About

Tandy Warnow is the Grainger Distinguished Chair in Engineering at the University of Illinois Urbana-Champaign, where she serves as Associate Director for the Siebel School of Computing and Data Science. She received her PhD in Mathematics from UC Berkeley in 1991 under the guidance of Gene Lawler, followed by postdoctoral training with Simon Tavare and Michael Waterman at the University of Southern California. Her academic career includes positions at Sandia National Laboratories, the University of Pennsylvania, and the University of Texas before joining the University of Illinois. Warnow's research focuses on algorithms for network science, computational biology, and historical linguistics, with significant contributions to the mathematical foundations of phylogenetics, methods for multiple sequence alignment, species tree estimation from multi-gene datasets, and metagenomic taxon identification. She has collaborated with linguist Don Ringe on inferring evolutionary histories for natural languages, settling several conjectures for Indo-European. Warnow has received numerous awards, including the NSF Young Investigator Award, the David and Lucile Packard Foundation Award, a Radcliffe Institute Fellowship, and a Guggenheim Fellowship. She is a Fellow of the ACM, ISCB, and AAAS, and was elected to the American Academy of Arts and Sciences in 2023. Her teaching includes courses in discrete mathematics, algorithm design, and computational genomics, emphasizing real-world applications and current research literature.

Research topics

• Biology
• Computer Science
• Genetics
• Evolutionary biology
• Artificial Intelligence
• Information Retrieval
• Computational biology
• Ecology
• Library science
• Data science
• Chemistry
• Paleontology

Selected publications

• Complexity of avian evolution revealed by family-level genomes

  Nature · 2024 · 270 citations

  • Evolutionary biology
  • Biology
  • Ecology

  (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

  PublisherOA PDFDOI

• Why sequence all eukaryotes?

  Proceedings of the National Academy of Sciences · 2022 · 121 citations

  • Computer Science
  • Biology
  • Evolutionary biology

  Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there on the origins of novelty and the continuing maintenance of biodiversity on Earth? The history of life and the code for the working parts of cells and systems are written in the genome. The Earth BioGenome Project has proposed that the genomes of all extant, named eukaryotes-about 2 million species-should be sequenced to high quality to produce a digital library of life on Earth, beginning with strategic phylogenetic, ecological, and high-impact priorities. Here we discuss why we should sequence all eukaryotic species, not just a representative few scattered across the many branches of the tree of life. We suggest that many questions of evolutionary and ecological significance will only be addressable when whole-genome data representing divergences at all of the branchings in the tree of life or all species in natural ecosystems are available. We envisage that a genomic tree of life will foster understanding of the ongoing processes of speciation, adaptation, and organismal dependencies within entire ecosystems. These explorations will resolve long-standing problems in phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, and medicine.

  DOI

• Towards complete and error-free genome assemblies of all vertebrate species

  Nature · 2021 · 2980 citations

  • Biology
  • Evolutionary biology
  • Computational biology

  has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

  DOI

• Towards complete and error-free genome assemblies of all vertebrate species

  bioRxiv (Cold Spring Harbor Laboratory) · 2020 · 195 citations

  • Biology
  • Evolutionary biology
  • Computational biology

  Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

  DOI

• Viewing computer science through citation analysis: Salton and Bergmark Redux

  Scientometrics · 2020 · 10 citations

  • Computer Science
  • Information Retrieval
  • Computer Science
  DOI

Recent grants

• Collaborative Research: OAC Core: Cyber-Infrastructure for Community Detection, Extraction, and Search in Large Networks

  NSF · $398k · 2024–2027

• Collaborative Research: Novel Methodologies for Genome-scale Evolutionary Analysis of Multi-locus data

  NSF · $350k · 2011–2014

• ITR: Collaborative Research, Algorithms for Inferring Reticulate Evolution in Historical Linguistics

  NSF · $345k · 2003–2009

• Collaborative Research: Large-scale simultaneous multiple alignment and phylogeny estimation

  NSF · $1.6M · 2007–2014

• AitF: Full: Collaborative Research: Graph-theoretic algorithms to improve phylogenomic analyses

  NSF · $360k · 2015–2020

Frequent coauthors

• Siavash Mirarab

  University of California, San Diego

  70 shared

• C. Randal Linder

  U.S. Vegetable Laboratory

  36 shared

• Bernard M. E. Moret

  35 shared

• Erin K. Molloy

  33 shared

• Nam Nguyen

  29 shared

• Li‐San Wang

  University of Pennsylvania

  28 shared

• Kevin Liu

  Harvard University

  24 shared

• Luay Nakhleh

  22 shared

Labs

• Warnow LabPI

Education

• Ph.D., Computer Science

  University of Texas at Austin

  1996

• M.S., Computer Science

  University of Texas at Austin

  1992

• B.S., Computer Science

  University of Texas at Austin

  1990

Awards & honors

• National Science Foundation Young Investigator Award (1994)
• David and Lucile Packard Foundation Award in Science and Eng…
• Radcliffe Institute Fellowship (2006)
• Guggenheim Foundation Fellowship (2011)
• Fellow of the Association for Computing Machinery (ACM) (201…

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