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The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation

Author: Kenneth Berendzen

Publisher: Bentham Science Publishers

Published: 2013-10-29

Total Pages: 225

ISBN-13: 1608054926

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A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors. This e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of TF - cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached. The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.

Book Synopsis The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation by : Kenneth Berendzen

Download or read book The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation written by Kenneth Berendzen and published by Bentham Science Publishers. This book was released on 2013-10-29 with total page 225 pages. Available in PDF, EPUB and Kindle. Book excerpt: A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors. This e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of TF - cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached. The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.

Artificial Intelligence: Theories, Models and Applications

Author: John Darzentas

Publisher: Springer

Published: 2008-09-22

Total Pages: 457

ISBN-13: 3540878815

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Artificial intelligence (AI) is a dynamic field that is constantly expanding into new application areas, discovering new research challenges and facilitating the devel- ment of innovative products. Today’s information overload and rapid technological advancement raise needs for effective management of the complexity and heteroge- ity of knowledge, for intelligent and adaptable man–machine interfaces and for pr- ucts and applications that can learn and take decisions by themselves. Although the mystery of human-level intelligence has just started to be uncovered in various int- disciplinary fields, AI is inspired by the respective scientific areas to explore certain theories and models that will provide the methods and techniques to design and - velop human-centered applications that address the above-mentioned needs. This volume contains papers selected for presentation at the 5th Hellenic Conference on Artificial Intelligence (SETN 2008), the official meeting of the Hellenic Society for Artificial Intelligence (EETN). Previous conferences were held at the University of Piraeus (1996), at the Aristotle University of Thessaloniki (2002), at the University of the Aegean (2004) and at the Institute of Computer Science at FORTH (Foundation for Research and Technology - Hellas) and the University of Crete (2006).

Book Synopsis Artificial Intelligence: Theories, Models and Applications by : John Darzentas

Download or read book Artificial Intelligence: Theories, Models and Applications written by John Darzentas and published by Springer. This book was released on 2008-09-22 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: Artificial intelligence (AI) is a dynamic field that is constantly expanding into new application areas, discovering new research challenges and facilitating the devel- ment of innovative products. Today’s information overload and rapid technological advancement raise needs for effective management of the complexity and heteroge- ity of knowledge, for intelligent and adaptable man–machine interfaces and for pr- ucts and applications that can learn and take decisions by themselves. Although the mystery of human-level intelligence has just started to be uncovered in various int- disciplinary fields, AI is inspired by the respective scientific areas to explore certain theories and models that will provide the methods and techniques to design and - velop human-centered applications that address the above-mentioned needs. This volume contains papers selected for presentation at the 5th Hellenic Conference on Artificial Intelligence (SETN 2008), the official meeting of the Hellenic Society for Artificial Intelligence (EETN). Previous conferences were held at the University of Piraeus (1996), at the Aristotle University of Thessaloniki (2002), at the University of the Aegean (2004) and at the Institute of Computer Science at FORTH (Foundation for Research and Technology - Hellas) and the University of Crete (2006).

The Regulatory Genome: Gene Regulatory Networks in Development and Evolution

Author: Eric H. Davidson

Publisher: Academic Press

Published: 2006-05

Total Pages: 304

ISBN-13: 9781483299983

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Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. * The only book in the market that is solely devoted to the genomic regulatory code for animal development * Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding * Presents a comprehensive treatment of molecular control elements that determine the function of genes * Provides a comparative treatment of development, based on principles rather than description of developmental processes * Considers the evolutionary processes in terms of the structural properties of gene regulatory networks * Includes 42 full-color descriptive figures and diagrams

Book Synopsis The Regulatory Genome: Gene Regulatory Networks in Development and Evolution by : Eric H. Davidson

Download or read book The Regulatory Genome: Gene Regulatory Networks in Development and Evolution written by Eric H. Davidson and published by Academic Press. This book was released on 2006-05 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. * The only book in the market that is solely devoted to the genomic regulatory code for animal development * Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding * Presents a comprehensive treatment of molecular control elements that determine the function of genes * Provides a comparative treatment of development, based on principles rather than description of developmental processes * Considers the evolutionary processes in terms of the structural properties of gene regulatory networks * Includes 42 full-color descriptive figures and diagrams

Database Systems for Advanced Applications

Author: Sang-goo Lee

Publisher: Springer

Published: 2012-04-05

Total Pages: 615

ISBN-13: 3642290388

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This two volume set LNCS 7238 and LNCS 7239 constitutes the refereed proceedings of the 17th International Conference on Database Systems for Advanced Applications, DASFAA 2012, held in Busan, South Korea, in April 2012. The 44 revised full papers and 8 short papers presented together with 2 invited keynote papers, 8 industrial papers, 8 demo presentations, 4 tutorials and 1 panel paper were carefully reviewed and selected from a total of 159 submissions. The topics covered are query processing and optimization, data semantics, XML and semi-structured data, data mining and knowledge discovery, privacy and anonymity, data management in the Web, graphs and data mining applications, temporal and spatial data, top-k and skyline query processing, information retrieval and recommendation, indexing and search systems, cloud computing and scalability, memory-based query processing, semantic and decision support systems, social data, data mining.

Book Synopsis Database Systems for Advanced Applications by : Sang-goo Lee

Download or read book Database Systems for Advanced Applications written by Sang-goo Lee and published by Springer. This book was released on 2012-04-05 with total page 615 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two volume set LNCS 7238 and LNCS 7239 constitutes the refereed proceedings of the 17th International Conference on Database Systems for Advanced Applications, DASFAA 2012, held in Busan, South Korea, in April 2012. The 44 revised full papers and 8 short papers presented together with 2 invited keynote papers, 8 industrial papers, 8 demo presentations, 4 tutorials and 1 panel paper were carefully reviewed and selected from a total of 159 submissions. The topics covered are query processing and optimization, data semantics, XML and semi-structured data, data mining and knowledge discovery, privacy and anonymity, data management in the Web, graphs and data mining applications, temporal and spatial data, top-k and skyline query processing, information retrieval and recommendation, indexing and search systems, cloud computing and scalability, memory-based query processing, semantic and decision support systems, social data, data mining.

Reproductive Genomics

Author: Xi Wang

Publisher: Frontiers Media SA

Published: 2022-09-27

Total Pages: 158

ISBN-13: 2889768694

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Book Synopsis Reproductive Genomics by : Xi Wang

Download or read book Reproductive Genomics written by Xi Wang and published by Frontiers Media SA. This book was released on 2022-09-27 with total page 158 pages. Available in PDF, EPUB and Kindle. Book excerpt:

A Cis-regulatory Lexicon of DNA Motif Combinations Mediating Cell Type-specific Gene Regulation

Author: Laura Kaitlin Hill Donohue

Publisher:

Published: 2021

Total Pages:

ISBN-13:

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The role of the DNA sequence in protein-coding genes has been widely established due to the obvious functional relevance and well-defined relationships between DNA variation and protein sequence. However, most disease-associated variants are not in protein-coding sequences. This has led to much investigation of non-coding variation as it relates to protein-coding gene regulation. Critically, non-coding regulatory elements within DNA are intricately linked to cell type-specific protein-coding gene expression. This dissertation contributes to the goal of uncovering the underlying cis-regulatory logic of non-coding DNA sequences driving cell type-specific gene expression in homeostasis and disease. Cell type-specific non-coding cis-regulatory elements are known to drive important gene expression programs. However, it is still unclear what combinatorial DNA sequences underlie cell type-specific gene regulatory mechanisms. The objective of this dissertation is to progress our understanding of cis-regulatory logic through integration of genome-wide regulatory maps followed by modeling of combinatorial DNA motif logic in cis-regulatory modules regulating cell type-specific gene expression programs and focused identification of functional regulatory DNA motif combinations (DMCs) in homeostasis and complex disease. In Chapter 2, I generate epigenomic and transcriptomic profiles of 15 primary human cell types and perform integrated analysis to define cell type-specific open chromatin peak-long range looped-expressed target gene transcripts (PLTs). I then incorporate disease-associated single nucleotide variants (SNVs) from the NHGRI GWAS catalog and Genotype-Tissue Expression (GTEx) data to link SNVs enriched in cell type-specific PLTs to putative target genes. In Chapter 3, I model the genomic information necessary to derive cis-regulatory modules linked to cell type-specific gene expression programs and nominate transcription factor (TF) DMCs underlying cell type-specific regulatory logic. Finally, in Chapter 4, I validate DMC logic in four primary human cell types and identify cancer-specific regulatory logic in human squamous cell carcinoma and melanoma cells. The findings and approaches described in this dissertation add to the existing annotation of functional combinatorial TF motif logic and help build a framework for future studies of cis-regulatory logic.

Book Synopsis A Cis-regulatory Lexicon of DNA Motif Combinations Mediating Cell Type-specific Gene Regulation by : Laura Kaitlin Hill Donohue

Download or read book A Cis-regulatory Lexicon of DNA Motif Combinations Mediating Cell Type-specific Gene Regulation written by Laura Kaitlin Hill Donohue and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The role of the DNA sequence in protein-coding genes has been widely established due to the obvious functional relevance and well-defined relationships between DNA variation and protein sequence. However, most disease-associated variants are not in protein-coding sequences. This has led to much investigation of non-coding variation as it relates to protein-coding gene regulation. Critically, non-coding regulatory elements within DNA are intricately linked to cell type-specific protein-coding gene expression. This dissertation contributes to the goal of uncovering the underlying cis-regulatory logic of non-coding DNA sequences driving cell type-specific gene expression in homeostasis and disease. Cell type-specific non-coding cis-regulatory elements are known to drive important gene expression programs. However, it is still unclear what combinatorial DNA sequences underlie cell type-specific gene regulatory mechanisms. The objective of this dissertation is to progress our understanding of cis-regulatory logic through integration of genome-wide regulatory maps followed by modeling of combinatorial DNA motif logic in cis-regulatory modules regulating cell type-specific gene expression programs and focused identification of functional regulatory DNA motif combinations (DMCs) in homeostasis and complex disease. In Chapter 2, I generate epigenomic and transcriptomic profiles of 15 primary human cell types and perform integrated analysis to define cell type-specific open chromatin peak-long range looped-expressed target gene transcripts (PLTs). I then incorporate disease-associated single nucleotide variants (SNVs) from the NHGRI GWAS catalog and Genotype-Tissue Expression (GTEx) data to link SNVs enriched in cell type-specific PLTs to putative target genes. In Chapter 3, I model the genomic information necessary to derive cis-regulatory modules linked to cell type-specific gene expression programs and nominate transcription factor (TF) DMCs underlying cell type-specific regulatory logic. Finally, in Chapter 4, I validate DMC logic in four primary human cell types and identify cancer-specific regulatory logic in human squamous cell carcinoma and melanoma cells. The findings and approaches described in this dissertation add to the existing annotation of functional combinatorial TF motif logic and help build a framework for future studies of cis-regulatory logic.

A Study of Local and Regional Gene Regulatory Features in the Human Genome

Author: Brett B. Maricque

Publisher:

Published: 2016

Total Pages: 102

ISBN-13:

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Living organisms depend on their genomes to exist, grow, and survive in different environments. Gene activity, or gene expression, underlies such biology and is controlled by regulatory DNA sequences, akin to switches in an electrical circuit. Understanding how a single genome encodes the information to establish, maintain, and modify hundreds of cellular states has been a leading challenge in basic research for many decades. My dissertation work builds on three long-standing observations and explores two open questions: Observation 1: Cells in different biological states express different sets of genes and gene expression changes cause changes in cell state. Observation 2: Regulatory DNA controls changes in gene expression. Observation 3: The DNA bases associated with gene expression differences depend on the biological context of the DNA bases. Question 1: How does cellular state contribute to the activity of a regulatory element? Question 2: To what extent does genomic context influence the relationship between DNA sequence and regulatory activity? I developed a new lentiviral-based method for measuring the activity of thousands of genome-integrated reporter genes, which we call LV-MPRA. I demonstrate that LV-MPRA generates reproducible data and deploy it in two neural cell types. I find that primary DNA sequence features such as GC content and dinucleotide composition can distinguish sequences with high activity in either glioblastoma cells or neural progenitor cells. I show proof-of-concept for the use of lentiviral reporter genes to study regulatory DNA sequences in mouse brains in vivo. Finally, I describe two applications of genome-integrated reporter genes that address distinct biological questions about the interactions between local and regional gene regulatory features. I believe the tools I developed and the ideas I pursued will lead to important discoveries about how the genome encoded information for gene regulation.

Book Synopsis A Study of Local and Regional Gene Regulatory Features in the Human Genome by : Brett B. Maricque

Download or read book A Study of Local and Regional Gene Regulatory Features in the Human Genome written by Brett B. Maricque and published by . This book was released on 2016 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living organisms depend on their genomes to exist, grow, and survive in different environments. Gene activity, or gene expression, underlies such biology and is controlled by regulatory DNA sequences, akin to switches in an electrical circuit. Understanding how a single genome encodes the information to establish, maintain, and modify hundreds of cellular states has been a leading challenge in basic research for many decades. My dissertation work builds on three long-standing observations and explores two open questions: Observation 1: Cells in different biological states express different sets of genes and gene expression changes cause changes in cell state. Observation 2: Regulatory DNA controls changes in gene expression. Observation 3: The DNA bases associated with gene expression differences depend on the biological context of the DNA bases. Question 1: How does cellular state contribute to the activity of a regulatory element? Question 2: To what extent does genomic context influence the relationship between DNA sequence and regulatory activity? I developed a new lentiviral-based method for measuring the activity of thousands of genome-integrated reporter genes, which we call LV-MPRA. I demonstrate that LV-MPRA generates reproducible data and deploy it in two neural cell types. I find that primary DNA sequence features such as GC content and dinucleotide composition can distinguish sequences with high activity in either glioblastoma cells or neural progenitor cells. I show proof-of-concept for the use of lentiviral reporter genes to study regulatory DNA sequences in mouse brains in vivo. Finally, I describe two applications of genome-integrated reporter genes that address distinct biological questions about the interactions between local and regional gene regulatory features. I believe the tools I developed and the ideas I pursued will lead to important discoveries about how the genome encoded information for gene regulation.

Animal Biotechnology

Author: Ashish S. Verma

Publisher: Academic Press

Published: 2013-11-04

Total Pages: 685

ISBN-13: 0123914345

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Animal Biotechnology introduces applications of animal biotechnology and implications for human health and welfare. It begins with an introduction to animal cell cultures and genome sequencing analysis and provides readers with a review of available cell and molecular tools. Topics here include the use of transgenic animal models, tissue engineering, nanobiotechnology, and proteomics. The book then delivers in-depth examples of applications in human health and prospects for the future, including cytogenetics and molecular genetics, xenografts, and treatment of HIV and cancers. All this is complemented by a discussion of the ethical and safety considerations in the field.Animal biotechnology is a broad field encompassing the polarities of fundamental and applied research, including molecular modeling, gene manipulation, development of diagnostics and vaccines, and manipulation of tissue. Given the tools that are currently available and the translational potential for these studies, animal biotechnology has become one of the most essential subjects for those studying life sciences. Highlights the latest biomedical applications of genetically modified and cloned animals with a focus on cancer and infectious diseases Provides firsthand accounts of the use of biotechnology tools, including molecular markers, stem cells, and tissue engineering

Book Synopsis Animal Biotechnology by : Ashish S. Verma

Download or read book Animal Biotechnology written by Ashish S. Verma and published by Academic Press. This book was released on 2013-11-04 with total page 685 pages. Available in PDF, EPUB and Kindle. Book excerpt: Animal Biotechnology introduces applications of animal biotechnology and implications for human health and welfare. It begins with an introduction to animal cell cultures and genome sequencing analysis and provides readers with a review of available cell and molecular tools. Topics here include the use of transgenic animal models, tissue engineering, nanobiotechnology, and proteomics. The book then delivers in-depth examples of applications in human health and prospects for the future, including cytogenetics and molecular genetics, xenografts, and treatment of HIV and cancers. All this is complemented by a discussion of the ethical and safety considerations in the field.Animal biotechnology is a broad field encompassing the polarities of fundamental and applied research, including molecular modeling, gene manipulation, development of diagnostics and vaccines, and manipulation of tissue. Given the tools that are currently available and the translational potential for these studies, animal biotechnology has become one of the most essential subjects for those studying life sciences. Highlights the latest biomedical applications of genetically modified and cloned animals with a focus on cancer and infectious diseases Provides firsthand accounts of the use of biotechnology tools, including molecular markers, stem cells, and tissue engineering

Basic Immunology and Its Clinical Application

Author: Mitsuru Matsumoto

Publisher: Springer Nature

Published:

Total Pages: 252

ISBN-13: 981999781X

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Book Synopsis Basic Immunology and Its Clinical Application by : Mitsuru Matsumoto

Download or read book Basic Immunology and Its Clinical Application written by Mitsuru Matsumoto and published by Springer Nature. This book was released on with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Applying Machine Learning Techniques to Bioinformatics: Few-Shot and Zero-Shot Methods

Author: Lilhore, Umesh Kumar

Publisher: IGI Global

Published: 2024-03-22

Total Pages: 418

ISBN-13:

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Why are cutting-edge data science techniques such as bioinformatics, few-shot learning, and zero-shot learning underutilized in the world of biological sciences?. In a rapidly advancing field, the failure to harness the full potential of these disciplines limits scientists ability to unlock critical insights into biological systems, personalized medicine, and biomarker identification. This untapped potential hinders progress and limits our capacity to tackle complex biological challenges. The solution to this issue lies within the pages of Applying Machine Learning Techniques to Bioinformatics. This book serves as a powerful resource, offering a comprehensive analysis of how these emerging disciplines can be effectively applied to the realm of biological research. By addressing these challenges and providing in-depth case studies and practical implementations, the book equips researchers, scientists, and curious minds with the knowledge and techniques needed to navigate the ever-changing landscape of bioinformatics and machine learning within the biological sciences.

Book Synopsis Applying Machine Learning Techniques to Bioinformatics: Few-Shot and Zero-Shot Methods by : Lilhore, Umesh Kumar

Download or read book Applying Machine Learning Techniques to Bioinformatics: Few-Shot and Zero-Shot Methods written by Lilhore, Umesh Kumar and published by IGI Global. This book was released on 2024-03-22 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: Why are cutting-edge data science techniques such as bioinformatics, few-shot learning, and zero-shot learning underutilized in the world of biological sciences?. In a rapidly advancing field, the failure to harness the full potential of these disciplines limits scientists ability to unlock critical insights into biological systems, personalized medicine, and biomarker identification. This untapped potential hinders progress and limits our capacity to tackle complex biological challenges. The solution to this issue lies within the pages of Applying Machine Learning Techniques to Bioinformatics. This book serves as a powerful resource, offering a comprehensive analysis of how these emerging disciplines can be effectively applied to the realm of biological research. By addressing these challenges and providing in-depth case studies and practical implementations, the book equips researchers, scientists, and curious minds with the knowledge and techniques needed to navigate the ever-changing landscape of bioinformatics and machine learning within the biological sciences.