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Comparative Genomics
This book constitutes the proceedings of the 21st International Conference on Comparative Genomics, RECOMB-CG 2024, which was held in Boston, MA, USA, during April 27-28, 2024. The 13 full papers presented in this book were carefully reviewed and selected from 21 submissions. The papers are divided into the following topical sections: phylogenetic networks; homology and phylogenetic reconstruction; tools for evolution reconstruction; genome rearrangements; and genome evolution.
Topological Data Analysis for Genomics and Evolution
Biology has entered the age of Big Data. A technical revolution has transformed the field, and extracting meaningful information from large biological data sets is now a central methodological challenge. Algebraic topology is a well-established branch of pure mathematics that studies qualitative descriptors of the shape of geometric objects. It aims to reduce comparisons of shape to a comparison of algebraic invariants, such as numbers, which are typically easier to work with. Topological data analysis is a rapidly developing subfield that leverages the tools of algebraic topology to provide robust multiscale analysis of data sets. This book introduces the central ideas and techniques of topological data analysis and its specific applications to biology, including the evolution of viruses, bacteria and humans, genomics of cancer, and single cell characterization of developmental processes. Bridging two disciplines, the book is for researchers and graduate students in genomics and evolutionary biology as well as mathematicians interested in applied topology.
Phylogenetic Networks
The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.
Information-theoretic causal inference of lexical flow
This volume seeks to infer large phylogenetic networks from phonetically encoded lexical data and contribute in this way to the historical study of language varieties. The technical step that enables progress in this case is the use of causal inference algorithms. Sample sets of words from language varieties are preprocessed into automatically inferred cognate sets, and then modeled as information-theoretic variables based on an intuitive measure of cognate overlap. Causal inference is then applied to these variables in order to determine the existence and direction of influence among the varieties. The directed arcs in the resulting graph structures can be interpreted as reflecting the exis...
Research in Computational Molecular Biology
This book constitutes the proceedings of the 24th Annual Conference on Research in Computational Molecular Biology, RECOMB 2020, held in Padua, Italy, in May 2020. The 13 regular and 24 short papers presented were carefully reviewed and selected from 206 submissions. The papers report on original research in all areas of computational molecular biology and bioinformatics.
The Post-Communist World in the Twenty-First Century
The Post-Communist World in the Twenty-First Century presents studies by senior scholars and practitioners that are highly relevant to contemporary political challenges. The democratic vision that accompanied the collapse of communist regimes in the Soviet Union and East Central Europe has been replaced by a range of authoritarian, semi-authoritarian and democratic regimes, and growing division between Western and Russian influence. Russia’s invasion of Ukraine has led to renewed tensions and international crisis. China, which presents major challenges to the US, Europe, and the global order, has emerged as a critical actor in the international conflict. The need to understand the internal...
Algorithms -- ESA 2010, Part II
This book constitutes the proceedings of the 18th Annual European Symposium on Algorithms, held in Liverpool, UK in September 2010.
Phylogeny
Phylogenetics is a topical and growing area of research. Phylogenies (phylogenetic trees and networks) allow biologists to study and graph evolutionary relationships between different species. These are also used to investigate other evolutionary processes?for example, how languages developed or how different strains of a virus (such as HIV or influenza) are related to each other.? This self-contained book addresses the underlying mathematical theory behind the reconstruction and analysis of phylogenies. The theory is grounded in classical concepts from discrete mathematics and probability theory as well as techniques from other branches of mathematics (algebra, topology, differential equations). The biological relevance of the results is highlighted throughout. The author supplies proofs of key classical theorems and includes results not covered in existing books, emphasizes relevant mathematical results derived over the past 20 years, and provides numerous exercises, examples, and figures.?
Research in Computational Molecular Biology
Zusammenfassung: This book constitutes the proceedings of the 28th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2024, held in Cambridge, MA, USA, during April 29-May 2, 2024. The 57 full papers included in this book were carefully reviewed and selected from 352 submissions. They were organized in topical sections as follows: theoretical and foundational algorithm contributions and more applied directions that engage with new technologies and intriguing biological questions
Handbook of Stemmatology
Stemmatology studies aspects of textual criticism that use genealogical methods to analyse a set of copies of a text whose autograph has been lost. This handbook is the first to cover the entire field, encompassing both theoretical and practical aspects of traditional as well as modern digital methods and their history. As an art (ars), stemmatology’s main goal is editing and thus presenting to the reader a historical text in the most satisfactory way. As a more abstract discipline (scientia), it is interested in the general principles of how texts change in the process of being copied. Thirty eight experts from all of the fields involved have joined forces to write this handbook, whose ei...
