Investigating Chromosome Dynamics Through Hi-C Assembly

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Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (119 download)

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Book Synopsis Investigating Chromosome Dynamics Through Hi-C Assembly by : Lyam Baudry

Download or read book Investigating Chromosome Dynamics Through Hi-C Assembly written by Lyam Baudry and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The advent of high-throughput DNA sequencing technologies has set off an expanding trend in genome assembling and scaffolding. Such genome quality is an essential preliminary to understand interactions between and among chromosomes. We built upon a computational and technological framework that let us tackle genome assembly problems of increasing complexity. Our methods are mainly based on chromosome conformation capture technologies such as Hi-C. In a Hi-C experiment, DNA molecules are cross-linked with the surrounding proteins and form a large, static protein-DNA complex. This captures the spatial conformation by trapping together molecules that are physically close to each other. Therefore, Hi-C is very suitable for 3D genome structure analysis, which lets us infer a wealth of information about the genome. It was indeed shown that the tridimensional structure of the genome can be unambiguously linked to its 1D structure thanks to the physical properties of DNA polymers. Moreover, such 3D proximity also gives access to cell compartment information, thus opening the way for an additional approach for metagenomic binning, known as meta3C. In this work, we expand upon these methods and apply them to use cases with more and more complexity. We first improve on tools for genome assembly and demonstrate their validity with the scaffolding of Ectocarpus sp., then unveil rearrangements in joint scaffoldings of Trichoderma reesei and Cataglyphis hispanica. Lastly, we use the same approach with metagenomic binning on live mouse microbiome samples to reconstruct hundreds of genomes.

Sex Determination in Plants

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Publisher : Garland Science
ISBN 13 : 1135325650
Total Pages : 201 pages
Book Rating : 4.1/5 (353 download)

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Book Synopsis Sex Determination in Plants by : CC Ainsworth

Download or read book Sex Determination in Plants written by CC Ainsworth and published by Garland Science. This book was released on 2004-08-02 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: Indispensable for all plant biologists, this is a fascinating and thorough examination of those factors which affect the sex determination of plant species, describing all of the main classes of plant with unisexual flowers hermaphrodite, monoecious and

The Barley Genome

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Publisher : Springer
ISBN 13 : 3319925288
Total Pages : 400 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis The Barley Genome by : Nils Stein

Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.

Hi-C Data Analysis

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Publisher : Humana
ISBN 13 : 9781071613924
Total Pages : 0 pages
Book Rating : 4.6/5 (139 download)

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Book Synopsis Hi-C Data Analysis by : Silvio Bicciato

Download or read book Hi-C Data Analysis written by Silvio Bicciato and published by Humana. This book was released on 2022-09-04 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.

HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing

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Publisher :
ISBN 13 : 9781523764426
Total Pages : 40 pages
Book Rating : 4.7/5 (644 download)

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Book Synopsis HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing by : Oldenburg Oldenburg Press

Download or read book HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing written by Oldenburg Oldenburg Press and published by . This book was released on 2016-01-29 with total page 40 pages. Available in PDF, EPUB and Kindle. Book excerpt: HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.

The Pear Genome

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Publisher : Springer
ISBN 13 : 3030110486
Total Pages : 315 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis The Pear Genome by : Schuyler S. Korban

Download or read book The Pear Genome written by Schuyler S. Korban and published by Springer. This book was released on 2019-07-03 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: Addressing the pear genome, this book covers the current state of knowledge regarding genetic and genomic resources, breeding approaches and strategies, as well as cutting-edge content on how these tools and resources are being / soon will be utilized to pursue genetic improvement efforts that will combine fruit quality, high productivity, precocious fruit bearing, and long postharvest storage life, along with elevated levels of resistance to various major diseases and insect pests. Throughout, the book also explores potential opportunities and challenges in genomic analysis, sequence assembly, structural features, as well as functional studies that will assist in future genetic improvement efforts for pears. The pear (Pyrus), an important tree fruit crop, is grown worldwide, and has several economically relevant cultivars. In recent years, modern genetic and genomic tools have resulted in the development of a wide variety of valuable resources for the pear. In the past few years, completion of whole genome assemblies of ‘Dangshansuli’, an Asian pear, and ‘Bartlett’, a European pear, have paved the way for new discoveries regarding for example, the pear’s genomic structure, chromosome evolution, and patterns of genetic variation. This wealth of new resources will have a major impact on our knowledge of the pear genome; in turn, these resources and knowledge will have significant impacts on future genetic improvement efforts.

Computational Predictions, Dynamic Tracking, and Evolutionary Analysis of Antibiotic Resistance Through the Mining of Microbial Genomes and Metagenomic Data

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Publisher : Frontiers Media SA
ISBN 13 : 2889760138
Total Pages : 138 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Computational Predictions, Dynamic Tracking, and Evolutionary Analysis of Antibiotic Resistance Through the Mining of Microbial Genomes and Metagenomic Data by : Qi Zhao

Download or read book Computational Predictions, Dynamic Tracking, and Evolutionary Analysis of Antibiotic Resistance Through the Mining of Microbial Genomes and Metagenomic Data written by Qi Zhao and published by Frontiers Media SA. This book was released on 2022-04-27 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Fruits and Nuts

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Publisher : Springer Science & Business Media
ISBN 13 : 3540345337
Total Pages : 370 pages
Book Rating : 4.5/5 (43 download)

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Book Synopsis Fruits and Nuts by : Chittaranjan Kole

Download or read book Fruits and Nuts written by Chittaranjan Kole and published by Springer Science & Business Media. This book was released on 2007-03-06 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Fruits and Nuts" form the largest group among crop plants. Several constraints such as long life cycle have caused comparatively slow research progress in the past. The chapters on 20 fruit and nut crops authored by 56 renowned scientists from 12 countries include for the first time comprehensive reviews on a variety of fruits and nuts. The huge amount of information hitherto dispersed in journals is now available in a clearly structured reference work.

Chromosome Architecture

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Publisher : Humana
ISBN 13 : 9781493936298
Total Pages : 0 pages
Book Rating : 4.9/5 (362 download)

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Book Synopsis Chromosome Architecture by : Mark C. Leake

Download or read book Chromosome Architecture written by Mark C. Leake and published by Humana. This book was released on 2016-06-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume details a valuable collection of protocols and reviews, such as emerging experimental and theoretical approaches. These approaches have resulted in a substantial improvement in the understanding of chromosome architecture. Chromosome Architecture: Methods and Protocols guides readers through cutting-edge interdisciplinary methods which allow for an understanding of architecture of chromosomes with exceptionally enhanced resolution, both in terms of space and time. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Chromosome Architecture: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Plant Molecular Evolution

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Publisher : Springer Science & Business Media
ISBN 13 : 9401142211
Total Pages : 272 pages
Book Rating : 4.4/5 (11 download)

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Book Synopsis Plant Molecular Evolution by : J.J. Doyle

Download or read book Plant Molecular Evolution written by J.J. Doyle and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant molecular biology has produced an ever-increasing flood of data about genes and genomes. Evolutionary biology and systematics provides the context for synthesizing this information. This book brings together contributions from evolutionary biologists, systematists, developmental geneticists, biochemists, and others working on diverse aspects of plant biology whose work touches to varying degrees on plant molecular evolution. The book is organized in three parts, the first of which introduces broad topics in evolutionary biology and summarizes advances in plant molecular phylogenetics, with emphasis on model plant systems. The second segment presents a series of case studies of gene family evolution, while the third gives overviews of the evolution of important plant processes such as disease resistance, nodulation, hybridization, transposable elements and genome evolution, and polyploidy.

Long-Range Control of Gene Expression

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Publisher : Academic Press
ISBN 13 : 0080877818
Total Pages : 415 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis Long-Range Control of Gene Expression by : Veronica van Heyningen

Download or read book Long-Range Control of Gene Expression written by Veronica van Heyningen and published by Academic Press. This book was released on 2011-09-02 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Long-Range Control of Gene Expression covers the current progress in understanding the mechanisms for genomic control of gene expression, which has grown considerably in the last few years as insight into genome organization and chromatin regulation has advanced. Discusses the evolution of cis-regulatory sequences in drosophila Includes information on genomic imprinting and imprinting defects in humans Includes a chapter on epigenetic gene regulation in cancer

The Yeast Nucleus

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Publisher :
ISBN 13 : 9781383049756
Total Pages : 0 pages
Book Rating : 4.0/5 (497 download)

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Book Synopsis The Yeast Nucleus by : Peter Fantes

Download or read book The Yeast Nucleus written by Peter Fantes and published by . This book was released on 2000 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Capturing Chromosome Conformation

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Publisher : Humana
ISBN 13 : 9781071606636
Total Pages : 322 pages
Book Rating : 4.6/5 (66 download)

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Book Synopsis Capturing Chromosome Conformation by : Beatrice Bodega

Download or read book Capturing Chromosome Conformation written by Beatrice Bodega and published by Humana. This book was released on 2020-10-29 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Capturing Chromosome Conformation: Methods and Protocols serves as an ideal guide for researchers working to further understand 3D genome organization.

The Amaranth Genome

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Publisher : Springer Nature
ISBN 13 : 3030723658
Total Pages : 181 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis The Amaranth Genome by : Dinesh Adhikary

Download or read book The Amaranth Genome written by Dinesh Adhikary and published by Springer Nature. This book was released on 2021-06-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

The Pangenome

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Publisher : Springer Nature
ISBN 13 : 3030382818
Total Pages : 311 pages
Book Rating : 4.0/5 (33 download)

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Book Synopsis The Pangenome by : Hervé Tettelin

Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Gene Drives on the Horizon

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Publisher : National Academies Press
ISBN 13 : 0309437873
Total Pages : 231 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Gene Drives on the Horizon by : National Academies of Sciences, Engineering, and Medicine

Download or read book Gene Drives on the Horizon written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-08-28 with total page 231 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research on gene drive systems is rapidly advancing. Many proposed applications of gene drive research aim to solve environmental and public health challenges, including the reduction of poverty and the burden of vector-borne diseases, such as malaria and dengue, which disproportionately impact low and middle income countries. However, due to their intrinsic qualities of rapid spread and irreversibility, gene drive systems raise many questions with respect to their safety relative to public and environmental health. Because gene drive systems are designed to alter the environments we share in ways that will be hard to anticipate and impossible to completely roll back, questions about the ethics surrounding use of this research are complex and will require very careful exploration. Gene Drives on the Horizon outlines the state of knowledge relative to the science, ethics, public engagement, and risk assessment as they pertain to research directions of gene drive systems and governance of the research process. This report offers principles for responsible practices of gene drive research and related applications for use by investigators, their institutions, the research funders, and regulators.

The Role of High-Order Chromatin Organization in Gene Regulation

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Publisher : Frontiers Media SA
ISBN 13 : 2832505295
Total Pages : 248 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis The Role of High-Order Chromatin Organization in Gene Regulation by : Alexey V. Pindyurin

Download or read book The Role of High-Order Chromatin Organization in Gene Regulation written by Alexey V. Pindyurin and published by Frontiers Media SA. This book was released on 2022-11-11 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: