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Computational Biology (Methods in Molecular Biology #673)
by David FenyöComputational biology is an interdisciplinary field that applies mathematical, statistical, and computer science methods to answer biological questions, and its importance has only increased with the introduction of high-throughput techniques such as automatic DNA sequencing, comprehensive expression analysis with microarrays, and proteome analysis with modern mass spectrometry. In Computational Biology, expert practitioners present a broad survey of computational biology methods by focusing on their applications, including primary sequence analysis, protein structure elucidation, transcriptomics and proteomics data analysis, and exploration of protein interaction networks. As a volume in the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results. Authoritative and easy to use, Computational Biology is an ideal guide for all scientists interested in quantitative biology.
Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology (Methods in Molecular Biology #2553)
by Kumar SelvarajooThis volume provides protocols for computational, statistical, and machine learning methods that are mainly applied to the study of metabolic engineering, synthetic biology, and disease applications. These techniques support the latest progress in cross-disciplinary research that integrates the different scales of biological complexity. The topics covered in this book are geared toward researchers with a background in engineering, computational analytical, and modeling experience and cover a broad range of topics in computational and machine learning approaches. 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.Comprehensive and practical, Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology is a valuable resource for any researcher or scientist who wants to learn more about the latest computational methods and how they are applied toward the understanding and prediction of complex biology.
Computational Biology of Non-Coding RNA: Methods and Protocols (Methods in Molecular Biology #1912)
by Julio Vera Xin Lai Shailendra K. GuptaThis volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. 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, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.
Computational Biology of Non-Coding RNA: Methods and Protocols (Methods in Molecular Biology #2883)
by Xin Lai Shailendra Gupta Julio Vera GonzalezThis second edition details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. 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, Computational Biology of Non-Coding RNA: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.
Computational Biology of Transcription Factor Binding (Methods in Molecular Biology #674)
by Istvan LadungaThrough great experimental difficulty, we've witnessed rapid, crucial developments at the intersection of computational biology, experimental technology, and statistics through which the vital process of transcriptional regulation can be further examined. In Computational Biology of Transcription Factor Binding, experts in the field examine the basic principles and provide detailed guidance for the computational analyses and biological interpretations of transcription factor binding, while disclosing critical practical information and caveats that are missing from many research publications. The volume serves not only computational biologists but experimentalists as well, who may want to better understand how to design and execute experiments and to communicate more effectively with computational biologists, computer scientists, and statisticians. Written for the highly successful Methods in Molecular BiologyTM series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results in the lab. Authoritative and easy to use, Computational Biology of Transcription Factor Binding guides scientists working in this area and demands not only new experiments but also the re-annotation of existing experimental data and computational predictions leading to important ongoing, major paradigm changes for us all.
Computational Biology: A Hypertextbook (ASM Books)
by Dennis Didulo Scott KelleyAn introduction to the world of bioinformatics Massive increases in computing power and the ability to routinely sequence whole genomes of living organisms have begun to fundamentally alter our understanding of biology, medicine, and agriculture. At the intersection of the growing information and genomics revolutions sits bioinformatics, which uses modern computational power to reveal patterns in biological data sets, especially DNA, RNA, and protein sequences. Computational Biology: A Hypertextbook, by Scott Kelley and Dennis Didulo, provides a wonderful introduction for anyone who wants to learn the basics of bioinformatics. This book is more than a textbook because of the wealth of online ancillary materials and how the print and electronic components are integrated to form a complete educational resource. Aspects that make Computational Biology: A Hypertextbook a unique and valuable tool for teaching and learning bioinformatics include Clear explanations of the basic biology of DNA, RNA, and proteins and how the related bioinformatics algorithms work Extensive exercises that enable students to practice with the same bioinformatics applications that are used by scientists worldwide Tutorials, sample data sets, and interactive learning tools developed with teachers in mind and field-tested by hundreds of students Online tutorials and curated web links that are accurate (instead of frustrating!) and won't lead to dead ends Online resources that work on multiple platforms and electronic devices Computational Biology: A Hypertextbook is written in an accessible voice, punctuated with humor, and designed to significantly increase computational competencies. Biology and computer science undergraduate and graduate students will thoroughly enjoy learning from this unique hypertextbook, as will anyone with an interest in exploring this burgeoning topic.
Computational Biology: A Practical Introduction to Bio Data Juggling with Worked Examples
by Röbbe WünschiersThis extensively expanded third edition offers a practical introduction to Bio Data Science. With a hands-on approach to learning, this book offers ample opportunities to practice: - Installing and utilizing Linux as a virtual machine or remotely - Processing bio data with the programming language AWK - Managing data with the relational database system MariaDB - Analyzing and visualizing data with R - Implementing good bioinformatics practices with Jupyter Notebook and GitHub This book targets both students and professionals in the life sciences. While it is aimed at beginners, it also provides valuable tips and tricks for experienced researchers dealing with large datasets. Worked examples illustrate how to utilize various bioinformatics tools such as BLAST, Clustal, PLINK, IGV, SAMtools, BCFtools, Mason2, Minimap, NCBI Datasets, Velvet, Jmol, and more for: - Identifying bacterial proteins potentially associated with pathogenicity - Querying molecular structures for redox-regulated enzymes - Mapping and assembling real or simulated sequence reads - Identifying and mapping molecular structure mutations in viruses - Conducting genome-wide association studies All software tools and datasets mentioned are freely available, and all code is accessible as Jupyter Notebooks on GitHub. Drawing from the author's experiences and knowledge gained from both academia and industry, this book provides a practical and comprehensive approach to bioinformatics.
Computational Biology: A Practical Introduction to BioData Processing and Analysis with Linux, MySQL, and R
by Röbbe WünschiersThis greatly expanded 2nd edition provides a practical introduction to - data processing with Linux tools and the programming languages AWK and Perl- data management with the relational database system MySQL, and- data analysis and visualization with the statistical computing environment R for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for - finding proteins potentially causing pathogenicity in bacteria, - supporting the significance of BLAST with homology modeling, or- detecting candidate proteins that may be redox-regulated, on the basis of their structure.All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author's experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.
Computational Biology: A Statistical Mechanics Perspective, Second Edition (Chapman & Hall/CRC Computational Biology Series)
by Ralf BlosseyComputational biology has developed rapidly during the last two decades following the genomic revolution which culminated in the sequencing of the human genome. More than ever it has developed into a field which embraces computational methods from different branches of the exact sciences: pure and applied mathematics, computer science, theoretical physics. This Second Edition provides a solid introduction to the techniques of statistical mechanics for graduate students and researchers in computational biology and biophysics. Material has been reorganized to clarify equilbrium and nonequilibrium aspects of biomolecular systems Content has been expanded, in particular in the treatment of the electrostatic interactions of biomolecules and the application of non-equilibrium statistical mechanics to biomolecules New network-based approaches for the study of proteins are presented. All treated topics are put firmly in the context of the current research literature, allowing the reader to easily follow an individual path into a specific research field. Exercises and Tasks accompany the presentations of the topics with the intention of enabling the readers to test their comprehension of the developed basic concepts.
Computational Biomechanics for Medicine: Challenges and Solutions in Computing (Lecture Notes in Bioengineering)
by Karol Miller Adam Wittek Poul M. F. Nielsen Martyn P. Nash Magdalena Kobielarz Anju R. BabuThis book presents peer-reviewed contributions from the MICCAI 2023 Computational Biomechanics for Medicine CBM XVIII Workshop held in conjunction with the 26th International MICCAI Conference. The content focuses on applications of computational biomechanics to computer-integrated medicine, which includes medical image computing, application of machine learning in image analysis and biomechanics, atlas based biomechanical simulations, novel algorithms of computational biomechanics and experimental methods for analysis of disease and injury mechanisms. The book details state-of-the-art progress in the above fields to researchers, students, and professionals.
Computational Biomechanics for Medicine: Deformation and Flow
by Poul M.F. Nielsen Karol Miller Adam WittekOne of the greatest challenges for mechanical engineers is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. This book is an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine.<P><P> Computational Biomechanics for Medicine: Deformation and Flow collects the papers from the Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2011) dedicated to research in the field of medical image computing and computer assisted medical interventions. The topics covered include: medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, injury mechanism analysis, implant and prostheses design, and medical robotics.
Computational Biomechanics for Medicine: From Algorithms to Models and Applications
by Poul M.F. Nielsen Karol Miller Adam Wittek Barry J. Doyle Grand JoldesMathematical modelling and computer simulation have proved tremendously successful in engineering. One of the greatest challenges for mechanists is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. The proposed workshop will provide an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine. For example, continuum mechanics models provide a rational basis for analysing biomedical images by constraining the solution to biologically reasonable motions and processes. Biomechanical modelling can also provide clinically important information about the physical status of the underlying biology, integrating information across molecular, tissue, organ, and organism scales. The main goal of this workshop is to showcase the clinical and scientific utility of computational biomechanics in computer-integrated medicine.
Computational Biomechanics for Medicine: Fundamental Science and Patient-specific Applications
by Karol Miller Adam Wittek Barry Doyle Poul M. F. NielsenOne of the greatest challenges facing the computational engineering community is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, the biomedical sciences and medicine. The Computational Biomechanics for Medicine series provides an opportunity for specialists in computational biomechanics to present their latest methodologies and advancements. This 5th edition comprises nine of the latest developments in both fundamental science and patient-specific applications, from researchers in Australia, New Zealand, USA, UK, France, Ireland and China. Some of the interesting topics discussed are: cellular mechanics; tumor growth and modeling; medical image analysis and both patient-specific fluid dynamics and solid mechanics simulations.
Computational Biomechanics for Medicine: Imaging, Modeling and Computing
by Poul M.F. Nielsen Karol Miller Adam Wittek Barry Doyle Grand R. JoldesThe Computational Biomechanics for Medicine titles provide an opportunity for specialists in computational biomechanics to present their latest methodologies and advancements. This volume comprises eighteen of the newest approaches and applications of computational biomechanics, from researchers in Australia, New Zealand, USA, UK, Switzerland, Scotland, France and Russia. Some of the interesting topics discussed are: tailored computational models; traumatic brain injury; soft-tissue mechanics; medical image analysis; and clinically-relevant simulations. <P><P>One of the greatest challenges facing the computational engineering community is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, the biomedical sciences, and medicine. We hope the research presented within this book series will contribute to overcoming this grand challenge.
Computational Biomechanics for Medicine: Models, Algorithms And Implementation
by Karol Miller Adam Wittek Barry Doyle Poul M. F. Nielsen Grand R. Joldes Martyn P. NashThis volume comprises the latest developments in both fundamental science and patient-specific applications, discussing topics such as: cellular mechanics, injury biomechanics, biomechanics of the heart and vascular system, algorithms of computational biomechanics for medical image analysis, and both patient-specific fluid dynamics and solid mechanics simulations. With contributions from researchers world-wide, Computational Biomechanics for Medicine: Measurments, Models, and Predictions provides an opportunity for specialists in the field to present their latest methodologies and advancements.
Computational Biomechanics for Medicine: Models, Algorithms And Implementation
by Poul M.F. Nielsen Karol MillerMathematical modelling and computer simulation have proved tremendously successful in engineering. One of the greatest challenges for mechanists is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. The proposed workshop will provide an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine. For example, continuum mechanics models provide a rational basis for analysing biomedical images by constraining the solution to biologically reasonable motions and processes. Biomechanical modelling can also provide clinically important information about the physical status of the underlying biology, integrating information across molecular, tissue, organ, and organism scales. The main goal of this workshop is to showcase the clinical and scientific utility of computational biomechanics in computer-integrated medicine.
Computational Biomechanics for Medicine: New Approaches and New Applications
by Karol Miller Adam Wittek Barry Doyle Poul M. F. NielsenOne of the greatest challenges facing the computational engineering community is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, the biomedical sciences and medicine. The Computational Biomechanics for Medicine series provides an opportunity for specialists in computational biomechanics to present their latest methodologies and advancements. This 5th edition comprises nine of the latest developments in both fundamental science and patient-specific applications, from researchers in Australia, New Zealand, USA, UK, France, Ireland and China. Some of the interesting topics discussed are: cellular mechanics; tumor growth and modeling; medical image analysis and both patient-specific fluid dynamics and solid mechanics simulations.
Computational Biomechanics for Medicine: Personalisation, Validation and Therapy
by Karol Miller Adam Wittek Poul M. F. Nielsen Grand R. Joldes Martyn P. NashThis book contains contributions from computational biomechanics specialists who present and exchange opinions on the opportunities for applying their techniques to computer-integrated medicine, including computer-aided surgery and diagnostic systems. Computational Biomechanics for Medicine collects peer-reviewed chapters from the annual Computational Biomechanics for Medicine Workshop, in conjunction with the Medical Image Computing and Computer Assisted Intervention [MICCAI] Society conference. The works are dedicated to research in the field of methods and applications of computational biomechanics to medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease diagnosis and prognosis, analysis of injury mechanisms, implant and prosthesis design, artificial organ design, and medical robotics. These chapters will appeal to a wide range of researchers and students within the fields of engineering and medicine, as well as those working in computational science.
Computational Biomechanics for Medicine: Progress in Research and Applications (Lecture Notes in Bioengineering)
by Karol Miller Adam Wittek Martyn P. Nash Poul Nielsen Magdalena Kobielarz Anju R. BabuThis book presents contributions from the MICCAI 2024 Computational Biomechanics for Medicine Workshop CBM XIX. The peer-reviewed chapters of the book were presented during the 27th International Conference on Medical Image Computing and Computer Assisted Intervention MICCAI held in Marrakesh, Morocco. The content focuses on applications of computational biomechanics to computer-integrated medicine, which includes medical image computing, application of machine learning in image analysis and biomechanics, new approaches to stress computing for biomechanics of soft tissues and evaluation of strain, new assumptions to computing pipelines for disease and injury mechanisms, novel algorithms of computational biomechanics, a unique application of artificial intelligence and neural network in computing and experimental methods for the analysis of disease and injury mechanisms. This book details the state-of-the-art and progress in above mentioned scientific fields for researchers, students, and professionals.
Computational Biomechanics for Medicine: Soft Tissues and the Musculoskeletal System
by Poul M.F. Nielsen Karol Miller Adam WittekOne of the greatest challenges for mechanical engineers is to extend the success of computational mechanics to fields outside traditional engineering, in particular to biology, biomedical sciences, and medicine. The proposed workshop will provide an opportunity for computational biomechanics specialists to present and exchange opinions on the opportunities of applying their techniques to computer-integrated medicine. <P><P> Computational Biomechanics for Medicine: Soft Tissues and the Musculoskeletal System collects the papers from the Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2010) in Beijing, dedicated to research in the field of medical image computing and computer assisted medical interventions. The topics covered include: medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, injury mechanism analysis, implant and prostheses design, medical robotics.
Computational Biomechanics for Medicine: Solid and Fluid Mechanics Informing Therapy
by Karol Miller Adam Wittek Poul M. F. Nielsen Martyn NashComputational Biomechanics for Medicine: Solid and fluid mechanics for the benefit of patients contributions and papers from the MICCAI Computational Biomechanics for Medicine Workshop help in conjunction with Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2020) in Lima, Peru. The content is dedicated to research in the field of methods and applications of computational biomechanics to medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book appeals to researchers, students and professionals in the field.
Computational Biomechanics for Medicine: Solid and Fluid Mechanics for the Benefit of Patients
by Karol Miller Adam Wittek Poul M. F. Nielsen Grand Joldes Martyn P. NashComputational Biomechanics for Medicine: Solid and fluid mechanics for the benefit of patients contributions and papers from the MICCAI Computational Biomechanics for Medicine Workshop help in conjunction with Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2019) in Shenzhen, China. The content is dedicated to research in the field of methods and applications of computational biomechanics to medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. These proceedings appeal to researchers, students and professionals in the field.
Computational Biomechanics for Medicine: Towards Automation and Robustness of Computations in the Clinic
by Karol Miller Adam Wittek Poul M. F. Nielsen Martyn P. Nash Magdalena Kobielarz Anju R. BabuThis book presents contributions from the MICCAI 2022 Computational Biomechanics for Medicine Workshop. "Computational Biomechanics for Medicine - towards translation and better patient outcomes” comprises papers accepted for the MICCAI Computational Biomechanics for Medicine Workshop held in 2022 in Singapore. The content focuses on applications of computational biomechanics to computer-integrated medicine, which includes MICCAI topics of Medical Image Computing, Computer-Aided Modeling and Evaluation of Surgical Procedures, and Imaging, Analysis Methods for Image Guided Therapies, Computational Physiology, and Medical Robotics. Specific topics covered include medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book details state-of-the-art progress in the above fields to researchers, students, and professionals.
Computational Biomechanics for Medicine: Towards Translation and Better Patient Outcomes
by Karol Miller Adam Wittek Poul M. F. Nielsen Martyn P. Nash Xinshan LiThis book presents contributions from the MICCAI 2021 Computational Biomechanics for Medicine Workshop. "Computational Biomechanics for Medicine - towards translation and better patient outcomes” comprises papers accepted for the MICCAI Computational Biomechanics for Medicine Workshop held virtually in conjunction with Medical Image Computing and Computer Assisted Intervention conference 2021, based in Strasbourg. The content focuses on methods and applications of computational biomechanics to medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book details state-of-the-art progress in the above fields to researchers, students, and professionals.
Computational Biomechanics of the Musculoskeletal System
by Ming Zhang Yubo FanComputational biomechanics is an emerging research field that seeks to understand the complex biomechanical behaviors of normal and pathological human joints to come up with new methods of orthopedic treatment and rehabilitation.Computational Biomechanics of the Musculoskeletal System collects the latest research and cutting-edge techniques used in