Systems Biology and Regulatory Genomics

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San ...

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Author: Eleazar Eskin

Publisher: Springer Science & Business Media

ISBN: 9783540482932

Category: Science

Page: 261

View: 487

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Systems Biology and Regulatory Genomics

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San ...

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Author: Eleazar Eskin

Publisher: Springer

ISBN: 3540832300

Category: Science

Page: 261

View: 584

This book constitutes the thoroughly refereed post-proceedings of two joint RECOMB 2005 satellite events: the First Annual Workshop on Systems Biology, RSB 2005 and the Second Annual Workshop on Regulatory Genomics, RRG 2005, held in San Diego, CA, USA in December 2005. It contains 21 revised full papers that address a broad variety of topics in systems biology and regulatory genomics.

Systems Biology for Signaling Networks

The first volume in this series, Systems Biology of Signaling Networks, contains a collection of work in regulatory signaling networks and the use of large-scale omics data.

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Author: Sangdun Choi

Publisher: Springer Science & Business Media

ISBN: 1441957979

Category: Science

Page: 908

View: 512

System Biology encompasses the knowledge from diverse fields such as Molecular Biology, Immunology, Genetics, Computational Biology, Mathematical Biology, etc. not only to address key questions that are not answerable by individual fields alone, but also to help in our understanding of the complexities of biological systems. Whole genome expression studies have provided us the means of studying the expression of thousands of genes under a particular condition and this technique had been widely used to find out the role of key macromolecules that are involved in biological signaling pathways. However, making sense of the underlying complexity is only possible if we interconnect various signaling pathways into human and computer readable network maps. These maps can then be used to classify and study individual components involved in a particular phenomenon. Apart from transcriptomics, several individual gene studies have resulted in adding to our knowledge of key components that are involved in a signaling pathway. It therefore becomes imperative to take into account of these studies also, while constructing our network maps to highlight the interconnectedness of the entire signaling pathways and the role of that particular individual protein in the pathway. This collection of articles will contain a collection of pioneering work done by scientists working in regulatory signaling networks and the use of large scale gene expression and omics data. The distinctive features of this book would be: Act a single source of information to understand the various components of different signaling network (roadmap of biochemical pathways, the nature of a molecule of interest in a particular pathway, etc.), Serve as a platform to highlight the key findings in this highly volatile and evolving field, and Provide answers to various techniques both related to microarray and cell signaling to the readers.

Emerging Research in the Analysis and Modeling of Gene Regulatory Networks

Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation.

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Author: Ivanov, Ivan V.

Publisher: IGI Global

ISBN: 9781522503545

Category: Medical

Page: 418

View: 574

While technological advancements have been critical in allowing researchers to obtain more and better quality data about cellular processes and signals, the design and practical application of computational models of genomic regulation continues to be a challenge. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks presents a compilation of recent and emerging research topics addressing the design and use of technology in the study and simulation of genomic regulation. Exploring both theoretical and practical topics, this publication is an essential reference source for students, professionals, and researchers working in the fields of genomics, molecular biology, bioinformatics, and drug development.

Systems Biology and Synthetic Biology

This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

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Author: Pengcheng Fu

Publisher: John Wiley & Sons

ISBN: 0470437979

Category: Technology & Engineering

Page: 672

View: 806

The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Practical Systems Biology

Practical Systems Biology provides a detailed overview of the different approaches used in this relatively new discipline, integrating bioinformatics, genomics, proteomics and metabolomics.

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Author: Alistair Hetherington

Publisher: Taylor & Francis

ISBN: 9781134133048

Category: Science

Page: 300

View: 315

Systems biology is the study of organisms as interacting networks of genes, proteins and reactions. Practical Systems Biology provides a detailed overview of the different approaches used in this relatively new discipline, integrating bioinformatics, genomics, proteomics and metabolomics. Various areas of research are also discussed, including the use of computational models of biological processes, and post-genomic research. Each chapter is written by an experienced researcher and gives an excellent account of various issues of systems biology that is suitable for postgraduate and postdoctoral researchers who are interested in this expanding area of science.

Systems Biology of Transcription Regulation

Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.

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Author: Ekaterina Shelest

Publisher: Frontiers Media SA

ISBN: 9782889199679

Category:

Page:

View: 814

Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.

Computational Modeling of Gene Regulatory Networks

This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind.

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Author: Hamid Bolouri

Publisher: Imperial College Press

ISBN: 9781848162204

Category: Medical

Page: 326

View: 235

This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Evolutionary Genomics and Systems Biology

The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology A special section on RNA biology—translation, evolution ...

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Author: Gustavo Caetano-Anollés

Publisher: John Wiley & Sons

ISBN: 9781118210710

Category: Science

Page: 480

View: 452

A comprehensive, authoritative look at an emergent area inpost-genomic science, Evolutionary genomics is an up-and-coming,complex field that attempts to explain the biocomplexity of theliving world. Evolutionary Genomics and Systems Biology isthe first full-length book to blend established and emergingconcepts in bioinformatics, evolution, genomics, and structuralbiology, with the integrative views of network and systems biology. Three key aspects of evolutionary genomics and systems biologyare covered in clear detail: the study of genomic history, i.e.,understanding organismal evolution at the genomic level; the studyof macromolecular complements, which encompasses the evolution ofthe protein and RNA machinery that propels life; and theevolutionary and dynamic study of wiringdiagrams—macromolecular components in interaction—inthe context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, theevolution of genomes, and the evolution of biological networks,within the framework of systems biology A special section on RNA biology—translation, evolutionof structure, and micro RNA and regulation of gene expression Chapters on the mapping of genotypes to phenotypes, the role ofinformation in biology, protein architecture and biologicalfunction, chromosomal rearrangements, and biological networks anddisease Contributions by leading authorities on each topic Evolutionary Genomics and Systems Biology is an idealbook for students and professionals in genomics, bioinformatics,evolution, structural biology, complexity, origins of life,systematic biology, and organismal diversity, as well as thoseindividuals interested in aspects of biological sciences as theyinterface with chemistry, physics, and computer science andengineering.

Bioinformatics of Genome Regulation and Structure II

Analysis, comprehension, and use of the tremendous volumes of experimental data reflecting the intricate processes underlying the functioning of molecular genetic systems are unfeasible in principle without the systems approach and ...

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Author: Nikolay Kolchanov

Publisher: Springer Science & Business Media

ISBN: 9780387294551

Category: Science

Page: 560

View: 148

The last 15 years in development of biology were marked with accumulation of unprecedentedly huge arrays of experimental data. The information was amassed with exclusively high rates due to the advent of highly efficient experimental technologies that provided for high throughput genomic sequencing; of functional genomics technologies allowing investigation of expression dynamics of large groups of genes using expression DNA chips; of proteomics methods giving the possibility to analyze protein compositions of cells, tissues, and organs, assess the dynamics of the cell proteome, and reconstruct the networks of protein-protein interactions; and of metabolomics, in particular, high resolution mass spectrometry study of cell metabolites, and distribution of metabolic fluxes in the cells with a concurrent investigation of the dynamics of thousands metabolites in an individual cell. Analysis, comprehension, and use of the tremendous volumes of experimental data reflecting the intricate processes underlying the functioning of molecular genetic systems are unfeasible in principle without the systems approach and involvement of the state-of-the-art information and computer technologies and efficient mathematical methods for data analysis and simulation of biological systems and processes. The need in solving these problems initiated the birth of a new science— postgenomic bioinformatics or systems biology in silico.

Genomic Control Process

This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development.

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Author: Isabelle Peter

Publisher: Academic Press

ISBN: 9780124047464

Category: Science

Page: 460

View: 675

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Frontiers in Computational and Systems Biology

Understanding the biology at a molecular and system level stands among the most exciting challenges faced by modern science. This text clearly demonstrates how computational and mathematical approaches continue to address this challenge.

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Author: Jianfeng Feng

Publisher: Springer Science & Business Media

ISBN: 1849961964

Category: Science

Page: 24

View: 178

Biological and biomedical studies have entered a new era over the past two decades thanks to the wide use of mathematical models and computational approaches. A booming of computational biology, which sheerly was a theoretician’s fantasy twenty years ago, has become a reality. Obsession with computational biology and theoretical approaches is evidenced in articles hailing the arrival of what are va- ously called quantitative biology, bioinformatics, theoretical biology, and systems biology. New technologies and data resources in genetics, such as the International HapMap project, enable large-scale studies, such as genome-wide association st- ies, which could potentially identify most common genetic variants as well as rare variants of the human DNA that may alter individual’s susceptibility to disease and the response to medical treatment. Meanwhile the multi-electrode recording from behaving animals makes it feasible to control the animal mental activity, which could potentially lead to the development of useful brain–machine interfaces. - bracing the sheer volume of genetic, genomic, and other type of data, an essential approach is, ?rst of all, to avoid drowning the true signal in the data. It has been witnessed that theoretical approach to biology has emerged as a powerful and st- ulating research paradigm in biological studies, which in turn leads to a new - search paradigm in mathematics, physics, and computer science and moves forward with the interplays among experimental studies and outcomes, simulation studies, and theoretical investigations.

Systems Biology

Written for a wide audience, each volume presents a timely compendium of essential information that is necessary for a comprehensive study of the subject. The chapters in the two volumes reflect the hierarchical nature of systems biology.

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Author: Isidore Rigoutsos

Publisher: Oxford University Press on Demand

ISBN: 9780195300819

Category: Science

Page: 314

View: 161

The genome is seen as a network of interacting components, explored in new ways by sub-discipline specialists. Systems biology is a powerful new computational approach to studying such complex living systems, made possible through technological breakthroughs such as the human genome project, and explosive interest in genetics and molecular biology. At once groundbreaking and synthetic, each chapter in this book treats systems and related technologies as seen by world renowned, trail-blazing experts in their respective fields. It will be useful for researchers in biology, genetics, bioinformatics, molecular biology, biochemical engineering, mathematics, computer science, physics, and chemistry who, using high throughput methods, seek ways to organize vast data sets at the molecular and sub-molecular levels.

Crop Systems Biology

This book will appeal to those interested in bridging fundamental plant biology and applied crop science using a diversity of systems modelling approaches.

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Author: Xinyou Yin

Publisher: Springer

ISBN: 9783319205625

Category: Technology & Engineering

Page: 233

View: 349

The sequencing of genomes has been completed for an increasing number of crop species, and researchers have now succeeded in isolating and characterising many important QTLs/genes. High expectations from genomics, however, are waving back toward the recognition that crop physiology is also important for realistic improvement of crop productivity. Complex processes and networks along various hierarchical levels of crop growth and development can be thoroughly understood with the help of their mathematical description – modelling. The further practical application of these understandings also requires quantitative predictions. In order to better support design, engineering and breeding for new crops and cultivars for improving agricultural production under global warming and climate change, there is an increasing call for an interdisciplinary research approach, which combines modern genetics and genomics, traditional physiology and biochemistry, and advanced bioinformatics and modelling. Such an interdisciplinary approach has been practised in various research groups for many years. However, it does not seem to be fully covered in the format of book publications. We want to initiate a book project on crop systems biology - narrowing the gaps between genotypes and phenotypes and the gaps between crop modelling and genetics/genomics, for publication in 2013/2014. The book will be meant for those scientists and graduate students from fundamental plant biology and applied crop science who are interested in bridging the gap between these two fields. We have invited a group of scientists (who have very good track records in publishing excellent papers in this field or in a closely related area) to contribute chapters to this new book, and they have agreed to do so.​

Systems Biology

Written for a wide audience, each volume presents a timely compendium of essential information that is necessary for a comprehensive study of the subject. The chapters in the two volumes reflect the hierarchical nature of systems biology.

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Author: Isidore Rigoutsos

Publisher: Oxford University Press

ISBN: 0195345789

Category: Science

Page: 366

View: 313

The advent of genome sequencing and associated technologies has transformed biologists' ability to measure important classes of molecules and their interactions. This expanded cellular view has opened the field to thousands of interactions that previously were outside the researchers' reach. The processing and interpretation of these new vast quantities of interconnected data call for sophisticated mathematical models and computational methods. Systems biology meets this need by combining genomic knowledge with theoretical, experimental and computational approaches from a number of traditional scientific disciplines to create a mechanistic explanation of cellular systems and processes. Systems Biology I: Genomics and Systems Biology II: Networks, Models, and Applications offer a much-needed study of genomic principles and their associated networks and models. Written for a wide audience, each volume presents a timely compendium of essential information that is necessary for a comprehensive study of the subject. The chapters in the two volumes reflect the hierarchical nature of systems biology. Chapter authors-world-recognized experts in their fields-provide authoritative discussions on a wide range of topics along this hierarchy. Volume I explores issues pertaining to genomics that range from prebiotic chemistry to noncoding RNAs. Volume II covers an equally wide spectrum, from mass spectrometry to embryonic stem cells. The two volumes are meant to provide a reliable reference for students and researchers alike.

Advances in Bioinformatics and Computational Biology

This book constitutes the refereed proceedings of the 7th Brazilian Symposium on Bioinformatics, BSB 2012, held in Campo Grande, Brazil, in August 2012.

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Author: Marcilio C.P. de Souto

Publisher: Springer

ISBN: 9783642319273

Category: Computers

Page: 204

View: 139

This book constitutes the refereed proceedings of the 7th Brazilian Symposium on Bioinformatics, BSB 2012, held in Campo Grande, Brazil, in August 2012. The 16 regular papers presented were carefully reviewed and selected for inclusion in this book. It also contains a joint paper from two of the guest speakers. The Brazilian Symposium on Bioinformatics covers all aspects of bioinformatics and computational biology, including sequence analysis; motifs, and pattern matching; biological databases, data management, data integration, and data mining; biomedical text mining; structural, comparative, and functional genomics; personal genomics; protein structure, modeling, and simulation; gene identification, regulation and expression analysis; gene and protein interaction and networks; molecular docking; molecular evolution and phylogenetics; computational systems biology; computational proteomics; statistical analysis of molecular sequences; algorithms for problems in computational biology; applications in molecular biology, biochemistry, genetics, medicine, microbiology and associated subjects.

Research in Computational Molecular Biology

This book constitutes the refereed proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, held in Vancouver, Canada, in March 2011.

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Author: Vineet Bafna

Publisher: Springer

ISBN: 3642200354

Category: Computers

Page: 580

View: 778

This book constitutes the refereed proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2011, held in Vancouver, Canada, in March 2011. The 43 revised full papers were carefully reviewed and selected from 153 submissions. The papers cover a wide range of topics including molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; population, statistical genetics; systems biology; imaging; computational proteomics; molecular structural biology.

Encyclopedia of Bioinformatics and Computational Biology

This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in ...

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Author:

Publisher: Elsevier

ISBN: 9780128114322

Category: Medical

Page: 3284

View: 975

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases