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
About the Author: 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".
