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Bioinformatics
"In this book, Andy Baxevanis and Francis Ouellette . . . haveundertaken the difficult task of organizing the knowledge in thisfield in a logical progression and presenting it in a digestibleform. And they have done an excellent job. This fine text will makea major impact on biological research and, in turn, on progress inbiomedicine. We are all in their debt." —Eric Lander from the Foreword Reviews from the First Edition "...provides a broad overview of the basic tools for sequenceanalysis ... For biologists approaching this subject for the firsttime, it will be a very useful handbook to keep on the shelf afterthe first reading, close to the computer." —Nature Structural Biology "...sho...
The Proteomics Protocols Handbook
Hands-on researchers describe in step-by-step detail 73 proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and post-translational modification. There are also readily reproducible methods for protein expression profiling, identifying protein-protein interactions, and protein chip technology, as well as a range of newly developed methodologies for determining the structure and function of a protein. The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. All laboratory-based protocols follow the successful Methods in Molecular BiologyTM series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
Handbook of Cell Signaling, Three-Volume Set
The Handbook of Cell Signaling is a comprehensive work covering all aspects of intracellular signal processing, including extra/intracellular membrane receptors, signal transduction, gene expression/translation, and cellular/organotypic signal responses. The subject matter has been divided into five main parts (each of which is headed by a recognized expert in the field):* Initiation: Extracellular and Membrane Events* Transmission: Effectors and Cytosolic Events * Nuclear Responses: Gene Expression and Translation* Events in Intracellular Compartments* Cell-Cell and Cell-Matrix Interactions Covered in extensive detail, these areas will appeal to a broad, cross-disciplinary audience interest...
Biological Network Analysis
Biological Network Analysis: Trends, Approaches, Graph Theory, and Algorithms considers three major biological networks, including Gene Regulatory Networks (GRN), Protein-Protein Interaction Networks (PPIN), and Human Brain Connectomes. The book's authors discuss various graph theoretic and data analytics approaches used to analyze these networks with respect to available tools, technologies, standards, algorithms and databases for generating, representing and analyzing graphical data. As a wide variety of algorithms have been developed to analyze and compare networks, this book is a timely resource.
Natural Language Processing in the Real World
Natural Language Processing in the Real World is a practical guide for applying data science and machine learning to build Natural Language Processing (NLP) solutions. Where traditional, academic-taught NLP is often accompanied by a data source or dataset to aid solution building, this book is situated in the real world where there may not be an existing rich dataset. This book covers the basic concepts behind NLP and text processing and discusses the applications across 15 industry verticals. From data sources and extraction to transformation and modelling, and classic Machine Learning to Deep Learning and Transformers, several popular applications of NLP are discussed and implemented. This book provides a hands-on and holistic guide for anyone looking to build NLP solutions, from students of Computer Science to those involved in large-scale industrial projects.
Data Integration in the Life Sciences
This book constitutes the refereed proceedings of the First International Workshop on Data Integration in the Life Sciences, DILS 2004, held in Leipzig, Germany, in March 2004. The 13 revised full papers and 2 revised short papers presented were carefully reviewed and selected from many submissions. The papers are organized in topical sections on scientific and clinical workflows, ontologies and taxonomies, indexing and clustering, integration tools and systems, and integration techniques.
Handbook of Systems Biology
This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress...
Visual Insights
A guide to the basics of information visualization that teaches nonprogrammers how to use advanced data mining and visualization techniques to design insightful visualizations. In the age of Big Data, the tools of information visualization offer us a macroscope to help us make sense of the avalanche of data available on every subject. This book offers a gentle introduction to the design of insightful information visualizations. It is the only book on the subject that teaches nonprogrammers how to use open code and open data to design insightful visualizations. Readers will learn to apply advanced data mining and visualization techniques to make sense of temporal, geospatial, topical, and net...
Data Management of Protein Interaction Networks
Current PPI databases do not offer sophisticated querying interfaces and especially do not integrate existing information about proteins. Current algorithms for PIN analysis use only topological information, while emerging approaches attempt to exploit the biological knowledge related to proteins and kinds of interaction, e.g. protein function, localization, structure, described in Gene Ontology or PDB. The book discusses technologies, standards and databases for, respectively, generating, representing and storing PPI data. It also describes main algorithms and tools for the analysis, comparison and knowledge extraction from PINs. Moreover, some case studies and applications of PINs are also discussed.
Be sparse! Be dense! Be robust!
In this thesis we study the computational complexity of five NP-hard graph problems. It is widely accepted that, in general, NP-hard problems cannot be solved efficiently, that is, in polynomial time, due to many unsuccessful attempts to prove the contrary. Hence, we aim to identify properties of the inputs other than their length, that make the problem tractable or intractable. We measure these properties via parameters, mappings that assign to each input a nonnegative integer. For a given parameter k, we then attempt to design fixed-parameter algorithms, algorithms that on input q have running time upper bounded by f(k(q)) * |q|^c , where f is a preferably slowly growing function, |q| is t...
