Search results for ""Author Paul A. Gagniuc""

ALGORITHMS IN BIOINFORMATICS Explore a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields Algorithms in Bioinformatics: Theory and Implementation delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment, detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. The text incorporates graphical illustrations to highlight and emphasize the technical details of computational algorithms found within, to further the reader’s understanding and retention of the material. Throughout, the book is written in an accessible and practical manner, showing how algorithms can be implemented and used in JavaScript on Internet Browsers. The author has included more than 120 open-source implementations of the material, as well as 33 ready-to-use presentations. The book contains original material that has been class-tested by the author and numerous cases are examined in a biological and medical context. Readers will also benefit from the inclusion of: A thorough introduction to biological evolution, including the emergence of life, classifications and some known theories and molecular mechanisms A detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementations Discussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matrices A detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fields An examination of information and entropy, including sequence logos and explanations related to their meaning An exploration of the current state of bioinformatics, including what is known and what issues are usually avoided in the field A chapter on philosophical transactions that allows the reader a broader view of the prediction process Native computer implementations in the context of the field of Bioinformatics Extensive worked examples with detailed case studies that point out the meaning of different results Perfect for professionals and researchers in biology, medicine, engineering, and information technology, as well as upper level undergraduate students in these fields, Algorithms in Bioinformatics: Theory and Implementation will also earn a place in the libraries of software engineers who wish to understand how to implement bioinformatic algorithms in their products.

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A fascinating and instructive guide to Markov chains for experienced users and newcomers alike This unique guide to Markov chains approaches the subject along the four convergent lines of mathematics, implementation, simulation, and experimentation. It introduces readers to the art of stochastic modeling, shows how to design computer implementations, and provides extensive worked examples with case studies. Markov Chains: From Theory to Implementation and Experimentation begins with a general introduction to the history of probability theory in which the author uses quantifiable examples to illustrate how probability theory arrived at the concept of discrete-time and the Markov model from experiments involving independent variables. An introduction to simple stochastic matrices and transition probabilities is followed by a simulation of a two-state Markov chain. The notion of steady state is explored in connection with the long-run distribution behavior of the Markov chain. Predictions based on Markov chains with more than two states are examined, followed by a discussion of the notion of absorbing Markov chains. Also covered in detail are topics relating to the average time spent in a state, various chain configurations, and n-state Markov chain simulations used for verifying experiments involving various diagram configurations. • Fascinating historical notes shed light on the key ideas that led to the development of the Markov model and its variants • Various configurations of Markov Chains and their limitations are explored at length • Numerous examples—from basic to complex—are presented in a comparative manner using a variety of color graphics • All algorithms presented can be analyzed in either Visual Basic, Java Script, or PHP • Designed to be useful to professional statisticians as well as readers without extensive knowledge of probability theory Covering both the theory underlying the Markov model and an array of Markov chain implementations, within a common conceptual framework, Markov Chains: From Theory to Implementation and Experimentation is a stimulating introduction to and a valuable reference for those wishing to deepen their understanding of this extremely valuable statistical tool. Paul A. Gagniuc, PhD, is Associate Professor at Polytechnic University of Bucharest, Romania. He obtained his MS and his PhD in genetics at the University of Bucharest. Dr. Gagniuc’s work has been published in numerous high profile scientific journals, ranging from the Public Library of Science to BioMed Central and Nature journals. He is the recipient of several awards for exceptional scientific results and a highly active figure in the review process for different scientific areas.

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