Alexander Zelikovsky - Böcker

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Introduces readers to core algorithmic techniques for next-generation sequencing (NGS) data analysis and discusses a wide range of computational techniques and applications This book provides an in-depth survey of some of the recent developments in NGS and discusses mathematical and computational challenges in various application areas of NGS technologies. The 18 chapters featured in this book have been authored by bioinformatics experts and represent the latest work in leading labs actively contributing to the fast-growing field of NGS. The book is divided into four parts: Part I focuses on computing and experimental infrastructure for NGS analysis, including chapters on cloud computing, modular pipelines for metabolic pathway reconstruction, pooling strategies for massive viral sequencing, and high-fidelity sequencing protocols.Part II concentrates on analysis of DNA sequencing data, covering the classic scaffolding problem, detection of genomic variants, including insertions and deletions, and analysis of DNA methylation sequencing data. Part III is devoted to analysis of RNA-seq data. This part discusses algorithms and compares software tools for transcriptome assembly along with methods for detection of alternative splicing and tools for transcriptome quantification and differential expression analysis. Part IV explores computational tools for NGS applications in microbiomics, including a discussion on error correction of NGS reads from viral populations, methods for viral quasispecies reconstruction, and a survey of state-of-the-art methods and future trends in microbiome analysis.Computational Methods for Next Generation Sequencing Data Analysis: Reviews computational techniques such as new combinatorial optimization methods, data structures, high performance computing, machine learning, and inference algorithmsDiscusses the mathematical and computational challenges in NGS technologiesCovers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and moreThis text is a reference for biomedical professionals interested in expanding their knowledge of computational techniques for NGS data analysis. The book is also useful for graduate and post-graduate students in bioinformatics.

The conference proceeding  LNCS 11346 constitutes the refereed proceedings of the 12th International Conference on Combinatorial Optimization and Applications, COCOA 2018, held in Atlanta, GA, USA, in December 2018.The 50 full papers presented were carefully reviewed and selected from 106 submissions. The papers cover most aspects of t graph algorithms, routing and network design problems, scheduling algorithms, network optimization, combinatorial algorithms, approximation algorithms, paths and connectivity problems and much more.

This book constitutes revised selected papers from the 9th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2019, held in Miami, Florida, USA in November 2019.The 15 papers presented in this volume were carefully reviewed and selected from 30 submissions. biomedical image analysis;

This book constitutes revised selected papers from the refereed proceedings of the 11th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2021, held as a virtual event during December 16–18, 2021.The 13 full papers included in this book were carefully reviewed and selected from 17 submissions. They were organized in topical sections as follows: Computational advances in bio and medical sciences; and computational advances in molecular epidemiology.

This book constitutes the refereed proceedings of the 12th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2023, held in Norman, Oklahoma, USA, during December 11–13, 2023. The 23 full papers included in this book were carefully reviewed and selected from 65 submissions.

This book constitutes the refereed proceedings of the 20th International Conference on Computing and Combinatorics, COCOON 2014, held in Atlanta, GA, USA, in August 2014. There was a co-organized workshop on computational social networks (CSoNet 2014) where 8 papers were accepted. scheduling algorithms and circuit complexity and CSoNet.

It gives me great pleasure to present the Special Issue of LNCS Transactions on Computational Systems Biology devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005). The IWBRA workshop was a part of the International Conference on Computational Science (ICCS 2005) which took place in Emory University, Atlanta, Georgia, USA, May 22-24, 2005. See http://www.cs.gsu.edu/pan/ iwbra.htm for more details. The 10 papers selected for the special issue cover a wide range of bioinformatics research. The first papers are devoted to problems in RNA structure prediction: Blin et al. contribute to the arc-preserving subsequence problem and Liu et al. develop an efficient search of pseudoknots. The coding schemes and structural alphabets for protein structure prediction are discussed in the contributions of Lei and Dai, and Zheng and Liu, respectively. Song et al. propose a novel technique for efficient extraction of biomedical information. Nakhleh and Wang discuss introducing hybrid speciation and horizontal gene transfer in phylogenetic networks.Practical algorithms minimizing recombinations in pedigree phasing are proposed by Zhang et al. Kolliet al. propose a new parallel implementation in OpenMP for finding the edit distance between two signed gene permutations. The issue is concluded with two papers devoted to bioinformatics problems that arise in DNA microarrays: improved tag set design for universal tag arrays is suggested by Mandoiu et al. and a new method of gene selection is discussed by Xu and Zhang.

This book constitutes the refereed proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA 2007, held in Atlanta, GA, USA in May 2007. The 55 revised full papers presented together with three invited talks cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.

This book constitutes the refereed proceedings of the Fourth International Symposium on Bioinformatics Research and Applications, ISBRA 2008, held in Atlanta, GA, USA in May 2008. The 35 revised full papers presented together with 6 workshop papers and 6 invited papers were carefully reviewed and selected from a total of 94 submissions. The papers cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.

This volume constitutes the refereed proceedings of the 7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011, held in Changsha, China, in May 2011.The 36 revised full papers presented together with 4 invited talks were carefully reviewed and selected from 92 submissions. Topics presented span all areas of bioinformatics and computational biology, including the development of experimental or commercial systems.