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The human brain can be organized using various different layers of information about the cells: epigenetic, genomic, transcriptomic, proteomic, etc. Recent endeavors have put tremendous effort into mapping the brain cell-by-cell using these layers of information. A challenge associated with these multi-modal approaches is being able to parse through the giga- to terabyte scale amount of data that is generated. My thesis work has focused on investigating the diversity of the brain's genome (DNA) and transcriptome (RNA) and developing bioinformatic tools to make that possible. My work can be broken into two general categories, addressing the genome and the transcriptome. On the genomic side, I focused on identifying novel features known as gencDNAs (genomic cDNAs). gencDNAs are hypothesized to result from transcription of a highly expressed gene which is then spliced, reverse-transcribed, and inserted back into the genome at the site of a DNA strand break. These novel sequences are predicted to be functional, resulting in additional translation of a protein. APP, the amyloid precursor protein gene, was the first gene to be identified as a gencDNA and was determined to be more prevalent in neurons of Alzheimer's disease (AD) patient brains. I developed an unbiased approach to identify additional gencDNAs in the genome from short-read sequencing data. The transcriptome can be studied at various resolutions. Through several projects, I examined gene expression at the single-cell level, and I additionally characterized full-length isoforms using long-read sequencing technologies. Recent advances in sequencing have made it possible to sequence the entire lengths of mRNA transcripts. This technology is relatively new, and bioinformatic tools need to be developed to handle this type of data. While several packages and tools exist for quality control, alignment, reduction of redundancy, and annotation, a tool for comparing isoforms (known and novel) across multiple samples and groups is not available. I made a database-driven tool for this purpose that is compatible with current analysis pipelines. The applications of this software were demonstrated by examining a dataset from the 1000 Genomes Project in addition to a large single-cell dataset investigating gene and isoform expression changes in several neurodegenerative diseases.
Medical Imaging Informatics provides an overview of this growing discipline, which stems from an intersection of biomedical informatics, medical imaging, computer science and medicine. Supporting two complementary views, this volume explores the fundamental technologies and algorithms that comprise this field, as well as the application of medical imaging informatics to subsequently improve healthcare research. Clearly written in a four part structure, this introduction follows natural healthcare processes, illustrating the roles of data collection and standardization, context extraction and modeling, and medical decision making tools and applications. Medical Imaging Informatics identifies core concepts within the field, explores research challenges that drive development, and includes current state-of-the-art methods and strategies.
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
Transcriptome analysis is the study of the transcriptome, of the complete set of RNA transcripts that are produced under specific circumstances, using high-throughput methods. Transcription profiling, which follows total changes in the behavior of a cell, is used throughout diverse areas of biomedical research, including diagnosis of disease, biomarker discovery, risk assessment of new drugs or environmental chemicals, etc. Transcriptome analysis is most commonly used to compare specific pairs of samples, for example, tumor tissue versus its healthy counterpart. In this volume, Dr. Pyo Hong discusses the role of long RNA sequences in transcriptome analysis, Dr. Shinichi describes the next-generation single-cell sequencing technology developed by his team, Dr. Prasanta presents transcriptome analysis applied to rice under various environmental factors, Dr. Xiangyuan addresses the reproductive systems of flowering plants and Dr. Sadovsky compares codon usage in conifers.
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Heritable human genome editing - making changes to the genetic material of eggs, sperm, or any cells that lead to their development, including the cells of early embryos, and establishing a pregnancy - raises not only scientific and medical considerations but also a host of ethical, moral, and societal issues. Human embryos whose genomes have been edited should not be used to create a pregnancy until it is established that precise genomic changes can be made reliably and without introducing undesired changes - criteria that have not yet been met, says Heritable Human Genome Editing. From an international commission of the U.S. National Academy of Medicine, U.S. National Academy of Sciences, and the U.K.'s Royal Society, the report considers potential benefits, harms, and uncertainties associated with genome editing technologies and defines a translational pathway from rigorous preclinical research to initial clinical uses, should a country decide to permit such uses. The report specifies stringent preclinical and clinical requirements for establishing safety and efficacy, and for undertaking long-term monitoring of outcomes. Extensive national and international dialogue is needed before any country decides whether to permit clinical use of this technology, according to the report, which identifies essential elements of national and international scientific governance and oversight.
Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.
This volume provides an introduction to the essential techniques required for studying the molecular biology of brain disease. The approaches and strategies for investigations of gene structure and regulation are described with reference to the molecular genetics of prion and Alzheimer's disease. The effects of aberrant gene regulation can also be examined at the protein level by immunocytochemistry and autoradiography. Improved understanding of basic biology has resulted in new approaches to animal models using transgenic techniques and new therapeutic approaches. The volume is structured to illustrate all these approaches and demonstrate the practice and promise of molecular neuropathology.
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.
Recent advances in drug discovery have been rapid. The second edition of Bioinformatics and Drug Discovery has been completely updated to include topics that range from new technologies in target identification, genomic analysis, cheminformatics, protein analysis, and network or pathway analysis. Each chapter provides an extended introduction that describes the theory and application of the technology. In the second part of each chapter, detailed procedures related to the use of these technologies and software have been incorporated. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Bioinformatics and Drug Discovery, Second Edition seeks to aid scientists in the further study of the rapidly expanding field of drug discovery.