Download or read book Computational Analysis of Biomolecular Data for Medical Applications from Bulk to Single cell written by Kaiyi Zhu and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput technologies have continuously driven the generation of different biomolecular data, including the genomics, epigenomics, transcriptomics, and other omics data in the last two decades. The developments and advances have revolutionized medical research. In this dissertation, a collection of computational analyses and tools, based on different types of biomolecular data with particular applications on human diseases are presented including 1) a cascade ensemble model based on the Dirichlet process mixture model for reconstructing tumor subclonality from tumor DNA sequencing data; 2) a meta-analysis of gene expression and DNA methylation data from prefrontal cortex samples of patients with neuropsychiatric disorders indicating a stress-related epigenetic mechanism; 3) 2DImpute, an imputation algorithm that is designed to alleviate the sparsity problem in single-cell RNA-sequencing data; and 4) a pan-cancer transformation from adipose-derived stromal cells to metastasis-associated fibroblasts revealed by single cell analysis.

Download or read book Bioinformatics Analysis of Single Cell Sequencing Data and Applications in Precision Medicine written by Jialiang Yang and published by Frontiers Media SA. This book was released on 2020-02-27 with total page 136 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Discovering Biomolecular Mechanisms with Computational Biology written by Frank Eisenhaber and published by Springer Science & Business Media. This book was released on 2007-03-20 with total page 152 pages. Available in PDF, EPUB and Kindle. Book excerpt: This anthology presents critical reviews of methods and high-impact applications in computational biology that lead to results that non-bioinformaticians must also know to design efficient experimental research plans. Discovering Biomolecular Mechanisms with Computational Biology explores the methodology of translating sequence strings into biological knowledge and considers exemplary groundbreaking results such as unexpected enzyme discoveries. This book also summarizes non-trivial theoretical predictions for regulatory and metabolic networks that have received experimental confirmation.

Download or read book Computational Medicine written by Zlatko Trajanoski and published by Springer. This book was released on 2016-08-23 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational methodologies and modeling play a growing role for investigating mechanisms, and for the diagnosis and therapy of human diseases. This progress gave rise to computational medicine, an interdisciplinary field at the interface of computer science and medicine. The main focus of computational medicine lies in the development of data analysis methods and mathematical modeling as well as computational simulation techniques specifically addressing medical problems. In this book, we present a number of computational medicine topics at several scales: from molecules to cells, organs, and organisms. At the molecular level, tools for the analysis of genome variations as well as cloud computing resources for medical genetics are reviewed. Then, an analysis of gene expression data and the application to the characterization of microbial communities are highlighted. At the protein level, two types of analyses for mass spectrometry data are reviewed: labeled quantitative proteomics and lipidomics, followed by protein sequence analysis and a 3D structure and drug design chapter. Finally, three chapters on clinical applications focus on the integration of biomolecular and clinical data for cancer research, biomarker discovery, and network-based methods for computational diagnostics.

Download or read book Research Awards Index written by and published by . This book was released on 1977 with total page 1368 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Introduction to Single Cell Omics written by Xinghua Pan and published by Frontiers Media SA. This book was released on 2019-09-19 with total page 129 pages. Available in PDF, EPUB and Kindle. Book excerpt: Single-cell omics is a progressing frontier that stems from the sequencing of the human genome and the development of omics technologies, particularly genomics, transcriptomics, epigenomics and proteomics, but the sensitivity is now improved to single-cell level. The new generation of methodologies, especially the next generation sequencing (NGS) technology, plays a leading role in genomics related fields; however, the conventional techniques of omics require number of cells to be large, usually on the order of millions of cells, which is hardly accessible in some cases. More importantly, harnessing the power of omics technologies and applying those at the single-cell level are crucial since every cell is specific and unique, and almost every cell population in every systems, derived in either vivo or in vitro, is heterogeneous. Deciphering the heterogeneity of the cell population hence becomes critical for recognizing the mechanism and significance of the system. However, without an extensive examination of individual cells, a massive analysis of cell population would only give an average output of the cells, but neglect the differences among cells. Single-cell omics seeks to study a number of individual cells in parallel for their different dimensions of molecular profile on genome-wide scale, providing unprecedented resolution for the interpretation of both the structure and function of an organ, tissue or other system, as well as the interaction (and communication) and dynamics of single cells or subpopulations of cells and their lineages. Importantly single-cell omics enables the identification of a minor subpopulation of cells that may play a critical role in biological process over a dominant subpolulation such as a cancer and a developing organ. It provides an ultra-sensitive tool for us to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. Besides, it also empowers the clinical investigation of patients when facing a very low quantity of cell available for analysis, such as noninvasive cancer screening with circulating tumor cells (CTC), noninvasive prenatal diagnostics (NIPD) and preimplantation genetic test (PGT) for in vitro fertilization. Single-cell omics greatly promotes the understanding of life at a more fundamental level, bring vast applications in medicine. Accordingly, single-cell omics is also called as single-cell analysis or single-cell biology. Within only a couple of years, single-cell omics, especially transcriptomic sequencing (scRNA-seq), whole genome and exome sequencing (scWGS, scWES), has become robust and broadly accessible. Besides the existing technologies, recently, multiplexing barcode design and combinatorial indexing technology, in combination with microfluidic platform exampled by Drop-seq, or even being independent of microfluidic platform but using a regular PCR-plate, enable us a greater capacity of single cell analysis, switching from one single cell to thousands of single cells in a single test. The unique molecular identifiers (UMIs) allow the amplification bias among the original molecules to be corrected faithfully, resulting in a reliable quantitative measurement of omics in single cells. Of late, a variety of single-cell epigenomics analyses are becoming sophisticated, particularly single cell chromatin accessibility (scATAC-seq) and CpG methylation profiling (scBS-seq, scRRBS-seq). High resolution single molecular Fluorescence in situ hybridization (smFISH) and its revolutionary versions (ex. seqFISH, MERFISH, and so on), in addition to the spatial transcriptome sequencing, make the native relationship of the individual cells of a tissue to be in 3D or 4D format visually and quantitatively clarified. On the other hand, CRISPR/cas9 editing-based In vivo lineage tracing methods enable dynamic profile of a whole developmental process to be accurately displayed. Multi-omics analysis facilitates the study of multi-dimensional regulation and relationship of different elements of the central dogma in a single cell, as well as permitting a clear dissection of the complicated omics heterogeneity of a system. Last but not the least, the technology, biological noise, sequence dropout, and batch effect bring a huge challenge to the bioinformatics of single cell omics. While significant progress in the data analysis has been made since then, revolutionary theory and algorithm logics for single cell omics are expected. Indeed, single-cell analysis exert considerable impacts on the fields of biological studies, particularly cancers, neuron and neural system, stem cells, embryo development and immune system; other than that, it also tremendously motivates pharmaceutic RD, clinical diagnosis and monitoring, as well as precision medicine. This book hereby summarizes the recent developments and general considerations of single-cell analysis, with a detailed presentation on selected technologies and applications. Starting with the experimental design on single-cell omics, the book then emphasizes the consideration on heterogeneity of cancer and other systems. It also gives an introduction of the basic methods and key facts for bioinformatics analysis. Secondary, this book provides a summary of two types of popular technologies, the fundamental tools on single-cell isolation, and the developments of single cell multi-omics, followed by descriptions of FISH technologies, though other popular technologies are not covered here due to the fact that they are intensively described here and there recently. Finally, the book illustrates an elastomer-based integrated fluidic circuit that allows a connection between single cell functional studies combining stimulation, response, imaging and measurement, and corresponding single cell sequencing. This is a model system for single cell functional genomics. In addition, it reports a pipeline for single-cell proteomics with an analysis of the early development of Xenopus embryo, a single-cell qRT-PCR application that defined the subpopulations related to cell cycling, and a new method for synergistic assembly of single cell genome with sequencing of amplification product by phi29 DNA polymerase. Due to the tremendous progresses of single-cell omics in recent years, the topics covered here are incomplete, but each individual topic is excellently addressed, significantly interesting and beneficial to scientists working in or affiliated with this field.

Download or read book Gene Expression Studies Using Affymetrix Microarrays written by Hinrich Gohlmann and published by Chapman and Hall/CRC. This book was released on 2009-07-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Affymetrix GeneChip® system is one of the most widely adapted microarray platforms. However, due to the overwhelming amount of information available, many Affymetrix users tend to stick to the default analysis settings and may end up drawing sub-optimal conclusions. Written by a molecular biologist and a biostatistician with a combined decade of experience in practical expression profiling experiments and data analyses, Gene Expression Studies Using Affymetrix Microarrays tears down the omnipresent language barriers among molecular biology, bioinformatics, and biostatistics by explaining the entire process of a gene expression study from conception to conclusion. Truly Multidisciplinary: Merges Molecular Biology, Bioinformatics, and Biostatistics This authoritative resource covers important technical and statistical pitfalls and problems, helping not only to explain concepts outside the domain of researchers, but to provide additional guidance in their field of expertise. The book also describes technical and statistical methods conceptually with illustrative, full-color examples, enabling those inexperienced with gene expression studies to grasp the basic principles. Gene Expression Studies Using Affymetrix Microarrays provides novices with a detailed, yet focused introductory course and practical user guide. Specialized experts will also find it useful as a translation dictionary to understand other involved disciplines or to get a broader picture of microarray gene expression studies in general. Although focusing on Affymetrix gene expression, this globally relevant guide covers topics that are equally useful for other microarray platforms and other Affymetrix applications.

Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.

Download or read book Bioinformatics Computing written by Bryan P. Bergeron and published by Prentice Hall Professional. This book was released on 2003 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive and concise, this handbook has chapters on computing visualization, large database designs, advanced pattern matching and other key bioinformatics techniques. It is a practical guide to computing in the growing field of Bioinformatics--the study of how information is represented and transmitted in biological systems, starting at the molecular level.

Download or read book Systems Genetics written by Florian Markowetz and published by Cambridge University Press. This book was released on 2015-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.

Download or read book The Science and Applications of Synthetic and Systems Biology written by Institute of Medicine and published by National Academies Press. This book was released on 2011-12-30 with total page 570 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Download or read book Feature Engineering Made Easy written by Sinan Ozdemir and published by Packt Publishing Ltd. This book was released on 2018-01-22 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: A perfect guide to speed up the predicting power of machine learning algorithms Key Features Design, discover, and create dynamic, efficient features for your machine learning application Understand your data in-depth and derive astonishing data insights with the help of this Guide Grasp powerful feature-engineering techniques and build machine learning systems Book Description Feature engineering is the most important step in creating powerful machine learning systems. This book will take you through the entire feature-engineering journey to make your machine learning much more systematic and effective. You will start with understanding your data—often the success of your ML models depends on how you leverage different feature types, such as continuous, categorical, and more, You will learn when to include a feature, when to omit it, and why, all by understanding error analysis and the acceptability of your models. You will learn to convert a problem statement into useful new features. You will learn to deliver features driven by business needs as well as mathematical insights. You'll also learn how to use machine learning on your machines, automatically learning amazing features for your data. By the end of the book, you will become proficient in Feature Selection, Feature Learning, and Feature Optimization. What you will learn Identify and leverage different feature types Clean features in data to improve predictive power Understand why and how to perform feature selection, and model error analysis Leverage domain knowledge to construct new features Deliver features based on mathematical insights Use machine-learning algorithms to construct features Master feature engineering and optimization Harness feature engineering for real world applications through a structured case study Who this book is for If you are a data science professional or a machine learning engineer looking to strengthen your predictive analytics model, then this book is a perfect guide for you. Some basic understanding of the machine learning concepts and Python scripting would be enough to get started with this book.

Download or read book RNA Seq Analysis Methods Applications and Challenges written by Filippo Geraci and published by Frontiers Media SA. This book was released on 2020-06-08 with total page 169 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Diagnostics Promises and Possibilities written by Mousumi Debnath and published by Springer Science & Business Media. This book was released on 2010-01-29 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt: A rapid development in diverse areas of molecular biology and genetic engineering resulted in emergence of variety of tools. These tools are not only applicable to basic researches being carried out world over, but also exploited for precise detection of abnormal conditions in plants, animals and human body. Although a basic researcher is well versed with few techniques used by him/her in the laboratory, they may not be well acquainted with methodologies, which can be used to work out some of their own research problems. The picture is more blurred when the molecular diagnostic tools are to be used by physicians, scientists and technicians working in diagnostic laboratories in hospitals, industry and academic institutions. Since many of them are not trained in basics of these methods, they come across several gray areas in understanding of these tools. The accurate application of molecular diagnostic tools demands in depth understanding of the methodology for precise detection of the abnormal condition of living body. To meet the requirements of a good book on molecular diagnostics of students, physicians, scientists working in agricultural, veterinary, medical and pharmaceutical sciences, it needs to expose the reader lucidly to: Give basic science behind commonly used tools in diagnostics Expose the readers to detailed applications of these tools and Make them aware the availability of such diagnostic tools The book will attract additional audience of pathologists, medical microbiologists, pharmaceutical sciences, agricultural scientists and veterinary doctors if the following topics are incorporated at appropriate places in Unit II or separately as a part of Unit-III in the book. Molecular diagnosis of diseases in agricultural crops Molecular diagnosis of veterinary diseases. Molecular epidemiology, which helps to differentiate various epidemic strains and sources of disease outbreaks. Even in different units of the same hospital, the infections could be by different strains of the same species and the information becomes valuable for infection control strategies. Drug resistance is a growing problem for bacterial, fungal and parasitic microbes and the molecular biology tools can help to detect the drug resistance genes without the cultivation and in vitro sensitivity testing. Molecular diagnostics offers faster help in the selection of the proper antibiotic for the treatment of tuberculosis, which is a major problem of the in the developing world. The conventional culture and drug sensitivity testing of tuberculosis bacilli is laborious and time consuming, whereas molecular diagnosis offers rapid drug resistant gene detection even from direct clinical samples. The same approach for HIV, malaria and many more diseases needs to be considered. Molecular diagnostics in the detection of diseases during foetal life is an upcoming area in the foetal medicine in case of genetic abnormalities and infectious like TORCH complex etc. The book will be equally useful to students, scientists and professionals working in the field of molecular diagnostics.

Download or read book Cardiac Regeneration written by Masaki Ieda and published by Springer. This book was released on 2017-10-27 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Volume of the series Cardiac and Vascular Biology offers a comprehensive and exciting, state-of-the-art work on the current options and potentials of cardiac regeneration and repair. Several techniques and approaches have been developed for heart failure repair: direct injection of cells, programming of scar tissue into functional myocardium, and tissue-engineered heart muscle support. The book introduces the rationale for these different approaches in cell-based heart regeneration and discusses the most important considerations for clinical translation. Expert authors discuss when, why, and how heart muscle can be salvaged. The book represents a valuable resource for stem cell researchers, cardiologists, bioengineers, and biomedical scientists studying cardiac function and regeneration.

Download or read book Omics Technologies and Bio engineering written by Debmalya Barh and published by Academic Press. This book was released on 2017-12-01 with total page 645 pages. Available in PDF, EPUB and Kindle. Book excerpt: Omics Technologies and Bio-Engineering: Towards Improving Quality of Life, Volume 1 is a unique reference that brings together multiple perspectives on omics research, providing in-depth analysis and insights from an international team of authors. The book delivers pivotal information that will inform and improve medical and biological research by helping readers gain more direct access to analytic data, an increased understanding on data evaluation, and a comprehensive picture on how to use omics data in molecular biology, biotechnology and human health care. - Covers various aspects of biotechnology and bio-engineering using omics technologies - Focuses on the latest developments in the field, including biofuel technologies - Provides key insights into omics approaches in personalized and precision medicine - Provides a complete picture on how one can utilize omics data in molecular biology, biotechnology and human health care

Download or read book Dynamic Force Spectroscopy and Biomolecular Recognition written by Anna Rita Bizzarri and published by CRC Press. This book was released on 2012-01-25 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular recognition, also known as biorecognition, is the heart of all biological interactions. Originating from protein stretching experiments, dynamic force spectroscopy (DFS) allows for the extraction of detailed information on the unbinding process of biomolecular complexes. It is becoming progressively more important in biochemical studies and is finding wider applications in areas such as biophysics and polymer science. In six chapters, Dynamic Force Spectroscopy and Biomolecular Recognition covers the most recent ideas and advances in the field of DFS applied to biorecognition: Chapter 1: Reviews the basic and novel aspects of biorecognition and discusses the emerging capabilities of single-molecule techniques to disclose kinetic properties and molecular mechanisms usually hidden in bulk measurements Chapter 2: Describes the basic principle of atomic force microsocopy (AFM) and DFS, with particular attention to instrumental and theoretical aspects more strictly related to the study of biomolecules Chapter 3: Overviews the theoretical background in which experimental data taken in nonequilibrum measurements of biomolecular unbinding forces are extrapolated to equilibrium conditions Chapter 4: Reviews the most common and efficient strategies adopted in DFS experiments to immobilize the interacting biomolecules to the AFM tip and to the substrate Chapter 5: Presents and discusses the most representative aspects related to the analysis of DFS data and the challenges of integrating well-defined criteria to calibrate data in automatic routinary procedures Chapter 6: Overviews the most relevant DFS applications to study biorecognition processes, including the biotin/avidin pair, and selected results on various biological complexes, including antigen/antibody, proteins/DNA, and complexes involved in adhesion processes Chapter 7: Summarizes the main results obtained by DFS applied to study biorecognition processes with forthcoming theoretical and experimental advances Although DFS is a widespread, worldwide technique, no books focused on this subject have been available until now. Dynamic Force Spectroscopy and Biomolecular Recognition provides the state of the art of experimental data analysis and theoretical procedures, making it a useful tool for researchers applying DFS to study biorecognition processes.