Mb
Release : 2011-11-06
Category : Science
ISBN : 9781461417439

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Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis Pdf

The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate 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. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Author : Jinhu Lü,Pei Wang
Publisher : Springer Nature
Page : 464 pages
File Size : 55,6 Mb
Release : 2020-12-06
Category : Science
ISBN : 9789811591440

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Modeling and Analysis of Bio-molecular Networks by Jinhu Lü,Pei Wang Pdf

This book addresses a number of questions from the perspective of complex systems: How can we quantitatively understand the life phenomena? How can we model life systems as complex bio-molecular networks? Are there any methods to clarify the relationships among the structures, dynamics and functions of bio-molecular networks? How can we statistically analyse large-scale bio-molecular networks? Focusing on the modeling and analysis of bio-molecular networks, the book presents various sophisticated mathematical and statistical approaches. The life system can be described using various levels of bio-molecular networks, including gene regulatory networks, and protein-protein interaction networks. It first provides an overview of approaches to reconstruct various bio-molecular networks, and then discusses the modeling and dynamical analysis of simple genetic circuits, coupled genetic circuits, middle-sized and large-scale biological networks, clarifying the relationships between the structures, dynamics and functions of the networks covered. In the context of large-scale bio-molecular networks, it introduces a number of statistical methods for exploring important bioinformatics applications, including the identification of significant bio-molecules for network medicine and genetic engineering. Lastly, the book describes various state-of-art statistical methods for analysing omics data generated by high-throughput sequencing. This book is a valuable resource for readers interested in applying systems biology, dynamical systems or complex networks to explore the truth of nature.

Author : Ziheng Yang
Publisher : OUP Oxford
Page : 374 pages
File Size : 53,9 Mb
Release : 2006-10-05
Category : Science
ISBN : 9780191513763

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Computational Molecular Evolution by Ziheng Yang Pdf

The field of molecular evolution has experienced explosive growth in recent years due to the rapid accumulation of genetic sequence data, continuous improvements to computer hardware and software, and the development of sophisticated analytical methods. The increasing availability of large genomic data sets requires powerful statistical methods to analyse and interpret them, generating both computational and conceptual challenges for the field. Computational Molecular Evolution provides an up-to-date and comprehensive coverage of modern statistical and computational methods used in molecular evolutionary analysis, such as maximum likelihood and Bayesian statistics. Yang describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. The book emphasizes essential concepts rather than mathematical proofs. It includes detailed derivations and implementation details, as well as numerous illustrations, worked examples, and exercises. It will be of relevance and use to students and professional researchers (both empiricists and theoreticians) in the fields of molecular phylogenetics, evolutionary biology, population genetics, mathematics, statistics and computer science. Biologists who have used phylogenetic software programs to analyze their own data will find the book particularly rewarding, although it should appeal to anyone seeking an authoritative overview of this exciting area of computational biology.

Author : Alexander Mehler,Andy Lücking,Sven Banisch,Philippe Blanchard,Barbara Job
Publisher : Springer
Page : 343 pages
File Size : 50,9 Mb
Release : 2015-07-07
Category : Technology & Engineering
ISBN : 9783662472385

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Towards a Theoretical Framework for Analyzing Complex Linguistic Networks by Alexander Mehler,Andy Lücking,Sven Banisch,Philippe Blanchard,Barbara Job Pdf

The aim of this book is to advocate and promote network models of linguistic systems that are both based on thorough mathematical models and substantiated in terms of linguistics. In this way, the book contributes first steps towards establishing a statistical network theory as a theoretical basis of linguistic network analysis the boarder of the natural sciences and the humanities. This book addresses researchers who want to get familiar with theoretical developments, computational models and their empirical evaluation in the field of complex linguistic networks. It is intended to all those who are interested in statistical models of linguistic systems from the point of view of network research. This includes all relevant areas of linguistics ranging from phonological, morphological and lexical networks on the one hand and syntactic, semantic and pragmatic networks on the other. In this sense, the volume concerns readers from many disciplines such as physics, linguistics, computer science and information science. It may also be of interest for the upcoming area of systems biology with which the chapters collected here share the view on systems from the point of view of network analysis.

Author : Raul Rabadan,Andrew J. Blumberg
Publisher : Cambridge University Press
Page : 521 pages
File Size : 48,6 Mb
Release : 2019-12-19
Category : Science
ISBN : 9781107159549

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Topological Data Analysis for Genomics and Evolution by Raul Rabadan,Andrew J. Blumberg Pdf

An introduction to geometric and topological methods to analyze large scale biological data; includes statistics and genomic applications.