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Computational Molecular Biology

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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.

Deciphering the Ends of DNA

Molecular biologist Elizabeth Blackburn--one of Time magazine’s 100 “Most Influential People in the World” in 2007--made headlines in 2004 when she was dismissed from the President’s Council on Bioethics after objecting to the council’s call for a moratorium on stem cell research and protesting the suppression of relevant scientific evidence in its final report. But it is Blackburn’s groundbreaking work on telomeric DNA, which launched the field of telomere research, that will have the more profound and long-lasting effect on science and society.

Bridging Nonliving and Living Matter

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.

A Survey of Practical Models, Algorithms, and Numerical Methods

There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis.

From Concepts to Nuts and Bolts

Research in systems biology requires the collaboration of researchers from diverse backgrounds, including biology, computer science, mathematics, statistics, physics, and biochemistry. These collaborations, necessary because of the enormous breadth of background needed for research in this field, can be hindered by differing understandings of the limitations and applicability of techniques and concerns from different disciplines.

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