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Cancer Genomics

Cancer Genomics
  • Author : Graham Dellaire,Jason N Berman,Robert J. Arceci
  • Publisher :Unknown
  • Release Date :2013-11-21
  • Total pages :510
  • ISBN : 9780123972743
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Summary : Cancer Genomics addresses how recent technological advances in genomics are shaping how we diagnose and treat cancer. Built on the historical context of cancer genetics over the past 30 years, the book provides a snapshot of the current issues and state-of-the-art technologies used in cancer genomics. Subsequent chapters highlight how these approaches have informed our understanding of hereditary cancer syndromes and the diagnosis, treatment and outcome in a variety of adult and pediatric solid tumors and hematologic malignancies. The dramatic increase in cancer genomics research and ever-increasing availability of genomic testing are not without significant ethical issues, which are addressed in the context of the return of research results and the legal considerations underlying the commercialization of genomic discoveries. Finally, the book concludes with "Future Directions", examining the next great challenges to face the field of cancer genomics, namely the contribution of non-coding RNAs to disease pathogenesis and the interaction of the human genome with the environment. Tools such as sidebars, key concept summaries, a glossary, and acronym and abbreviation definitions make this book highly accessible to researchers from several fields associated with cancer genomics. Contributions from thought leaders provide valuable historical perspective to relate the advances in the field to current technologies and literature.

Cancer Genomics

Cancer Genomics
  • Author : Ulrich Pfeffer
  • Publisher :Unknown
  • Release Date :2013-02-12
  • Total pages :588
  • ISBN : 9789400758421
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Summary : The combination of molecular biology, engineering and bioinformatics has revolutionized our understanding of cancer revealing a tight correlation of the molecular characteristics of the primary tumor in terms of gene expression, structural alterations of the genome, epigenetics and mutations with its propensity to metastasize and to respond to therapy. It is not just one or a few genes, it is the complex alteration of the genome that determines cancer development and progression. Future management of cancer patients will therefore rely on thorough molecular analyses of each single case. Through this book, students, researchers and oncologists will obtain a comprehensive picture of what the first ten years of cancer genomics have revealed. Experts in the field describe, cancer by cancer, the progress made and its implications for diagnosis, prognosis and treatment of cancer. The deep impact on the clinics and the challenge for future translational research become evident.

Cancer Genomics for the Clinician

Cancer Genomics for the Clinician
  • Author : Ramaswamy Govindan, MD,Ashiq Masood, MD
  • Publisher :Unknown
  • Release Date :2019-01-28
  • Total pages :184
  • ISBN : 9780826168689
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Summary : Cancer Genomics for the Clinician is a practical guide to cancer genomics and its application to cancer diagnosis and care. The book begins with a brief overview of the various types of genetic alterations that are encountered in cancer, followed by accessible and applicable information on next generation sequencing technology and bioinformatics; tumor heterogeneity; whole genome, exome, and transcriptome sequencing; epigenomics; and data analysis and interpretation. Each chapter provides essential explanations of concepts, terminology, and methods. Also included are tips for interpreting and analyzing molecular data, as well as a discussion of molecular predictors for targeted therapies covering hematologic malignancies and solid tumors. The final chapter explains the use of FDA-approved genomic-based targeted therapies for breast cancer, lung cancer, sarcomas, gastrointestinal cancers, urologic cancers, head and neck cancer, thyroid cancer, and many more. Assembled in an accessible format specifically designed for the non-expert, this book provides the clinical oncologist, early career practitioner, and trainee with an essential understanding of the molecular and genetic basis of cancer and the clinical aspects that have led to advancements in diagnosis and treatment. With this resource, physicians and trainees will increase their breadth of knowledge and be better equipped to educate patients and families who want to know more about their genetic predispositions to cancer and the targeted therapies that could be considered and prescribed. Key Features: Describes how cancer genomics and next generation sequencing informs cancer screening, risk factors, therapeutic options, and clinical management across cancer types Explains what mutations are, what tests are needed, and how to interpret the results Provides information on FDA-approved targeted therapies that are being used in the clinic Covers different sequencing platforms and technologies and how they perform in research settings Includes access to the fully searchable eBook

Cancer Genomics

Cancer Genomics
  • Author : Katayoon Kasaian,Yvonne Y. Li,Steven J.M. Jones
  • Publisher :Unknown
  • Release Date :2013-11-21
  • Total pages :510
  • ISBN : 9780128061060
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Summary : Advances in high-throughput sequencing technologies have enabled cost-effective sequencing of a single human genome at an unprecedented rate, facilitating scientific endeavours never imagined possible before. These improvements have transformed the field of cancer genomics, allowing the complete molecular characterization of individual cancer genomes. However, the promise of unveiling the complexity of cancer has lent itself to yet another level of complexity, the task of managing and integrating the massive amount of data that is generated as part of such experiments. There is a need to manage and store large sequence datasets such that they can be accessed and shared readily but, more importantly, there is a need for their thorough and efficient analysis. Developments and improvements in computer hardware and processing power have eliminated the data storage and access issues. Additionally, bioinformatic algorithms and software, designed specifically for the analysis of cancer genomic data, are now able comprehensively to profile the mutations in a cancer sample, to provide a probability score for their role as disease drivers and to identify potential actionable targets. Although the functional validation of putative driver mutations will remain a necessity, continued improvements in sequencing technologies and analysis tools promise to provide increasingly reliable computational analysis of cancer genomes.

Cancer Genetics and Genomics for Personalized Medicine

Cancer Genetics and Genomics for Personalized Medicine
  • Author : Il-Jin Kim
  • Publisher :Unknown
  • Release Date :2017-04-11
  • Total pages :286
  • ISBN : 9781315341101
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Summary : This book covers almost all fields of cancer genetics and genomics for personalized medicine. Targeted therapy, or precision medicine, or personalized medicine is becoming a standard treatment for many diseases, including cancer. However, how much do we know about the personalized medicine approach? This lucid book helps undergraduate and graduate students, professional researchers, and clinicians to better understand the key concept of personalized medicine. The most up-to-date topics on personalized medicine in this book cover the recent trends in and updates on lung, gastric, liver, breast, and other types of cancers. Circulating tumor cell, cell-free circulating DNA, and microRNAs are discussed as new diagnostic and prognostic markers for cancer. The avatar mouse model is also discussed for maximizing treatment efficacy and prognosis prediction, and so is microenvironment as a drug resistance mechanism. With classical and new pathological approaches, the book provides a systemic overview of personalized immunotherapies and hyperthermic intraperitoneal chemotherapy, followed by new emerging fields of hereditary cancer, thereby equipping readers to eventually contribute in developing more advanced tools and therapies for curing cancer.

'Essentials of Cancer Genomic, Computational Approaches and Precision Medicine

'Essentials of Cancer Genomic, Computational Approaches and Precision Medicine
  • Author : Nosheen Masood,Saima Shakil Malik
  • Publisher :Unknown
  • Release Date :2020-03-20
  • Total pages :499
  • ISBN : 9789811510670
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Summary : This book concisely describes the role of omics in precision medicine for cancer therapies. It outlines our current understanding of cancer genomics, shares insights into the process of oncogenesis, and discusses emerging technologies and clinical applications of cancer genomics in prognosis and precision-medicine treatment strategies. It then elaborates on recent advances concerning transcriptomics and translational genomics in cancer diagnosis, clinical applications, and personalized medicine in oncology. Importantly, it also explains the importance of high-performance analytics, predictive modeling, and system biology in cancer research. Lastly, the book discusses current and potential future applications of pharmacogenomics in clinical cancer therapy and cancer drug development.

Collaborative Genomics Projects: A Comprehensive Guide

Collaborative Genomics Projects: A Comprehensive Guide
  • Author : Margi Sheth,Julia Zhang,Jean C Zenklusen
  • Publisher :Unknown
  • Release Date :2016-02-24
  • Total pages :142
  • ISBN : 9780128023686
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Summary : Collaborative Genomics Projects: A Comprehensive Guide contains operational procedures, policy considerations, and the many lessons learned by The Cancer Genome Atlas Project. This book guides the reader through methods in patient sample acquisition, the establishment of data generation and analysis pipelines, data storage and dissemination, quality control, auditing, and reporting. This book is essential for those looking to set up or collaborate within a large-scale genomics research project. All authors are contributors to The Cancer Genome Atlas (TCGA) Program, a NIH- funded effort to generate a comprehensive catalog of genomic alterations in more than 35 cancer types. As the cost of genomic sequencing is decreasing, more and more researchers are leveraging genomic data to inform the biology of disease. The amount of genomic data generated is growing exponentially, and protocols need to be established for the long-term storage, dissemination, and regulation of this data for research. The book's authors create a complete handbook on the management of research projects involving genomic data as learned through the evolution of the TCGA program, a project that was primarily carried out in the US, but whose impact and lessons learned can be applied to international audiences. Establishes a framework for managing large-scale genomic research projects involving multiple collaborators Describes lessons learned through TCGA to prepare for potential roadblocks Evaluates policy considerations that are needed to avoid pitfalls Recommends strategies to make project management more efficient

Cancer Genome and Tumor Microenvironment

Cancer Genome and Tumor Microenvironment
  • Author : Andrei Thomas-Tikhonenko
  • Publisher :Unknown
  • Release Date :2010-01-23
  • Total pages :480
  • ISBN : 1441907114
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Summary : Oncogenes and tumor suppressor genes had been traditionally studied in the context of cell proliferation, differentiation, senescence, and survival, four relatively cell-autonomous processes. Consequently, in the late ’80s-early ’90s, neoplastic growth was described largely as an imbalance between net cell accumulation and loss, brought about through mutations in cancer genes. In the last ten years, a more holistic understanding of cancer has slowly emerged, stressing the importance of interactions between neoplastic and various stromal components: extracellular matrix, basement membranes, fibroblasts, endothelial cells of blood and lymphatic vessels, tumor-infiltrating lymphocytes, etc. The commonly held view is that changes in tumor microenvironment are “soft-wired”, i.e., epigenetic in nature and often reversible. Yet, there exists a large body of evidence suggesting that well-known mutations in cancer genes profoundly affect tumor milieu. In fact, these non-cell-autonomous changes might be one of the primary reasons such mutations are preserved in late-stage tumors.

Cancer Genomics and Proteomics

Cancer Genomics and Proteomics
  • Author : Paul B. Fisher
  • Publisher :Unknown
  • Release Date :2007-09-27
  • Total pages :358
  • ISBN : 1588295044
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Summary : Cancer Genomics and Proteomics provides a compendium of techniques and applications in gene identification and function. The approaches described in detail are state-of-the art and can be tailored to individual ongoing or planned research projects. This volume is a valuable laboratory resource for designing experiments to identify and analyze genes that are relevant to complex biological phenomena.

Cancer Genomics

Cancer Genomics
  • Author : Ryan D. Morin,Stephen B. Montgomery
  • Publisher :Unknown
  • Release Date :2013-11-21
  • Total pages :510
  • ISBN : 9780128061008
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Summary : Identifying gene expression changes in cancer provides opportunities to identify biomarkers that can be informative in regard to risk and in the choice of treatment options. In recent years, advances in sequencing have provided not only a quantitative measure of gene expression, but the resolution of diverse species of RNA, alternative transcripts and allele-specific expression. As well, such data have revealed novel sequences such as those from pathogens, mutations resulting in amino acid differences and fusion transcripts resulting from translocations and other structural alterations, each of which can inform the development of novel treatment strategies or potential preventive measures. In this chapter, we will discuss how transcriptome sequencing is conducted and analyzed and provide examples that illustrate its utility in studying cancer samples.

Cancer Genomics and Proteomics

Cancer Genomics and Proteomics
  • Author : Narendra Wajapeyee
  • Publisher :Unknown
  • Release Date :2016-09-17
  • Total pages :262
  • ISBN : 1493946544
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Summary : Cancer Genomics and Proteomics: Methods and Protocols, Second Edition includes methods for the analyses of cancer genome and proteome that have illuminated us about the changes in cancer cells. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Cancer Genomics and Proteomics: Methods and Protocols, Second Edition seeks to aid scientists in the further study into various aspects of tumor initiation and progression.

Genomics

Genomics
  • Author : Julian Parkhill,Sarah J. Lindsay,Phil Jones,Lia Chappell,Jonathon Roberts,Nancy Holroyd,Michal Spzak,Francesca (Wellcome Sanger Institute) Gale
  • Publisher :Unknown
  • Release Date :2020-04-15
  • Total pages :200
  • ISBN : 9780198848387
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Summary : This Oxford Biology Primer will introduce students to the field of genomics and its applications. From the early days of the Human Genome Project, sequencing technology has rapidly developed and is now cheaper and more accessible than ever before. The resulting pervasive nature of these technologies make them more likely to be experienced by people as patients, consumers and citizens. The primer introduces the basic principles of genomics and then uses these to consider human genetics, through examples of some of the rare diseases linked to single genes. The impact of these rare diseases is far-reaching and the knowledge gained through genome sequencing is proving invaluable in their diagnosis. Genome sequencing is revolutionising the diagnosis and treatment of cancer, and the primer introduces students to some of the key breakthroughs which have taken place in recent years. These include the identification of specific genes indicating cancer risk, and the sequencing of tumours throughout treatment to identify further mutations and modify treatment accordingly. The primer aims to address a number of the ethical issues which are raised by this rapidly-growing area of biology. Students are challenged to consider some of the decisions they may need to make relating to these technologies in their own lives, and are given opportunities to explore different aspects of these issues in a way which allows discussion to be both informed and meaningful. The study of infectious disease is also feeling the impact of genomics: the primer discusses the concept of pathogen genome sequencing, and illustrates the various ways in which this can be used - for example, enabling us to find different solutions to infections, to track outbreaks of disease to their source, and to identify and possibly ultimately combat antibiotic resistance. Many of the major diseases which impact the global population are caused by parasites, which come in a wide variety of shapes and sizes. The primer introduces students to the importance of understanding parasite genomes. Parasite genome sequencing makes it possible to develop both new medicines, and new treatments such as gene drive systems to wipe out disease-causing mosquito populations. For many years, our views of classification and evolution have been based on observational techniques going back to Darwin and Linnaeus. Focusing on human evolution, the primer will open students' eyes to the ways in which genome sequencing is being used to reveal evolutionary links that have never before been recognised, and to elucidate the way humans spread out of Africa across the world. Students are not always aware of the role technological developments play in enabling the progress of science. The final chapter delves into how genome sequencing technologies have developed, considering both the speed of change in the technology, its implications for usefulness, availability and cost, and the growing issue of big data and how it can be manipulated. The different technologies described in this chapter are referenced throughout the book.

Cancer Genomics

Cancer Genomics
  • Author : Jason N. Berman,Priscilla P.L. Chiu,Graham Dellaire
  • Publisher :Unknown
  • Release Date :2013-11-21
  • Total pages :510
  • ISBN : 9780128061053
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Summary : Genome-wide association (GWA) studies and tumor-specific epigenome, transcriptome and genome sequencing projects are generating an ever-growing list of susceptibility alleles, as well as putative gain- and loss-of-function gene mutations associated with cancer. These genetic changes ultimately need to be validated to determine their contribution to the initiation, progression and likelihood of treatment response for various cancers. The bottle-neck is no longer obtaining sequence data or completion of the GWA studies, but rather the ability efficiently to validate candidate genes identified by these projects. In vivo studies in animal models are the “gold standard” for validation of these candidate drivers and modifiers of cancer. Furthermore, once a gene product or molecular pathway has been validated as playing an important role in the development or progression of cancer, animal models provide the necessary preclinical data for evaluation of the efficacy and toxicity of new therapeutics targeting that gene or pathway. As such, animal models play an essential role in cancer research by facilitating the translation of genomic discoveries into preclinical studies that precede new targeted therapies for cancer. In this chapter, we will discuss vertebrate and invertebrate animal models as they apply to cancer genomics, as well as key technologies employed. In particular, we will focus on the use of murine and zebrafish human tumor xenografts and transgenic models.

Genomic and Precision Medicine

Genomic and Precision Medicine
  • Author : Geoffrey S. Ginsburg,Huntington F Willard,Sean P. David
  • Publisher :Unknown
  • Release Date :2017-03-30
  • Total pages :370
  • ISBN : 9780128006542
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Summary : Genomic and Precision Medicine: Primary Care, Third Edition is an invaluable resource on the state-of-the-art tools, technologies and policy issues that are required to fully realize personalized health care in the area of primary care. One of the major areas where genomic and personalized medicine is most active is the realm of the primary care practitioner. Risk, family history, personal genomics and pharmacogenomics are becoming increasingly important to the PCP and their patients, and this book discusses the implications as they relate to primary care practitioners. Presents a comprehensive volume for primary care providers Provides succinct commentary and key learning points that will assist providers with their local needs for the implementation of genomic and personalized medicine Includes a current overview on major opportunities for genomic and personalized medicine in practice Highlights case studies that illustrate the practical use of genomics in the management in patients

Cancer Genomics

Cancer Genomics
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2001
  • Total pages :82
  • ISBN : 6000003595
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Summary : This work states that we are no longer satisfied to study a gene or gene product in isolation, but rather we strive to view each gene within the complex circuitry of a cell. It states that as a family of diseases, all cancer results from changes in the genome.

Healthcare and Artificial Intelligence

Healthcare and Artificial Intelligence
  • Author : Bernard Nordlinger,Cédric Villani,Daniela Rus
  • Publisher :Unknown
  • Release Date :2020-03-17
  • Total pages :279
  • ISBN : 9783030321611
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Summary : This book provides an overview of the role of AI in medicine and, more generally, of issues at the intersection of mathematics, informatics, and medicine. It is intended for AI experts, offering them a valuable retrospective and a global vision for the future, as well as for non-experts who are curious about this timely and important subject. Its goal is to provide clear, objective, and reasonable information on the issues covered, avoiding any fantasies that the topic “AI” might evoke. In addition, the book seeks to provide a broad kaleidoscopic perspective, rather than deep technical details.

Clinical Genomics

Clinical Genomics
  • Author : Shashikant Kulkarni,John Pfeifer
  • Publisher :Unknown
  • Release Date :2014-11-10
  • Total pages :488
  • ISBN : 9780124051737
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Summary : Clinical Genomics provides an overview of the various next-generation sequencing (NGS) technologies that are currently used in clinical diagnostic laboratories. It presents key bioinformatic challenges and the solutions that must be addressed by clinical genomicists and genomic pathologists, such as specific pipelines for identification of the full range of variants that are clinically important. This book is also focused on the challenges of diagnostic interpretation of NGS results in a clinical setting. Its final sections are devoted to the emerging regulatory issues that will govern clinical use of NGS, and reimbursement paradigms that will affect the way in which laboratory professionals get paid for the testing. Simplifies complexities of NGS technologies for rapid education of clinical genomicists and genomic pathologists towards genomic medicine paradigm Tried and tested practice-based analysis for precision diagnosis and treatment plans Specific pipelines and meta-analysis for full range of clinically important variants

Cancer Genomics

Cancer Genomics
  • Author : Robert L. Strausberg
  • Publisher :Unknown
  • Release Date :2002
  • Total pages :120
  • ISBN : 1586032518
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Summary : This volume explores the genomics of cancer. Contributions explain how advances in biomedical research in the 1990s launched the genomics era - we are no longer satisfied to study a gene or gene product in isolation, but rather we strive to view each gene within the complex circuitry of a cell. In rapid succession, this mindset has invigorated the analysis of all molecular entities, from the genome, to transcripts (transciptome) and proteins (proteome).

Precision Cancer Medicine

Precision Cancer Medicine
  • Author : Sameek Roychowdhury,Eliezer M. Van Allen
  • Publisher :Unknown
  • Release Date :2020-01-02
  • Total pages :196
  • ISBN : 9783030236373
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Summary : Genomic sequencing technologies have augmented the classification of cancer beyond tissue of origin and towards a molecular taxonomy of cancer. This has created opportunities to guide treatment decisions for individual patients with cancer based on their cancer’s unique molecular characteristics, also known as precision cancer medicine. The purpose of this text will be to describe the contribution and need for multiple disciplines working together to deliver precision cancer medicine. This entails a multi-disciplinary approach across fields including molecular pathology, computational biology, clinical oncology, cancer biology, drug development, genetics, immunology, and bioethics. Thus, we have outlined a current text on each of these fields as they work together to overcome various challenges and create opportunities to deliver precision cancer medicine. As trainees and junior faculty enter their respective fields, this text will provide a framework for understanding the role and responsibility for each specialist to contribute to this team science approach.

Big Data Analytics in Genomics

Big Data Analytics in Genomics
  • Author : Ka-Chun Wong
  • Publisher :Unknown
  • Release Date :2016-10-24
  • Total pages :428
  • ISBN : 9783319412795
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Summary : This contributed volume explores the emerging intersection between big data analytics and genomics. Recent sequencing technologies have enabled high-throughput sequencing data generation for genomics resulting in several international projects which have led to massive genomic data accumulation at an unprecedented pace. To reveal novel genomic insights from this data within a reasonable time frame, traditional data analysis methods may not be sufficient or scalable, forcing the need for big data analytics to be developed for genomics. The computational methods addressed in the book are intended to tackle crucial biological questions using big data, and are appropriate for either newcomers or veterans in the field.This volume offers thirteen peer-reviewed contributions, written by international leading experts from different regions, representing Argentina, Brazil, China, France, Germany, Hong Kong, India, Japan, Spain, and the USA. In particular, the book surveys three main areas: statistical analytics, computational analytics, and cancer genome analytics. Sample topics covered include: statistical methods for integrative analysis of genomic data, computation methods for protein function prediction, and perspectives on machine learning techniques in big data mining of cancer. Self-contained and suitable for graduate students, this book is also designed for bioinformaticians, computational biologists, and researchers in communities ranging from genomics, big data, molecular genetics, data mining, biostatistics, biomedical science, cancer research, medical research, and biology to machine learning and computer science. Readers will find this volume to be an essential read for appreciating the role of big data in genomics, making this an invaluable resource for stimulating further research on the topic.

Computational Genomics with R

Computational Genomics with R
  • Author : Altuna Akalin
  • Publisher :Unknown
  • Release Date :2020-11-26
  • Total pages :462
  • ISBN : 1498781853
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Summary : 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.