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Analysis and Control of Cellular Ensembles. Exploiting dimensionality reduction in single-cell data and models
An ensemble system is a collection of nearly identical dynamical systems which admit a certain degree of heterogeneity, and which are subject to the restriction that they may only be manipulated or observed as a whole. This thesis presents analysis and control methods for cellular ensembles by considering reduced 1-dimensional dynamics of biological processes in high-dimensional single-cell data and models. To be more specific, we address the quest for real-time analysis of biological processes within single-cell data by introducing the measure-preserving map of pseudotime into real-time, in short MAPiT. MAPiT enables the reconstruction of temporal and spatial dynamics from single-cell snaps...
Emerging Applications of Control and Systems Theory
This book celebrates Professor Mathukumalli Vidyasagar’s outstanding achievements in systems, control, robotics, statistical learning, computational biology, and allied areas. The contributions in the book summarize the content of invited lectures given at the workshop “Emerging Applications of Control and Systems Theory” (EACST17) held at the University of Texas at Dallas in late September 2017 in honor of Professor Vidyasagar’s seventieth birthday. These contributions are the work of twenty-eight distinguished speakers from eight countries and are related to Professor Vidyasagar’s areas of research. This Festschrift volume will remain as a permanent scientific record of this event.
A mathematical modeling framework to simulate and analyze cell type transitions
The quantitative understanding of changes in cell types, referred to as cell type transitions, is fundamental to advance fields such as stem cell research, immunology, and cancer therapies. This thesis provides a mathematical modeling framework to simulate and analyze cell type transitions. The novel methodological approaches and models presented here address diverse levels which are essential in this context: Gene regulatory network models represent the cell type-determining gene expression dynamics. Here, a novel construction method for gene regulatory network models is introduced, which allows to transfer results from generic low-dimensional to realistic high-dimensional gene regulatory n...
Recent Advances in Density Functional Methods
Of all the different areas in computational chemistry, density functional theory (DFT) enjoys the most rapid development. Even at the level of the local density approximation (LDA), which is computationally less demanding, DFT can usually provide better answers than Hartree-Fock formalism for large systems such as clusters and solids. For atoms and molecules, the results from DFT often rival those obtained by ab initio quantum chemistry, partly because larger basis sets can be used. Such encouraging results have in turn stimulated workers to further investigate the formal theory as well as the computational methodology of DFT. This Part II expands on the methodology and applications of DFT. ...
Infectious Disease Management in Animal Shelters
Since the publication of the first edition of Infectious Disease Management in Animal Shelters in 2009, research and practice in the field of shelter medicine have advanced significantly. This updated second edition of that seminal work provides the most up-to-date and comprehensive guide to preventing, managing, and treating infectious diseases affecting cats, dogs and exotic small companion mammals in animal shelters. Throughout the book, the authors—noted experts on the topic—bridge the gap between medicine (both individual and group) and management. The book is filled with practical strategies that draw on the latest research and evidence-based medicine as well as the authors’ pers...
Microorganisms in Environmental Management
Microbes and their biosynthetic capabilities have been invaluable in finding solutions for several intractable problems mankind has encountered in maintaining the quality of the environment. They have, for example, been used to positive effect in human and animal health, genetic engineering, environmental protection, and municipal and industrial waste treatment. Microorganisms have enabled feasible and cost-effective responses which would have been impossible via straightforward chemical or physical engineering methods. Microbial technologies have of late been applied to a range of environmental problems, with considerable success. This survey of recent scientific progress in usefully applyi...
Mr Bligh's Bad Language
Captain Bligh and the mutiny on the Bounty have become proverbial in their capacity to evoke the extravagant and violent abuse of power. But William Bligh was one of the least violent disciplinarians in the British navy. It is this paradox which inspired Greg Dening to ask why the mutiny took place. His book explores the theatrical nature of what was enacted in the power-play on deck, on the beaches at Tahiti and in the murderous settlement at Pitcairn, on the altar stones and temples of sacrifice, and on the catheads from which men were hanged. Part of the key lies in the curious puzzle of Mr Bligh's bad language.
Computational Cell Biology
This textbook provides an introduction to dynamic modeling in molecular cell biology, taking a computational and intuitive approach. Detailed illustrations, examples, and exercises are included throughout the text. Appendices containing mathematical and computational techniques are provided as a reference tool.
