Integrative Computational Approaches To Study Protein Nucleic Acid Interactions PDF Download
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| Author | : Anob Mauli Chakrabarti |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2020 |
| Genre | : |
| ISBN | : |
Download Integrative Computational Approaches to Study Protein-nucleic Acid Interactions Book in PDF, ePub and Kindle
Interactions between proteins and nucleic acid molecules are central to the cellular regulation and homeostasis. To study them, I employ a wide range of computational analysis methods to integrate genomic data from many types of experiment. This thesis has three parts. In the first part, I explore the patterns of indels created by CRISPR-Cas9 genome editing. By thorough characterisation of the precision of editing at thousands of genomic target sites, we identify simple sequence rules that can help predict these outcomes. Furthermore, we examine the role of the structural chromatin context in fine-tuning Cas9-DNA interactions. In the second part, I explore methods to study protein-RNA interactions. I use comparative computational analyses to assess both the data quality of, and data analysis methods for, different crosslinking and immunoprecipitation (CLIP) technologies. I then develop new methods to analyse data generated by hybrid individual-nucleotide resolution CLIP (hiCLIP). By tailoring computational solutions to an understanding of experimental conditions, I improve the overall sensitivity of hiCLIP, and ultimately feedback to drive ongoing experimental development. In the third part, I focus on the Staufen family of double-stranded RNA binding proteins and using hiCLIP data to define transcriptome-wide atlases of RNA duplexes bound by these proteins both in a cell line and in rat brain tissue. Through integration with other data sets, both publicly available and newly generated, I derive insights into their function in RNA metabolism, and in how these interactions change during the course of mammalian brain development with putative roles in ribonucleoprotein complex formation. In summary, I present a range of tailored computational methods and analyses developed to understand interactions between proteins and nucleic acids; aiming to link these interactions to functional outcomes.
| Author | : Kuan-Bei Chen |
| Publisher | : |
| Total Pages | : 96 |
| Release | : 2013 |
| Genre | : |
| ISBN | : |
Download Computational Approaches for Integrative Detection of Protein-DNA Interactions Book in PDF, ePub and Kindle
| Author | : Sriganesh Srihari |
| Publisher | : Morgan & Claypool |
| Total Pages | : 297 |
| Release | : 2017-05-30 |
| Genre | : Science |
| ISBN | : 1970001534 |
Download Computational Prediction of Protein Complexes from Protein Interaction Networks Book in PDF, ePub and Kindle
Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.
| Author | : Annette Höglund |
| Publisher | : |
| Total Pages | : 0 |
| Release | : 2006 |
| Genre | : |
| ISBN | : |
Download Computational Approaches for Analyzing the Role of Protein-DNA Interactions in Gene Regulation Book in PDF, ePub and Kindle
| Author | : Phoebe A. Rice |
| Publisher | : Royal Society of Chemistry |
| Total Pages | : 417 |
| Release | : 2008-05-22 |
| Genre | : Science |
| ISBN | : 0854042725 |
Download Protein-Nucleic Acid Interactions Book in PDF, ePub and Kindle
This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
| Author | : Shula Shazman (Dotor.) |
| Publisher | : |
| Total Pages | : 103 |
| Release | : 2011 |
| Genre | : |
| ISBN | : |
Download Computational Approaches for Characterizing Protein-nucleic-acid Binding Book in PDF, ePub and Kindle
| Author | : |
| Publisher | : Academic Press |
| Total Pages | : 1571 |
| Release | : 2020-08-24 |
| Genre | : Science |
| ISBN | : 0128160780 |
Download Systems Medicine Book in PDF, ePub and Kindle
Technological advances in generated molecular and cell biological data are transforming biomedical research. Sequencing, multi-omics and imaging technologies are likely to have deep impact on the future of medical practice. In parallel to technological developments, methodologies to gather, integrate, visualize and analyze heterogeneous and large-scale data sets are needed to develop new approaches for diagnosis, prognosis and therapy. Systems Medicine: Integrative, Qualitative and Computational Approaches is an innovative, interdisciplinary and integrative approach that extends the concept of systems biology and the unprecedented insights that computational methods and mathematical modeling offer of the interactions and network behavior of complex biological systems, to novel clinically relevant applications for the design of more successful prognostic, diagnostic and therapeutic approaches. This 3 volume work features 132 entries from renowned experts in the fields and covers the tools, methods, algorithms and data analysis workflows used for integrating and analyzing multi-dimensional data routinely generated in clinical settings with the aim of providing medical practitioners with robust clinical decision support systems. Importantly the work delves into the applications of systems medicine in areas such as tumor systems biology, metabolic and cardiovascular diseases as well as immunology and infectious diseases amongst others. This is a fundamental resource for biomedical students and researchers as well as medical practitioners who need to need to adopt advances in computational tools and methods into the clinical practice. Encyclopedic coverage: ‘one-stop’ resource for access to information written by world-leading scholars in the field of Systems Biology and Systems Medicine, with easy cross-referencing of related articles to promote understanding and further research Authoritative: the whole work is authored and edited by recognized experts in the field, with a range of different expertise, ensuring a high quality standard Digitally innovative: Hyperlinked references and further readings, cross-references and diagrams/images will allow readers to easily navigate a wealth of information
| Author | : Siddhartha Roy |
| Publisher | : Royal Society of Chemistry |
| Total Pages | : 399 |
| Release | : 2020-12-14 |
| Genre | : Science |
| ISBN | : 1839160500 |
Download Protein–Protein Interaction Regulators Book in PDF, ePub and Kindle
New genomic information has revealed the crucial role that protein–protein interactions (PPIs) play in regulating numerous cellular functions. Aberrant forms of these interactions are common in numerous diseases and thus PPIs have emerged as a vast class of critical drug targets. Despite the importance of PPIs in biology, it has been extremely challenging to convert targets into therapeutics and targeting PPIs had long been considered a very difficult task. However, over the past decade the field has advanced with increasing growth in the number of successful PPI regulators. Protein–Protein Interaction Regulators surveys the latest advances in the structural understanding of PPIs as well as recent developments in modulator discovery.
| Author | : Kiyoshi Nagai |
| Publisher | : Oxford University Press, USA |
| Total Pages | : 302 |
| Release | : 1994 |
| Genre | : Medical |
| ISBN | : |
Download RNA-protein Interactions Book in PDF, ePub and Kindle
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
| Author | : Siddhartha Roy |
| Publisher | : Academic Press |
| Total Pages | : 352 |
| Release | : 2021-05-14 |
| Genre | : Science |
| ISBN | : 0128176458 |
Download Chemical Biology of the Genome Book in PDF, ePub and Kindle
Chemical Biology of the Genome provides a comprehensive overview of essential concepts and principles of genomic and epigenomics dynamics as explored through the lens of chemical biology. Key examples and case studies illustrate chemical biology methods for study and analysis of the genome and epigenome, with an emphasis on relevance to physiological and pathophysiological processes and drug discovery. Authors and international leaders in biochemical studies of the genome, Drs. Siddhartha Roy and Tapas Kundu, adopt an integrated, interdisciplinary approach throughout, demonstrating how fast evolving chemical and mass-scale sequencing tools are increasingly used to interpret biochemical processes of the genome. Later sections discuss chemical modifications of the genome, DNA sequence recognition by proteins and gene regulation, GWAS and EpiGWAS studies, 3D architecture of the genome, and functional genome architecture. In-depth, discovery focused chapters examine intervention in gene networks using SiRNA/ShRNA, miRNA, and anti-miR, small molecule modulation of iPS, drug resistance pathways altered DNA methylation as drug targets, anti-miR as therapeutics, and nanodelivery of drugs. Offers an interdisciplinary discussion of the chemical biology of the genome and epigenome, employing illustrative case studies in both physiological and pathophysiological contexts Supports researchers in employing chemical and mass-scale sequencing approaches to interpret genomic and epigenomic dynamics Highlights innovative pathways and molecular targets for new disease study and drug discovery
