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| atac-seq analysis pipeline: Computational Genomics with R Altuna Akalin, 2020-12-16 Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015. |
| atac-seq analysis pipeline: Unraveling New Frontiers and Advances in Bioinformatics Amit Chaudhary, |
| atac-seq analysis pipeline: Statistical Genomics Ewy Mathé, Sean Davis, 2016-03-24 This volume expands on statistical analysis of genomic data by discussing cross-cutting groundwork material, public data repositories, common applications, and representative tools for operating on genomic data. Statistical Genomics: Methods and Protocols is divided into four sections. The first section discusses overview material and resources that can be applied across topics mentioned throughout the book. The second section covers prominent public repositories for genomic data. The third section presents several different biological applications of statistical genomics, and the fourth section highlights software tools that can be used to facilitate ad-hoc analysis and data integration. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible analysis protocols, and tips on troubleshooting and avoiding known pitfalls. Through and practical, Statistical Genomics: Methods and Protocols, explores a range of both applications and tools and is ideal for anyone interested in the statistical analysis of genomic data. |
| atac-seq analysis pipeline: Genomic Control Process Isabelle S. Peter, Eric H. Davidson, 2015-01-21 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 |
| atac-seq analysis pipeline: Epigenetics in Psychiatry Jacob Peedicayil, Dennis R. Grayson, Dimitri Avramopoulos, 2021-08-21 Epigenetics in Psychiatry, Second Edition covers all major areas of psychiatry in which extensive epigenetic research has been performed, fully encompassing a diverse and maturing field, including drug addiction, bipolar disorder, epidemiology, cognitive disorders, and the uses of putative epigenetic-based psychotropic drugs. Uniquely, each chapter correlates epigenetics with relevant advances across genomics, transcriptomics, and proteomics. The book acts as a catalyst for further research in this growing area of psychiatry. This new edition has been fully revised to address recent advances in epigenetic understanding of psychiatric disorders, evoking data consortia (e.g., CommonMind, ATAC-seq), single cell analysis, and epigenome-wide association studies to empower new research. The book also examines epigenetic effects of the microbiome on psychiatric disorders, and the use of neuroimaging in studying the role of epigenetic mechanisms of gene expression. Ongoing advances in epigenetic therapy are explored in-depth. - Fully revised to discuss new areas of research across neuronal stem cells, cognitive disorders, and transgenerational epigenetics in psychiatric disease - Relates broad advances in psychiatric epigenetics to a modern understanding of the genome, transcriptome, and proteins - Catalyzes knowledge discovery in both basic epigenetic biology and epigenetic targets for drug discovery - Provides guidance in research methods and protocols, as well how to employ data from consortia, single cell analysis, and epigenome-wide association studies (EWAS) - Features chapter contributions from international leaders in the field |
| atac-seq analysis pipeline: Chromatin Accessibility Georgi K. Marinov, William J. Greenleaf, 2023-02-20 This detailed volume provides a comprehensive resource covering the existing and state-of-the-art tools in the field of profiling chromatin accessibility and its dynamics. Beginning with a section on bulk-cell methods for profiling chromatin accessibility and nucleosome positioning that rely on enzymatic cleavage of accessible DNA and produce information about relative accessibility, the book continues with methods that use single-molecule and enzymatic approaches to solving the problem of mapping absolute occupancy/accessibility, emerging tools for mapping DNA accessibility and nucleosome positioning in single cells, imaging-based methods for visualizing accessible chromatin in its nuclear context, as well as computational methods for the processing and analysis of chromatin accessibility datasets. 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 and readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, Chromatin Accessibility: Methods and Protocols serves as an extensive and useful reference for researchers studying different facets of chromatin accessibility in a wide variety of biological contexts. Chapter 6 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. |
| atac-seq analysis pipeline: Computational Exome and Genome Analysis Peter N. Robinson, Rosario Michael Piro, Marten Jager, 2017-09-13 Exome and genome sequencing are revolutionizing medical research and diagnostics, but the computational analysis of the data has become an extremely heterogeneous and often challenging area of bioinformatics. Computational Exome and Genome Analysis provides a practical introduction to all of the major areas in the field, enabling readers to develop a comprehensive understanding of the sequencing process and the entire computational analysis pipeline. |
| atac-seq analysis pipeline: Genomics and Bioinformatics Tore Samuelsson, 2012-06-07 With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems. |
| atac-seq analysis pipeline: Chromatin Immunoprecipitation Neus Visa, Antonio Jordán-Pla, 2017-10-14 This up-to-date volume includes protocols that illustrate the broad use of chromatin immunoprecipitation (ChIP) and ChIP-related methods in a variety of biological research areas. The collection also includes protocols designed to improve the performance of ChIP for specific applications. Written in the highly successful Methods in Molecular Biology series format, chapters include introduction to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromatin Immunoprecipitation: Methods and Protocols features techniques, including bioinformatic analysis of ChIP data, will be of interest to a very broad research community in the fields of biochemistry, molecular biology, microbiology, and biomedicine. |
| atac-seq analysis pipeline: Echinoderms Part B , 2019-04-02 Echinoderms, Volume 151, the latest release in the Methods in Cell Biology series, highlights advances in the field, with this update presenting chapters on Echinoderm Genome Databases, analysis of gene regulatory networks, using ATAC-seq and RNA-seq to increase resolution in GRN connectivity, multiplex cis-regulatory analysis, experimental approaches GRN/signal pathways, BACs, analysis of chromatin accessibility using ATAC-seq, analysis of sea urchin proteins /Click IT, CRISPR/Cas9-mediated genome editing in sea urchins, super-resolution and in toto imaging of echinoderm embryos, and methods for analysis of intracellular ion signals in sperm, eggs and embryos. - Presents clear, concise protocols provided by experts who have established the echinoderms as a model systems - Highlights new advances in the field, with this update presenting interesting chapters on echinoderms |
| atac-seq analysis pipeline: The Mouse Nervous System Charles Watson, George Paxinos, Luis Puelles, 2011-11-28 The Mouse Nervous System provides a comprehensive account of the central nervous system of the mouse. The book is aimed at molecular biologists who need a book that introduces them to the anatomy of the mouse brain and spinal cord, but also takes them into the relevant details of development and organization of the area they have chosen to study. The Mouse Nervous System offers a wealth of new information for experienced anatomists who work on mice. The book serves as a valuable resource for researchers and graduate students in neuroscience. Systematic consideration of the anatomy and connections of all regions of the brain and spinal cord by the authors of the most cited rodent brain atlases A major section (12 chapters) on functional systems related to motor control, sensation, and behavioral and emotional states A detailed analysis of gene expression during development of the forebrain by Luis Puelles, the leading researcher in this area Full coverage of the role of gene expression during development and the new field of genetic neuroanatomy using site-specific recombinases Examples of the use of mouse models in the study of neurological illness |
| atac-seq analysis pipeline: Genomics of Cereal Crops Shabir Hussain Wani, Anuj Kumar, 2022-06-13 This volume details different genomic methods and resources to explore cereal genomics. Chapters guide readers through crop genomes, Next Generation Sequencing (NGS) technologies, protocol for CRISPR editing, transgenic wheat, NGS approach, virus induced gene silencing (VIGS), genomic tools, computational prediction of ncRNAs (miRNAs & ceRNAs) in cereal crops, genotyping-by-sequencing (GBS), Bayesian method, single cell sequencing, genome-wide association study (GWAS), QTL interval mapping, whole genome bisulfite sequencing, genome imprinting, and methods for study the receptor-metabolite interaction. Authoritative and cutting-edge, Genomics of Cereal Crops aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge. |
| atac-seq analysis pipeline: Rigor and Reproducibility in Genetics and Genomics , 2023-11-08 Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students, and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians, and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices, and common pitfalls. Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists. - Provides practical approaches and step-by-step protocols to strengthen genetic and genomic research conducted in the laboratory or classroom - Presents illustrative case studies and training exercises, discussing common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, genomic sequencing, and gene editing, among other genetic and genomic approaches - Examines best practices for microarray analysis, DNA-seq, RNA-seq, gene expression validation, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis - Written to provide trainees and educators with highly applicable tools and strategies to learn or refine a method toward identifying meaningful results with high confidence in their reproducibility |
| atac-seq analysis pipeline: Computational Epigenetics and Diseases , 2019-02-06 Computational Epigenetics and Diseases, written by leading scientists in this evolving field, provides a comprehensive and cutting-edge knowledge of computational epigenetics in human diseases. In particular, the major computational tools, databases, and strategies for computational epigenetics analysis, for example, DNA methylation, histone modifications, microRNA, noncoding RNA, and ceRNA, are summarized, in the context of human diseases. This book discusses bioinformatics methods for epigenetic analysis specifically applied to human conditions such as aging, atherosclerosis, diabetes mellitus, schizophrenia, bipolar disorder, Alzheimer disease, Parkinson disease, liver and autoimmune disorders, and reproductive and respiratory diseases. Additionally, different organ cancers, such as breast, lung, and colon, are discussed. This book is a valuable source for graduate students and researchers in genetics and bioinformatics, and several biomedical field members interested in applying computational epigenetics in their research. - Provides a comprehensive and cutting-edge knowledge of computational epigenetics in human diseases - Summarizes the major computational tools, databases, and strategies for computational epigenetics analysis, such as DNA methylation, histone modifications, microRNA, noncoding RNA, and ceRNA - Covers the major milestones and future directions of computational epigenetics in various kinds of human diseases such as aging, atherosclerosis, diabetes, heart disease, neurological disorders, cancers, blood disorders, liver diseases, reproductive diseases, respiratory diseases, autoimmune diseases, human imprinting disorders, and infectious diseases |
| atac-seq analysis pipeline: Epigenetics Methods Trygve O Tollefsbol, 2020-07-08 In recent years, the field of epigenetics has grown significantly, driving new understanding of human developmental processes and disease expression, as well as advances in diagnostics and therapeutics. As the field of epigenetics continues to grow, methods and technologies have multiplied, resulting in a wide range of approaches and tools researchers might employ. Epigenetics Methods offers comprehensive instruction in methods, protocols, and experimental approaches applied in field of epigenetics. Here, across thirty-five chapters, specialists offer step-by-step overviews of methods used to study various epigenetic mechanisms, as employed in basic and translational research. Leading the reader from fundamental to more advanced methods, the book begins with thorough instruction in DNA methylation techniques and gene or locus-specific methylation analyses, followed by histone modification methods, chromatin evaluation, enzyme analyses of histone methylation, and studies of non-coding RNAs as epigenetic modulators. Recently developed techniques and technologies discussed include single-cell epigenomics, epigenetic editing, computational epigenetics, systems biology epigenetic methods, and forensic epigenetic approaches. Epigenetics methods currently in-development, and their implication for future research, are also considered in-depth. In addition, as with the wider life sciences, reproducibility across experiments, labs, and subdisciplines is a growing issue for epigenetics researchers. This volume provides consensus-driven methods instruction and overviews. Tollefsbol and contributing authors survey the range of existing methods; identify best practices, common themes, and challenges; and bring unity of approach to a diverse and ever-evolving field. - Includes contributions by leading international investigators involved in epigenetic research and clinical and therapeutic application - Integrates technology and translation with fundamental chapters on epigenetics methods, as well as chapters on more novel and advanced epigenetics methods - Written at verbal and technical levels that can be understood by scientists and students alike - Includes chapters on state-of-the-art techniques such as single-cell epigenomics, use of CRISPR/Cas9 for epigenetic editing, and epigenetics methods applied to forensics |
| atac-seq analysis pipeline: Next Steps for Functional Genomics National Academies of Sciences, Engineering, and Medicine, Division on Earth and Life Studies, Board on Life Sciences, 2020-12-18 One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from -omics screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop. |
| atac-seq analysis pipeline: Organoids, organs-on-chip, nanoparticles and in silico approaches to dissect the tumorimmune dynamics and to unveil the drug resistance mechanisms to therapy in the tumor microenvironment Fabrizio Mattei, Jason T. George, Mohit Kumar Jolly, 2023-08-03 |
| atac-seq analysis pipeline: Hi-C Data Analysis Silvio Bicciato, Francesco Ferrari, 2022-09-04 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. |
| atac-seq analysis pipeline: Photochemistry Angelo Albini, Stefano Protti, 2019-09-23 Drawing on the continued wealth of photochemical research, this volume combines reviews on the latest advances in the field with specific topical highlights. Starting with periodical reports of the recent literature on physical and inorganic aspects, light induced reactions in cryogenic matrices, properties of transition-metal compounds, time-resolved spectroscopy, the exploitation of solar energy and the molecules of colour. Coverage continues with highlighted topics, in the second part, from photoresponsive hydrogels, the tunable photoredox properties of organic dyes, light-driven asymmetric organocatalytic processes, dual gold–photoredox catalysis, the preparation and characterization of photosensitizers for triplet–triplet annihilation photon upconversion and the role of photochemistry on traditional synthetic processes. This volume will include for the first time a section entitled ‘SPR Lectures on Photochemistry’, providing examples for academic readers to introduce a photochemistry topic and precious help for students in photochemistry. Providing critical analysis of the topics, this book is essential reading for anyone wanting to keep up to date with the literature on photochemistry and its applications. |
| atac-seq analysis pipeline: Computational Biomedicine Peter Coveney, Vanessa Díaz-Zuccarini, Peter Hunter, Marco Viceconti, 2014-06 Computational Biomedicine unifies the different strands of a broad-ranging subject to demonstrate the power of a tool that has the potential to revolutionise our understanding of the human body, and the therapeutic strategies available to maintain and protect it. |
| atac-seq analysis pipeline: Deep Sequencing Data Analysis Noam Shomron, 2013-07-20 The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis, expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. These included techniques for compressing of data generated, Chromatin Immunoprecipitation (ChIP-seq), and various approaches for the identification of sequence variants. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data analysis procedures for deep sequencing data interpretation. |
| atac-seq analysis pipeline: Programmed Cell Death in Plants John Gray, 2004 The recognition of cell death as an active process has changed the way in which biologists view living things. Geneticists re-evaluate long known mutants, research strategies are redesigned, and new model systems are sought. This volume reviews our new understanding of programmed cell death as it applies to plants. The book draws comparisons with programmed cell death in animals and unicellular organisms. The book is directed at researchers and professionals in plant cell biology, biochemistry, physiology, developmental biology and genetics. |
| atac-seq analysis pipeline: Multi-omic Data Integration in Oncology Chiara Romualdi, Enrica Calura, Davide Risso, Sampsa Hautaniemi, Francesca Finotello, 2020-12-03 This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact. |
| atac-seq analysis pipeline: Developmental Hematopoiesis Margaret H. Baron, 2005-01-01 This volume presents the first collection of methods to study embryonic and fetal hematopoiesis in both invertebrate (fruit flies) and vertebrate (frog, fish, mouse, chick, and human) organisms. These state-of-the-art techniques range from the genetic, molecular, and cellular, to cell and embryo explant culture and whole animals, including in vivo imaging. Bioinformatic and functional genomic approaches for studying stem cells and their supportive stromal cells are also discussed. |
| atac-seq analysis pipeline: Microbial Omics in Environment and Health Minu Kesheri, |
| atac-seq analysis pipeline: In VIVO Footprinting I.L. Cartwright, 1997-08-22 The revolution in biological research initiated by the demonstration that particular DNA molecules could be isolated, recombined in novel ways, and conveniently replicated to high copy number in vivo for further study, that is, the recombinant DNA era, has spawned many additional advances, both methodological and intellectual, that have enhanced our understanding of cellular processes to an astonishing degree. As part of the subsequent outpouring of information, research exploring the mechanisms of gene regulation, both in prokaryotes and eukaryotes (but particularly the latter), has been particularly well represented. Although no one technical approach can be said to have brought the filed to its current level of sophistication, the ability to map the interactions of trans-acting factors with their DNA recognition sequences to a high level of precision has certainly been one of the more important advances. This footprinting approach has become almost ubiquitous in gene regulatory studies; however, it is in its in vivo application that ambiguities, confusions, and inconsistencies that may arise from a purely in vitro-based approach can often be resolved and placed in their proper perspective. Put more simply, that an interaction can be demonstrated to occur between purified factors and a particular piece of DNA in a test tube does not, of course, say anything regarding whether such interactions are occurring in vivo. The ability to probe for such interactions as they occur inside cells, with due attention paid to the relevant developmental stage, or to the tissue specificity of the interaction being probed, has made in vivo footprinting approach an invaluable adjunct to the gene jockey's arsenal of weapons. |
| atac-seq analysis pipeline: Bioinformatics: Sequences, Structures, Phylogeny Asheesh Shanker, 2018-10-13 This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files. |
| atac-seq analysis pipeline: HiC-Pro: an Optimized and Flexible Pipeline for Hi-C Data Processing Oldenburg Oldenburg Press, 2016-01-29 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. |
| atac-seq analysis pipeline: Computational Systems Biology in Medicine and Biotechnology Sonia Cortassa, Miguel A. Aon, 2022-05-23 This volume addresses the latest state-of-the-art systems biology-oriented approaches that--driven by big data and bioinformatics--are utilized by Computational Systems Biology, an interdisciplinary field that bridges experimental tools with computational tools to tackle complex questions at the frontiers of knowledge in medicine and biotechnology. The chapters in this book are organized into six parts: systems biology of the genome, epigenome, and redox proteome; metabolic networks; aging and longevity; systems biology of diseases; spatiotemporal patterns of rhythms, morphogenesis, and complex dynamics; and genome scale metabolic modeling in biotechnology. In every chapter, readers will find varied methodological approaches applied at different levels, from molecular, cellular, organ to organisms, genome to phenome, and health and disease. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; criteria utilized for applying specific methodologies; lists of the necessary materials, reagents, software, databases, algorithms, mathematical models, and dedicated analytical procedures; step-by-step, readily reproducible laboratory, bioinformatics, and computational protocols all delivered in didactic and clear style and abundantly illustrated with express case studies and tutorials; and tips on troubleshooting and advice for achieving reproducibility while avoiding mistakes and misinterpretations. The overarching goal driving this volume is to excite the expert and stimulate the newcomer to the field of Computational Systems Biology. Cutting-edge and authoritative, Computational Systems Biology in Medicine and Biotechnology: Methods and Protocols is a valuable resource for pre- and post-graduate students in medicine and biotechnology, and in diverse areas ranging from microbiology to cellular and organismal biology, as well as computational and experimental biologists, and researchers interested in utilizing comprehensive systems biology oriented methods. |
| atac-seq analysis pipeline: A Time for Metabolism and Hormones Paolo Sassone-Corsi, Yves Christen, 2016-04-04 Recent years have seen spectacular advances in the field of circadian biology. These have attracted the interest of researchers in many fields, including endocrinology, neurosciences, cancer, and behavior. By integrating a circadian view within the fields of endocrinology and metabolism, researchers will be able to reveal many, yet-unsuspected aspects of how organisms cope with changes in the environment and subsequent control of homeostasis. This field is opening new avenues in our understanding of metabolism and endocrinology. A panel of the most distinguished investigators in the field gathered together to discuss the present state and the future of the field. The editors trust that this volume will be of use to those colleagues who will be picking up the challenge to unravel how the circadian clock can be targeted for the future development of specific pharmacological strategies toward a number of pathologies. |
| atac-seq analysis pipeline: Epigenomics Gurbachan Singh Miglani, 2023-06-13 Epigenomics deals in detail with the concepts, principles, procedures, developments, limitations, advantages, applications and future prospects of different areas of epigenomics in a comprehensive manner. It provides concise yet complete knowledge on the many aspects of the basic and most recent methods and applications in epigenomics, a branch of epigenetics that deals with the mechanisms such as DNA modifications, histone modifications, RNA modifications, small and long non-coding RNAs, chromatin remodeling, which are involved in epigenetic control of gene expression without involving variations in DNA sequences. These regulatory mechanisms lead to phenotypic variations. These epigenetic mechanisms can be exploited for crop improvement and cure of human diseases. Epigenomics strives to understand the role of epigenetic marks (chemical tags) in the development of phenotype. This understanding provides epigeneticists to apply epigenomics in medicine and agriculture. Self-explanatory adequately labelled figures have been the special emphasis throughout. This book is primarily designed for senior undergraduate and graduate level (M.Sc. and Ph.D.) students studying epigenetics in conventional, agricultural and medicinal universities. This book will be a useful reference text for teachers and researcher in any discipline of life sciences, agricultural sciences, medicine, and biotechnology. |
| atac-seq analysis pipeline: CpG Islands Tanya Vavouri, Miguel A. Peinado, 2018-04-01 This detailed volume examines bioinformatic and molecular biological methods useful to identify and to explore the functions of CpG islands, key navigation points to understand gene regulation in fundamental processes such as development and cell differentiation as well as in diseases like cancer. Beginning with a historical perspective and important properties of CpG islands, the book continues with sections on computational and wet lab methods related to the study of DNA methylation, and in-depth protocols for the analysis of CpG island functional features including epigenetic profiling and chromatin interactions. 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, CpG Islands: Methods and Protocols aims to provide readers with the information and methodologies necessary to continue to decipher how a genome’s structure and organization contribute to regulate biological processes. |
| atac-seq analysis pipeline: Gene Network Inference Alberto Fuente, 2014-01-03 This book presents recent methods for Systems Genetics (SG) data analysis, applying them to a suite of simulated SG benchmark datasets. Each of the chapter authors received the same datasets to evaluate the performance of their method to better understand which algorithms are most useful for obtaining reliable models from SG datasets. The knowledge gained from this benchmarking study will ultimately allow these algorithms to be used with confidence for SG studies e.g. of complex human diseases or food crop improvement. The book is primarily intended for researchers with a background in the life sciences, not for computer scientists or statisticians. |
| atac-seq analysis pipeline: Enhancers and Promoters Tilman Borggrefe, Benedetto Daniele Giaimo, 2021-09-09 This volume contains cutting-edge techniques to study the function of enhancers and promoters in depth. Chapters are divided into six sections and describe enhancer-promoter transcripts, nucleosome occupancy, DNA accessibility, chromatin interactions, protein-DNA interactions, functional analyses, and DNA methylation assays. Written in the Methods in Molecular Biology series format, chapters include comprehensive introductions, lists of the necessary materials and reagents, step-by-step laboratory protocols, and useful suggestions for troubleshooting. Authoritative and cutting-edge, Enhancers and Promoters: Methods and Protocols is a useful guide for future experiments. |
| atac-seq analysis pipeline: Environmental Genomics C. Cristofre Martin, 2008-01-18 Here is a manual for an environmental scientist who wishes to embrace genomics to answer environmental questions. The volume covers: gene expression profiling, whole genome and chromosome mutation detection, and methods to assay genome diversity and polymorphisms within a particular environment. This book provides a systematic framework for determining environmental impact and ensuring human health and the sustainability of natural populations. |
| atac-seq analysis pipeline: The Maize Genome Jeffrey Bennetzen, Sherry Flint-Garcia, Candice Hirsch, Roberto Tuberosa, 2018-11-24 This book discusses advances in our understanding of the structure and function of the maize genome since publication of the original B73 reference genome in 2009, and the progress in translating this knowledge into basic biology and trait improvement. Maize is an extremely important crop, providing a large proportion of the world’s human caloric intake and animal feed, and serving as a model species for basic and applied research. The exceptionally high level of genetic diversity within maize presents opportunities and challenges in all aspects of maize genetics, from sequencing and genotyping to linking genotypes to phenotypes. Topics covered in this timely book range from (i) genome sequencing and genotyping techniques, (ii) genome features such as centromeres and epigenetic regulation, (iii) tools and resources available for trait genomics, to (iv) applications of allele mining and genomics-assisted breeding. This book is a valuable resource for researchers and students interested in maize genetics and genomics. |
| atac-seq analysis pipeline: Whole-Body Regeneration Simon Blanchoud, Brigitte Galliot, 2022 This Open Access volume provides a comprehensive overview of the latest tools available to scientists to study the many facets of whole-body regeneration (WBR). The chapters in this book are organized into six parts. Part One provides a historical overview on the study of the WBR phenomena focusing on the primary challenges of this research. Parts Two and Three explore a series of non-vertebrate zoological contexts that provide experimental models for WBR, showing how they can be approached with cellular tools. Parts Four, Five, and Six discuss the future advancements of WBR, reporting about the cutting-edge techniques in genetics and omics used to dissect the underlying mechanisms of WBR, and systems biology approaches to reach a synthetic view of WBR. 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 thorough, Whole-Body Regeneration: Methods and Protocols is a valuable resource for scientists and researchers who want to learn more about this important and developing field. |
| atac-seq analysis pipeline: Alien Introgression in Wheat Márta Molnár-Láng, Carla Ceoloni, Jaroslav Doležel, 2015-11-20 This book provides an overview of the latest advancements in the field of alien introgression in wheat. The discovery and wide application of molecular genetic techniques including molecular markers, in situ hybridization, and genomics has led to a surge in interspecific and intergeneric hybridization in recent decades. The work begins with the taxonomy of cereals, especially of those species which are potential gene sources for wheat improvement. The text then goes on to cover the origin of wheat, breeding in connection with alien introgressions, and the problems of producing intergeneric hybrids and backcross derivatives. These problems can include crossability, sterility, and unequal chromosome transmission. The work then covers alien introgressions according to the related species used, as well as new results in the field of genomics of wild wheat relatives and introgressions. |
| atac-seq analysis pipeline: Toxicoepigenetics Shaun D. McCullough, Dana Dolinoy, 2018-11-02 Toxicoepigenetics: Core Principles and Applications examines the core aspects of epigenetics, including chromatin biology, DNA methylation, and non-coding RNA, as well as fundamental techniques and considerations for studying each of these mechanisms of epigenetic regulation. Although its integration into the field of toxicology is in its infancy, epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. Increasing the presence of epigenetics in toxicological research allows for a more in-depth understanding of important aspects of toxicology such as the role of the environment and lifestyle influencing the individual susceptibility to these effects and the trans-generational transmission of these health effects and susceptibilities. Methods chapters are included to help improve efficacy and efficiency of protocols in both the laboratory and the classroom. Toxicoepigenetics: Core Principles and Applications is an essential book for researchers and academics using epigenetics in toxicology research and study. - Introduces the fundamental principles and practices for understanding the role of the epigenome in toxicology - Presents the foundation of epigenetics for toxicologists with a broad range of backgrounds - Discusses the incorporation of epigenetics and epigenomics into current toxicological studies and interpretation of epigenetic data in toxicological applications |
| atac-seq analysis pipeline: Epigenetics in Human Disease Trygve O Tollefsbol, 2018-05-18 Epigenetics in Human Disease, Second Edition examines the diseases and conditions on which we have advanced knowledge of epigenetic mechanisms, such as cancer, autoimmune disorders, aging, metabolic disorders, neurobiological disorders and cardiovascular disease. In addition to detailing the role of epigenetics in the etiology, progression, diagnosis and prognosis of these diseases, novel epigenetic approaches to treatment are also explored. Fully revised and up-to-date, this new edition discusses topics of current interest in epigenetic research, including stem cell epigenetic therapy, bioinformatic analysis of NGS data, and epigenetic mechanisms of imprinting disorders. Further sections explore online epigenetic tools and datasets, early-life programming of epigenetics in age-related diseases, the epigenetics of addiction and suicide, and epigenetic approaches to regulating and preventing diabetes, cardiac disease, allergic disorders, Alzheimer's disease, respiratory diseases, and many other human maladies. - Includes contributions from leading international investigators involved in translational epigenetic research and therapeutic applications - Integrates methods and applications with fundamental chapters on epigenetics in human disease, along with an evaluation of recent clinical breakthroughs - Presents side-by-side coverage of the basis of epigenetic diseases and treatment pathways - Provides a fully revised resource covering current developments, including stem cell epigenetic therapy, the bioinformatic analysis of NGS data, epigenetic mechanisms of imprinting disorders, online epigenetic tools and datasets, and more |
什么是「ATAC-seq 技术」？现在用于哪些生物学研究？ - 知乎
ATAC-seq程序的优化也已广泛用于神经组织和生物样本库中的细胞。 ATAC-seq可以测量低至500个细胞的样品，但是它无法在单细胞水平上破译细胞之间的差异。单细胞测序技术的出现 …
什么是「ATAC-seq 技术」？现在用于哪些生物学研究？ - 知乎
atac思路：通过tn5转座酶（在染色质开放区域各种切割，形成复合物后插入到靶序列）来富集开放染色质的dna序列，pcr扩增后ngs测序。 官方一点的话：DNA转座，是一种把DNA序列从染色 …
atac-seq和chip-seq的区别？ - 知乎
ATAC-seq（Assay for Transposase – Accessible Chromatin with highthroughput sequencing），通过Tn5转座酶将测序接头插入染色质的开放区域，然后通过测序数据来推断 …
ATAC 或 chip-seq中peak 图，下方基因位置中方框、箭头代表什么 …
Oct 24, 2022 · 对每个区域进行ATAC-seq peaks检测。首先比较了多个大脑区域之间共有的可重复peaks基因组特征分布。发现区域特异性peaks通常分布基因间或内含子区域。同时，更保守 …
分析单细胞atac数据比较全面的工具是只有archar和signac麽？ - 知乎
Jan 12, 2023 · SnapATAC ：151次 Fang R, Preissl S, Li Y, et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC[J]. Nature communications, 2021, 12(1): 1-15. …
这种热图怎么看啊，求大神们解惑？ - 知乎
就是不同条件下，相关修饰和染色质开放程度(atac-seq)的水平比较。每一个柱子(不知道是不是恰当)的一条横线表示一个基因，中间表示TSS，颜色表示read映射到该位置的强度。为什么会 …
什么是「ATAC-seq 技术」？现在用于哪些生物学研究？ - 知乎
ATAC-seq程序的优化也已广泛用于神经组织和生物样本库中的细胞。 ATAC-seq可以测量低至500个细胞的样品，但是它无法在单细胞水平上破译细胞之间的差异。单细胞测序技术的出现 …
什么是「ATAC-seq 技术」？现在用于哪些生物学研究？ - 知乎
atac思路：通过tn5转座酶（在染色质开放区域各种切割，形成复合物后插入到靶序列）来富集开放染色质的dna序列，pcr扩增后ngs测序。 官方一点的话：DNA转座，是一种把DNA序列从染色 …
atac-seq和chip-seq的区别？ - 知乎
ATAC-seq（Assay for Transposase – Accessible Chromatin with highthroughput sequencing），通过Tn5转座酶将测序接头插入染色质的开放区域，然后通过测序数据来推断 …
ATAC 或 chip-seq中peak 图，下方基因位置中方框、箭头代表什么 …
Oct 24, 2022 · 对每个区域进行ATAC-seq peaks检测。首先比较了多个大脑区域之间共有的可重复peaks基因组特征分布。发现区域特异性peaks通常分布基因间或内含子区域。同时，更保守 …
分析单细胞atac数据比较全面的工具是只有archar和signac麽？ - 知乎
Jan 12, 2023 · SnapATAC ：151次 Fang R, Preissl S, Li Y, et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC[J]. Nature communications, 2021, 12(1): 1-15. …
这种热图怎么看啊，求大神们解惑？ - 知乎
就是不同条件下，相关修饰和染色质开放程度(atac-seq)的水平比较。每一个柱子(不知道是不是恰当)的一条横线表示一个基因，中间表示TSS，颜色表示read映射到该位置的强度。为什么会 …
