Pooling designs have been widely used in various aspects of DNA sequencing. In biological applications, the well-studied mathematical problem called “group testing” shifts its focus to nonadaptive algorithms while the focus of traditional group testing is on sequential algorithms. Biological applications also bring forth new models not previously considered, such as the error-tolerant model, the complex model, and the inhibitor model. This book is the first attempt to collect all the significant research on pooling designs in one convenient place.The coverage includes many real biological applications such as clone library screening, contig sequencing, exon boundary finding and protein-protein interaction detecting and introduces the mathematics behind it.

This book constitutes the proceedings of the 8th International Conference on Algorithms for Computational Biology, AlCoB 2020, was planned to be held in Missoula, MT, USA in June 2021. Due to the Covid-19 pandemic, AlCoB 2020 and AlCoB 2021 were merged and held on these dates together. AlCoB 2020 proceedings were published as LNBI 12099. The 12 full papers included in this volume were carefully reviewed and selected from 22 submissions. They were organized in topical sections on genomics, phylogenetics, and RNA-Seq and other biological processes. The scope of AlCoB includes topics of either theoretical or applied interest, namely: sequence analysis; sequence alignment; sequence assembly; genome rearrangement; regulatory motif finding; phylogeny reconstruction; phylogeny comparison; structure prediction; compressive genomics; proteomics: molecular pathways, interaction networks, mass spectrometry analysis; transcriptomics: splicing variants, isoform inference and quantification, differential analysis; next-generation sequencing: population genomics, metagenomics, metatranscriptomics, epigenomics; genome CD architecture; microbiome analysis; cancer computational biology; and systems biology.

This book constitutes the refereed proceedings of the 16th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2012, held in Barcelona, Spain, in April 2012. The 31 revised full papers presented together with 5 keynote lectures were carefully reviewed and selected from 200 submissions. The papers feature current research in all areas of computational molecular biology, including: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging.

This book constitutes the proceedings of the 26th International Conference on Algorithmic Learning Theory, ALT 2015, held in Banff, AB, Canada, in October 2015, and co-located with the 18th International Conference on Discovery Science, DS 2015. The 23 full papers presented in this volume were carefully reviewed and selected from 44 submissions. In addition the book contains 2 full papers summarizing the invited talks and 2 abstracts of invited talks. The papers are organized in topical sections named: inductive inference; learning from queries, teaching complexity; computational learning theory and algorithms; statistical learning theory and sample complexity; online learning, stochastic optimization; and Kolmogorov complexity, algorithmic information theory.

This two volume set LNCS 14422-14423 constitutes the refereed proceedings of the 29th International Conference, COCOON 2023, held in Hawaii, HI, USA, during December 2023. The 60 full papers were carefully reviewed and selected from 146 submissions. They are organized in the following topical sections: Part I : Combinatorics and Algorithms; Algorithmic Solution in Applications; and Algorithm in Networks. Part II: Complexity and Approximation; Graph Algorithms; and Applied Algorithms.

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 algorithms Discusses the mathematical and computational challenges in NGS technologies Covers NGS error correction, de novo genome transcriptome assembly, variant detection from NGS reads, and more This 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 two-volume set LNCS 14461 and LNCS 14462 constitutes the refereed proceedings of the 17th International Conference on Combinatorial Optimization and Applications, COCOA 2023, held in Hawaii, HI, USA, during December 15–17, 2023. The 73 full papers included in the proceedings were carefully reviewed and selected from 117 submissions. They were organized in topical sections as follows: Part I: Optimization in graphs; scheduling; set-related optimization; applied optimization and algorithm; Graph planer and others; Part II: Modeling and algorithms; complexity and approximation; combinatorics and computing; optimization and algorithms; extreme graph and others; machine learning, blockchain and others.