MSMS 6211, BCOR 5585 - Genomics
Course guide for Genomics (MSMS 6211, BCOR 5585)
Genomics
MSMS 6211, BCOR 5585
Fall 2024
The primary goal of this course is to introduce and describe the latest advances in molecular biology, genomics, computational biotechnology, and their interrelationships to all biology and human society through classroom and computer exercises. We will review milestone discoveries, which led to the rise of genomics science, characteristics of the wide spectrum of different genomes (prokaryotic, eukaryotic and organellar), and innovative molecular techniques and tools (e.g. high throughput DNA sequencing, CRISPRs) used to study and manipulate genomes. We will study genomes including their architecture in different organisms and the gene products that underlie development and basic metabolism. Genomics will also be viewed in the context of “Big Data” sets, and its integration with computational methods. The impact of genomics on human health (personalized medicine, diagnostics and new treatments to cure genetic diseases), ecology, ethical issues and problems will be discussed in depth.
Required Textbooks:
Genomes 5 by
Genomes 5 has been completely revised and updated. It is a thoroughly modern textbook about genomes and how they are investigated. As with previous Genomes editions, techniques come first, then genome anatomies, followed by genome function, and finally genome evolution. The genomes of all types of organism are covered: viruses, bacteria, fungi, plants, and animals, including humans and other hominids. Genome sequencing and assembly methods have been thoroughly revised to include new developments in long-read DNA sequencing. Coverage of genome annotation emphasizes genome-wide RNA mapping, with CRISPR-Cas 9 and GWAS methods of determining gene function covered. The knowledge gained from these techniques forms the basis of the chapters that describe the three main types of genomes: eukaryotic, prokaryotic (including eukaryotic organelles), and viral (including mobile genetic elements). Coverage of genome expression and replication is truly genomic, concentrating on the genome-wide implications of DNA packaging, epigenome modifications, DNA-binding proteins, non-coding RNAs, regulatory genome sequences, and protein-protein interactions. Also included are examples of the applications of metabolomics and systems biology. The final chapter is on genome evolution, including the evolution of the epigenome, using genomics to study human evolution, and using population genomics to advance plant breeding. Established methods of molecular biology are included if they are still relevant today and there is always an explanation as to why the method is still important. Genomes 5 is the ideal text for upper-level courses focused on genomes and genomics. Key Features A highly accessible and well-structured book with chapters organized into four parts to aid navigation Superb artwork illustrates the key concepts and mechanisms Each chapter has a set of short-answer questions and in-depth problems to test the reader's understanding of the material Thoroughly up to date with references to the latest research from the 2020s
Call Number: E-BOOKISBN: 9781000832280Publication Date: 2023-04-28
Genomes 5 by
Completely updated and rewritten, with 150 new figures Genomes from a wide variety of organisms included, from viruses to humans Techniques fully integrated into the text, including those investigating the genome, transcriptome, and proteome Coverage of expression, regulation, and evolution is on a genomic scale Short answer questions and in-depth problems at the end of each chapter Same structure as Genomes 3 but streamlined
Call Number: QH447 .B76 2023ISBN: 9780367674076Publication Date: 2023-04-28
Recommended Textbooks:
The Genome Generation by
The year 2001 marked the moment when scientists first read the 3 billion letters of DNA that make up the human genome. This breakthrough begged questions such as What have we learned about evolution? How has it changed the way we practice medicine, grow crops, and breed livestock? and Is the genomic revolution an overhyped flop? Answering these and many other queries, this account covers revolutionary genetic developments in areas as diverse as medicine, agriculture, and evolution. From Botswana to Boston and from Australia to Mexico, the contributors to this work reveal what it means to be part of the genome generation.
Call Number: QH447 .F56 2012ISBN: 9780522856477Publication Date: 2012-04-01
Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea by
Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea: Uncovering Buried Treasures and the Value of the Benthos examines marine benthic habitats around the world that are linked by their physical location at the bottom of the oceans. The book approaches deep sea marine biodiversity with perspectives on genetics, microbiology and evolution, weaving a narrative of vital expert linkages with the goal of protecting something that most people cannot witness or experience. It provides a full assessment of biological diversity within benthic habitats, from coral reefs to plankton and fish species, and offers global case studies. It is the ideal resource for marine conservationists and biologists aiming to expand their knowledge and efforts to the rarely seen, yet equally important, realms of the ocean and respective benthic species. As these deep-sea ecosystems and their species face unprecedented threats of destruction and extinction due to factors including climate change, this book provides the most current knowledge of this undersea world along with solutions for its conservation. Compares and contrasts between shallow and marine habitats to reveal revolutionary connections and continuity Analyzes modern threats and gaps in biological knowledge regarding benthic communities Examines benthic biodiversity through vertical vs. horizontal gradients Poses possible solutions for the conservation of benthic habitats and organisms
Call Number: E-BOOKISBN: 9780128241134Publication Date: 2023-11-30
Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea by
Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea: Uncovering Buried Treasures and the Value of the Benthos examines marine benthic habitats around the world that are linked by their physical location at the bottom of the oceans. The book approaches deep sea marine biodiversity with perspectives on genetics, microbiology and evolution, weaving a narrative of vital expert linkages with the goal of protecting something that most people cannot view or experience. Heterogeneity becomes operative across one of the largest continuous habitats of the planet. The book provides a full assessment of biological diversity within various benthic habitats, from coral reefs to plankton and fish species, and offers global case studies. It is the ideal resource for marine conservationists and biologists aiming to expand their knowledge and efforts to the rarely seen, yet equally important, realms of the ocean and respective benthic species. As deep-sea ecosystems and their species face unprecedented threats of disruption and extinction due to factors including disease, disinformation, pollution and climate change, this book provides current, sweeping knowledge of this undersea world along with remedies for its conservation.
Call Number: QH95.8 .L67 2024ISBN: 9780128241127Publication Date: 2023-12-04
A Primer of Genome Science by Call Number: QH447 .G534 2009ISBN: 9780878932368Publication Date: 2008-12-01
The Eighth Day of Creation: Makers of the Revolution in Biology, Commemorative Edition by
In this classic book, the distinguished science writer Horace Freeland Judson tells the story of the birth and early development of molecular biology in the US, the UK, and France. The fascinating story of the golden period from the revelation of the double helix of DNA to the cracking of the genetic code and first glimpses of gene regulation is told largely in the words of the main players, all of whom Judson interviewed extensively. The result is a book widely regarded as the best history of recent biological science yet published. This commemorative edition, honoring the memory of the author who died in 2011, contains essays by his daughter Olivia Judson, Matthew Meselson, and Mark Ptashne and an obituary by Jason Pontin. It contains all the content added to previous editions, including essays on some of the principal historical figures involved, such as Rosalind Franklin, and a sketch of the further development of molecular biology in the era of recombinant DNA.
Call Number: QH506 .J83 1996ISBN: 0879694785Publication Date: 1996-01-01
Evolutionary Genomics and Systems Biology by
A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. Evolutionary Genomics and Systems Biology is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology. Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams-macromolecular components in interaction-in the context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biology A special section on RNA biology-translation, evolution of structure, and micro RNA and regulation of gene expression Chapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and disease Contributions by leading authorities on each topic Evolutionary Genomics and Systems Biology is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.
Call Number: E-BOOKISBN: 9781282707535Publication Date: 2010-03-15
Bioinformatics and Functional Genomics by
The bestselling introduction to bioinformatics and genomics - now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research. This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: Extensive revisions and a slight reorder of chapters for a more effective organization A brand new chapter on next-generation sequencing An expanded companion website, also updated as and when new information becomes available Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations: www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.
Call Number: QH441.2 .P48 2015ISBN: 9781118581780Publication Date: 2015-10-26
Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past by Call Number: E-BOOKISBN: 9781101870334Publication Date: 2018
- Demonstrate proficient library and computer skills in data gathering and analysis.
- Analyze macromolecular sequences in the context of specific biological questions.
- Navigate and apply diverse, modern genetic databases and software to specific questions.
- Apply current bioinformatics and genomics methods to current organismal systems and problems.
- Prepare oral and written reports in an acceptable standard scientific format.
- Understand some of the larger questions and issues within genomics and large scale data collection and analysis.
- Learn to work and cooperate as part of an interdisciplinary team.
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