Algorithms in Bioinformatics

Algorithms in Bioinformatics

An improved model for statistical alignment (I. Mikls, Z. Toroczkai). Improving profile-profile alignments via log average scoring (N. von ohsen, R. Zimmer). False positive s in genomic map assembly and sequence validation (T. Anantharaman, B. Mishra). Boosting EM for radiation hybrid and genetic mapping (T. Schiex, P. Chabrier, M. Bouchez, D. Milan). Placing probes along the genome using pairwise distance data (W. Casey, B. Mishra, M. Wigler). Comparing a Hidden Markov model and a stochastic context-free grammar (A. Jagota, R. B. Lyngso, C. N. S. Pedersen). Assessing the statistical significance of overrepresented oligonucleotides (A. Denise, M. Rgnier, M. vandenbogaert). Pattern matching and pattern discovery algorithms for protein topologies (J. Viksna, D. Gilbert). Computing linking numbers of a filtration (H. Edelsbrusnner, A. Zomorodian). Side chain-positioning as an integer programming problem (O. Eriksson, Y. Zhou, A. Elofsson). A chemical-distance-based test for positive darwinian selection (T. Pupko, R. Sharan, M. Hasegawa, R. Shamir, D. Graur). Finding a maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynominal time (G. Ganapathysaravanabavan, T. Warnow). Experiments in computing sequences of reversals (A. Bergeron, Franois Strasbourg). Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes (Li-San Wang). Finding an optimal inversion median: experimental results (A. C. Siepel, B. M. E. Moret). Analytic solutions for three-taxon MLMC trees with variable rates across sites (B. Chor, M. Hendy, D. Penny). The performance of phylogenetic methods on trees of bounded diameter (L. nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow). (1+E)- approximation of sorting by reversals and transpositions (N. Eriksen). On the practical solution of the reversal median problem (A. Caprara). Algorithms for finding gene clusters (S. Heber, J. Stoye). Determination of binding amino acids based on random peptide array screening data (P. J. van der Veen, L. F. A. Wessels, J. W. Sloostra, R. H. Meloen, M. J. T. Reinders, J. Hellendoorn). A simple hyper-geometric approach for discovering putative transcription factor binding sites (Y. Barash, G. Bejerano, N. Friedman). Comparing assemblies using fragments and mate-pairs (D. H. Huson, A. L. Halpern, Z. Lai, E. W. myers, K. Reinert, G. G. Sutton). Author index.

Algorithms in Bioinformatics

Visualization of Hydrogen-Bond Dynamics

Visualization of Hydrogen-Bond Dynamics

The hydrogen bond represents an important interaction between molecules, and the dynamics of hydrogen bonds in water create an ever-present question associated with the process of chemical and biological reactions. In spite of numerous studies, the process remains poorly understood at the microscopic level because hydrogen-bond dynamics, such as bond rearrangements and hydrogen/proton transfer reactions, are extremely difficult to probe. Those studies have been carried out by means of spectroscopic methods where the signal stems from the ensemble of a system and the hydrogen-bond dynamics were inferred indirectly. This book addresses the direct imaging of hydrogen-bond dynamics within water-based model systems assembled on a metal surface, using a scanning tunneling microscope (STM). The dynamics of individual hydrogen bonds in water clusters, hydroxyl clusters, and water-hydroxyl complexes are investigated in conjunction with density functional theory. In these model systems, quantum dynamics of hydrogen bonds, such as tunneling and zero-point nuclear motion, are observed in real space. Most notably, hydrogen atom relay reactions, which are frequently invoked across many fields of chemistry, are visualized and controlled by STM. This work presents a means of studying hydrogen-bond dynamics at the single-molecule level, providing an important contribution to wide fields beyond surface chemistry.

Visualization of Hydrogen-Bond Dynamics

Clusters in Nuclei, Volume 1

Clusters in Nuclei, Volume 1

Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is presently one of the domains of heavy-ion nuclear physics facing both the greatest challenges and opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physics decided to team up in producing a comprehensive collection of lectures and tutorial reviews covering the field. This first volume, gathering seven extensive lectures, covers the follow topics: * Cluster Radioactivity * Cluster States and Mean Field Theories * Alpha Clustering and Alpha Condensates * Clustering in Neutron-rich Nuclei * Di-neutron Clustering * Collective Clusterization in Nuclei * Giant Nuclear Molecules By promoting new ideas and developments while retaining a pedagogical nature of presentation throughout, these lectures will both serve as a reference and as advanced teaching material for future courses and schools in the fields of nuclear physics and nuclear astrophysics.

Clusters in Nuclei, Volume 1

Cosmic Update

Cosmic Update

‘…The Multiversal book series is equally unique, providing book-length extensions of the lectures with enough additional depth for those who truly want to explore these fields, while also providing the kind of clarity that is appropriate for interested lay people to grasp the general principles involved.’ – Lawrence M. KraussCosmic Update Covers:A novel approach to uncover the dark faces of the Standard Model of cosmology.The possibility that Dark Energy and Dark Matter are manifestations of the inhomogeneous geometry of our Universe.On the history of cosmological model building and the general architecture of cosmological modes.Illustrations on the Large Scale Structure of the Universe.A new perspective on the classical static Einstein Cosmos.Global properties of World Models including their Topology.The Arrow of Time in a Universe with a Positive Cosmological Constant.Exploring the consequences of a fundamental Cosmological Constant for our Universe. Exploring why the current observed acceleration of the Universe may not be its final destiny.Demonstrating that nature forbids the existence of a pure Cosmological Constant.Our current understanding of the long term (in time scales that greatly exceed the current age of the Universe) future of the Universe.The long term fate and eventual destruction of the astrophysical objects that populate the universe — including clusters, galaxies, stars, planets, and black holes. The material is presented in a layperson-friendly language followed by addition technical sections that explain the basic equations and principles. This feature is very attractive to readers who want to learn more about the theories involved beyond the basic description. ‘Multiversal Journeys is a trademark of Farzad Nekoogar and Multiversal Journeys, a 501 (c) (3) nonprofit organization.’

Cosmic Update

Clusters in Nuclei, Volume 3

Clusters in Nuclei, Volume 3

Following the pioneering discovery of alpha clustering and of molecular resonances, the field of nuclear clustering is today one of those domains of heavy-ion nuclear physics that faces the greatest challenges, yet also contains the greatest opportunities. After many summer schools and workshops, in particular over the last decade, the community of nuclear molecular physicists has decided to collaborate in producing a comprehensive collection of lectures and tutorial reviews covering the field. This third volume follows the successful Lect. Notes Phys. 818 (Vol. 1) and 848 (Vol. 2), and comprises six extensive lectures covering the following topics:

Clusters in Nuclei, Volume 3

Best Jobs for the 21st Century, Sixth Edition

Best Jobs for the 21st Century, Sixth Edition

This bestseller has helped thousands discover their best career options through a unique and useful format. This book features the 500 jobs with the best pay, fastest growth, and most openings and presents more than 65 best jobs lists. In just two steps, Best Jobs for the 21st Century helps readers quickly and easily focus their career options (step 1: the lists) and learn more about jobs of interest (step 2: the job descriptions). This completely revised edition turns the government s latest occupational data into a helpful, interesting reference for job seekers, students, career changers, and others. The book now gives information on each jobs career cluster and pathway, plus the top three industries for its growth and employment. New lists include best jobs in the 16 career clusters and best jobs in urban and rural areas.

Best Jobs for the 21st Century, Sixth Edition

Linux System Administration

Linux System Administration

If you’re an experienced system administrator looking to acquire , skills, or a seasoned Linux user facing a new challenge, Linux System , offers practical knowledge for managing a complete range of Linux systems and servers. The book summarizes the steps you need to build everything from standalone SOHO hubs, web servers, and LAN servers to load-balanced clusters and servers consolidated through virtualization. Along the way, you’ll learn about all of the tools you need to set up and maintain these working environments.,

Linux is now a standard corporate platform with users numbering in the hundreds of millions, and there is a definite shortage of talented administrators. Linux System Administration is ideal as an introduction to Linux for Unix veterans, MCSEs, and mainframe administrators, and as an advanced (and refresher) guide for existing Linux administrators who will want to jump into the middle of the book.

Linux System Administration