Bioinformatics and Phylogenetics

This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret's research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest.

Topics and features:

• Addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem
• Describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees
• Discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events
• Reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches
• Examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation
• Highlights how evolution can provide a framework within which to understand comparative and functional genomics
• Provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem

Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

Dr. Tandy Warnow is the Founder Professor of Computer Science at the University of Illinois at Urbana-Champaign, where she is also an affiliate in the departments of Mathematics, Statistics, Bioengineering, Electrical and Computer Engineering, Animal Biology, Entomology, and Plant Biology.

Autorentext

Dr. Tandy Warnow is the Founder Professor of Computer Science at the University of Illinois at Urbana-Champaign, where she is also an affiliate in the departments of Mathematics, Statistics, Bioengineering, Electrical and Computer Engineering, Animal Biology, Entomology, and Plant Biology. Tandy received her PhD in Mathematics in 1991 at UC Berkeley under the direction of Gene Lawler, and did postdoctoral training with Simon Tavaré and Michael Waterman at USC. Her research combines computer science, statistics, and discrete mathematics, focusing on developing improved models and algorithms for reconstructing complex and large-scale evolutionary histories in biology and historical linguistics. She has published more than 160 papers and one textbook, graduated 11 PhD students, and has 5 current PhD students. Her awards include the NSF Young Investigator Award (1994), the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2006), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the International Society for Computational Biology (ISCB) in 2017. Warnow succeeded Bernard Moret as the director of the NSF-funded CIPRES (Cyber-Infrastructure for Phylogenetic Research) project, whose goal was To provide the computational infrastructure needed to reconstruct phylogenies for millions of taxa.

Inhalt

Introduction: A Biography of Bernard Moret
Tandy Warnow

A Review of Approaches for Optimizing Phylogenetic Likelihood Calculations
Alexandros Stamatakis

Numerical Optimization Techniques in Maximum Likelihood Tree Inference
Stéphane Guindon and Olivier Gascuel

High-Performance Phylogenetic Inference
David A. Bader and Kamesh Madduri

Hands-On Introduction to Sequence-Length Requirements in Phylogenetics
Sébastien Roch

Gene Family Evolution An Algorithmic Framework
Nadia El-Mabrouk and Emmanuel Noutahi

Divide-and-Conquer Tree Estimation: Opportunities and Challenges
Tandy Warnow

Taxonomic Supertree Construction with incertae sedis Taxa
Benjamin D. Redelings and Mark T. Holder

Evolutionary Rate Change and the Transformation from Additive to Ultrametric: Modal Similarity of Orthologs in Fish and Flower Phylogenomics
Daniella Santos Muñoz, Eric Lam and David Sankoff

Ancestral Genome Reconstruction
Jijun Tang

Genome Rearrangement Problems with Single and Multiple Gene Copies: A Review
Ron Zeira and Ron Shamir Computational Models for Cancer Phylogenetics
Russell Schwartz

Clusters, Trees and Phylogenetic Network Classes
Louxin Zhang

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
R. A. Leo Elworth, Huw A. Ogilvie, Jiafan Zhu and Luay Nakhleh

A Perspective on Comparative and Functional Genomics
Daniel Doerr and Jens Stoye

Integer Linear Programming in Computational Biology: Overview of ILP, and New Results for Traveling Salesman Problems in Biology
Dan Gusfield