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Author: Kenneth Berendzen Publisher: Bentham Science Publishers ISBN: 1608054926 Category : Science Languages : en Pages : 225
Book Description
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.
Author: Kenneth Berendzen Publisher: Bentham Science Publishers ISBN: 1608054926 Category : Science Languages : en Pages : 225
Book Description
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.
Author: Eric H. Davidson Publisher: Elsevier ISBN: 0080455573 Category : Science Languages : en Pages : 303
Book Description
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
Author: Junhong Luo Publisher: ISBN: Category : Languages : en Pages : 512
Book Description
Uncovering the system-level transcriptional regulatory architecture of gene expression in human has been a major focal point in modern systems biology researches. Human genes are commonly under coordinated and combinatorial transcriptional regulation mediated by a class of proteins known as transcription factors. Recent technological advancements have enabled comprehensive mapping of transcription factor binding motifs in human genome through both experimental (e.g. ChIP-seq) and computational (e.g. comparative sequence analysis) methods. Collections of defined transcription factor binding motifs and their corresponding target genes in a given species can be used as a "dictionary" to define groups of genes that have the potential of being under coordinated control. Utilising a large-scale transcription factor binding motif location data in human genome, this study has defined a comprehensive genome-wide binding motif dictionary of human transcription factors. Instead of inferring transcriptional regulatory networks from co-expression, this study attempted to take the opposite approach in which, by using simple multivariate data analysis methods and graph theory, groups of genes under putative transcriptional co-regulation were defined based on the promoter motif content similarity between genes. These defined networks of genes could be used as a platform for incorporating other biological datasets to clarify the system-level regulatory architecture of human genes. In this thesis, independent gene function annotation, gene expression and ChIP-seq datasets were employed to bring in functional and biological insights, and also to provide independent validations for the regulatory networks defined based on promoter motif content similarity. The results showed the regulatory networks defined in this work were of biological significance. More specifically, groups of genes under putative co-regulation defined in this study on the basis of sharing common transcription factor binding motifs were likely to share common function and expression. Overall, the affirmative findings described in this thesis demonstrated the feasibility of identifying putative gene regulatory networks by using large-scale motif dictionaries.
Author: Brett B. Maricque Publisher: ISBN: Category : Electronic dissertations Languages : en Pages : 102
Book Description
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.
Author: Laura Kaitlin Hill Donohue Publisher: ISBN: Category : Languages : en Pages :
Book Description
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.
Author: John Darzentas Publisher: Springer ISBN: 3540878815 Category : Computers Languages : en Pages : 457
Book Description
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).
Author: Sang-goo Lee Publisher: Springer ISBN: 3642290388 Category : Computers Languages : en Pages : 615
Book Description
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.
Author: Ashish S. Verma Publisher: Academic Press ISBN: 0123914345 Category : Science Languages : en Pages : 685
Book Description
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
Author: Kenneth Berendzen
Author: Kenneth Berendzen
Author: Eric H. Davidson
Author: Junhong Luo
Author: Brett B. Maricque
Author: Laura Kaitlin Hill Donohue
Author: John Darzentas
Author: Sang-goo Lee
Author: Xi Wang
Author: Ashish S. Verma
Author: Mitsuru Matsumoto