In this book, Dan Gusfield examines combinatorial algorithms to construct genealogical and exact phylogenetic networks, particularly ancestral recombination graphs (ARGs). The algorithms produce networks (or information about networks) that serve as hypotheses about the true genealogical history of observed biological sequences and can be applied to practical biological problems.
Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology.
The introduction of high-throughput methods has transformed biology into a data-rich science. Knowledge about biological entities and processes has traditionally been acquired by thousands of scientists through decades of experimentation and analysis. The current abundance of biomedical data is accompanied by the creation and quick dissemination of new information. Much of this information and knowledge, however, is represented only in text form--in the biomedical literature, lab notebooks, Web pages, and other sources.
Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules.
Biomedical signal analysis has become one of the most important visualization and interpretation methods in biology and medicine. Many new and powerful instruments for detecting, storing, transmitting, analyzing, and displaying images have been developed in recent years, allowing scientists and physicians to obtain quantitative measurements to support scientific hypotheses and medical diagnoses. This book offers an overview of a range of proven and new methods, discussing both theoretical and practical aspects of biomedical signal analysis and interpretation.
Computational systems biology aims to develop algorithms that uncover the structure and parameterization of the underlying mechanistic model—in other words, to answer specific questions about the underlying mechanisms of a biological system—in a process that can be thought of as learning or inference. This volume offers state-of-the-art perspectives from computational biology, statistics, modeling, and machine learning on new methodologies for learning and inference in biological networks.
Issues of regulation and control are central to the study of biological and biochemical systems. Thus it is not surprising that the tools of feedback control theory—engineering techniques developed to design and analyze self-regulating systems—have proven useful in the study of these biological mechanisms. Such interdisciplinary work requires knowledge of the results, tools and techniques of another discipline, as well as an understanding of the culture of an unfamiliar research community.
From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs dramatically, and the mutations that affect this organization are known as genome rearrangements. Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems.
Recent research in molecular biology has produced a remarkably detailed understanding of how living things operate. Becoming conversant with the intricacies of molecular biology and its extensive technical vocabulary can be a challenge, though, as introductory materials often seem more like a barrier than an invitation to the study of life.
Protocells offers a comprehensive resource on current attempts to create simple forms of life from scratch in the laboratory. These minimal versions of cells, known as protocells, are entities with lifelike properties created from nonliving materials, and the book provides in-depth investigations of processes at the interface between nonliving and living matter. Chapters by experts in the field put this state-of-the-art research in the context of theory, laboratory work, and computer simulations on the components and properties of protocells.