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Research Output 1990 2019

Article

Indo-European and computational cladistics

Ringe, D., Warnow, T. & Taylor, A., Jan 1 2002, In : Transactions of the Philological Society. 100, 1, p. 59-129 71 p.

Research output: Contribution to journalArticle

phylogeny
methodology
experiment
Methodology
Cladistics

Inferring evolutionary history from DNA sequences

Kannan, S. K. & Warnow, T. J., Jan 1 1994, In : SIAM Journal on Computing. 23, 4, p. 713-737 25 p.

Research output: Contribution to journalArticle

DNA sequences
DNA Sequence
Molecular biology
Phylogenetic Tree
Compatibility

In Memoriam Eugene L. Lawler

Gustfield, D., Shmoys, D., Lenstra, J. K. & Warnow, T., Jan 1 1994, In : Journal of Computational Biology. 1, 4, p. 255-256 2 p.

Research output: Contribution to journalArticle

Kaikoura tree theorems: Computing the maximum agreement subtree

Steel, M. & Warnow, T., Nov 8 1993, In : Information Processing Letters. 48, 2, p. 77-82 6 p.

Research output: Contribution to journalArticle

Computing
Theorem
Binary trees
Leaves
Binary Tree

Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule

ErdH os, P., Steel, M. A., Székely, L. & Warnow, T. J., 1997, In : Computing and Informatics. 16, 2, p. 217-227 11 p.

Research output: Contribution to journalArticle

Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods

Roch, S., Nute, M. & Warnow, T., Mar 1 2019, In : Systematic biology. 68, 2, p. 281-297 17 p.

Research output: Contribution to journalArticle

topology
loci
methodology
gene
genomics

Mathematical approaches to comparative linguistics

Warnow, T., Jun 24 1997, In : Proceedings of the National Academy of Sciences of the United States of America. 94, 13, p. 6585-6590 6 p.

Research output: Contribution to journalArticle

Linguistics
Language
History

Minimizing phylogenetic number to find good evolutionary trees

Goldberg, L. A., Goldberg, P. W., Phillips, C. A., Sweedyk, E. & Warnow, T., Dec 5 1996, In : Discrete Applied Mathematics. 71, 1-3, p. 111-136 26 p.

Research output: Contribution to journalArticle

Evolutionary Tree
Phylogenetics
Topology
Polynomials
Parsimony

MRL and SuperFine+MRL: New supertree methods

Nguyen, N., Mirarab, S. & Warnow, T., Jan 26 2012, In : Algorithms for Molecular Biology. 7, 1, 3.

Research output: Contribution to journalArticle

Matrix Representation
Parsimony
Likelihood
Trinitrotoluene
Heuristics

Multiple sequence alignment: A major challenge to large-scale phylogenetics

Liu, K., Linder, C. R. & Warnow, T., Dec 1 2010, In : PLoS Currents. NOV, ecurrents.RRN1198.

Research output: Contribution to journalArticle

Sequence Alignment
Phylogeny
Benchmarking
Datasets
Research Personnel

Naive binning improves phylogenomic analyses

Bayzid, M. S. & Warnow, T., Sep 15 2013, In : Bioinformatics. 29, 18, p. 2277-2284 8 p.

Research output: Contribution to journalArticle

Binning
Genes
Sorting
Gene
Coalescence

New approaches for reconstructing phytogenies from gene order data

Moret, B. M. E., Wang, L. S., Warnow, T. & Wyman, S. K., Jan 1 2001, In : Bioinformatics. 17, SUPPL. 1, p. S165-S173

Research output: Contribution to journalArticle

Gene Order
Campanulaceae
Genes
Genome
Chloroplast Genome

OCTAL: Optimal Completion of gene trees in polynomial time

Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Mar 15 2018, In : Algorithms for Molecular Biology. 13, 1, 6.

Research output: Contribution to journalArticle

Completion
Polynomial time
Genes
Polynomials
Gene

One thousand plant transcriptomes and the phylogenomics of green plants

One Thousand Plant Transcriptomes Initiative, Oct 31 2019, In : Nature. 574, 7780, p. 679-685 7 p.

Research output: Contribution to journalArticle

Open Access
Viridiplantae
Transcriptome
Plant Genome
Rhodophyta
Glaucophyta

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

Roch, S. & Warnow, T., Jul 1 2015, In : Systematic biology. 64, 4, p. 663-676 14 p.

Research output: Contribution to journalArticle

gene
Genes
genes
sorting
methodology

PASTA: Ultra-large multiple sequence alignment for nucleotide and amino-acid sequences

Mirarab, S., Nguyen, N., Guo, S., Wang, L. S., Kim, J. & Warnow, T., May 1 2015, In : Journal of Computational Biology. 22, 5, p. 377-386 10 p.

Research output: Contribution to journalArticle

Multiple Sequence Alignment
Sequence Alignment
Amino Acid Sequence
Nucleotides
Amino acids

PASTA for proteins

Collins, K. & Warnow, T., Nov 15 2018, In : Bioinformatics. 34, 22, p. 3939-3941 3 p.

Research output: Contribution to journalArticle

Proteins
Protein
Bioinformatics
Large Data Sets
Availability

Pattern identification in biogeography

Ganapathy, G., Goodson, B., Jansen, R., Le, H. S., Ramachandran, V. & Warnow, T., Oct 1 2006, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 3, 4, p. 334-346 13 p.

Research output: Contribution to journalArticle

biogeography
Identification Problem
Linear-time Algorithm
Formalization
Efficient Algorithms

Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages

Nakhleh, L., Ringe, D. & Warnow, T., Jun 1 2005, In : Language. 81, 2, p. 382-420 39 p.

Research output: Contribution to journalArticle

methodology
history
language
contact
candidacy

Performance study of phylogenetic methods: (Unweighted) quartet methods and neighbor-joining

St. John, K., Warnow, T., Moret, B. M. E. & Vawter, L., Aug 2003, In : Journal of Algorithms. 48, 1, p. 173-193 21 p.

Research output: Contribution to journalArticle

Phylogenetics
Joining
Cleaning
Experiments
Sample space

Phylogenetic networks: Modeling, reconstructibility, and accuracy

Moret, B. M. E., Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J. & Timme, R., Jan 1 2004, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 1, 1, p. 13-23 11 p.

Research output: Contribution to journalArticle

Phylogenetic Network
Network Modeling
Horizontal Gene Transfer
phylogeny
Gene transfer

Phylogenomic analyses data of the avian phylogenomics project

The Avian Phylogenomics Consortium, Feb 12 2015, In : GigaScience. 4, 1, 4.

Research output: Contribution to journalArticle

Genes
Genome
DNA Transposable Elements
Sequence Alignment
Expressed Sequence Tags

Phylogenomics from whole genome sequences using aTRAM

Allen, J. M., Boyd, B., Nguyen, N. P., Vachaspati, P., Warnow, T., Huang, D. I., Grady, P. G. S., Bell, K. C., Cronk, Q. C. B., Mugisha, L., Pittendrigh, B. R., Leonardi, M. S., Reed, D. L. & Johnson, K. P., Sep 1 2017, In : Systematic biology. 66, 5, p. 786-798 13 p.

Research output: Contribution to journalArticle

genome
Genome
application coverage
Anoplura
gene

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Davidson, R., Vachaspati, P., Mirarab, S. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-12 12 p.

Research output: Contribution to journalArticle

Horizontal Gene Transfer
Biological Phenomena
Genes

Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola)

Boyd, B. M., Allen, J. M., Nguyen, N. P., Sweet, A. D., Warnow, T., Shapiro, M. D., Villa, S. M., Bush, S. E., Clayton, D. H. & Johnson, K. P., Nov 1 2017, In : Systematic biology. 66, 6, p. 896-911 16 p.

Research output: Contribution to journalArticle

Columbicola
Phthiraptera
Psocodea
louse
lice

Phylotranscriptomic analysis of the origin and early diversification of land plants

Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., Rothfels, C. J. & 22 others, Pokorny, L., Shaw, A. J., De Gironimo, L., Stevenson, D. W., Surek, B., Villarreal, J. C., Roure, B., Philippe, H., De Pamphilis, C. W., Chen, T., Deyholos, M. K., Baucom, R. S., Kutchan, T. M., Augustin, M. M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G. K. S. & Leebens-Mack, J., Nov 11 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 45, p. E4859-E4868

Research output: Contribution to journalArticle

Embryophyta
Hepatophyta
Plant Genome
Bryophyta
Chlorophyta

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice

Boyd, B. M., Allen, J. M., Nguyen, N. P., Vachaspati, P., Quicksall, Z. S., Warnow, T., Mugisha, L., Johnson, K. P. & Reed, D. L., Jul 1 2017, In : Molecular biology and evolution. 34, 7, p. 1743-1757 15 p.

Research output: Contribution to journalArticle

Phthiraptera
louse
hominid
lice
Hominidae

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

Liu, K., Raghavan, S., Nelesen, S., Linder, C. R. & Warnow, T., Jun 19 2009, In : Science. 324, 5934, p. 1561-1564 4 p.

Research output: Contribution to journalArticle

Sequence Alignment
Molecular Sequence Data
DNA
Datasets

RAxML and FastTree: Comparing two methods for large-scale maximum likelihood phylogeny estimation

Liu, K., Linder, C. R. & Warnow, T., Nov 21 2011, In : PloS one. 6, 11, e27731.

Research output: Contribution to journalArticle

Maximum likelihood estimation
Phylogeny
Maximum likelihood
phylogeny
Sequence Alignment
Datasets
Heuristics

Reconstructing chromosomal evolution

Wang, L. S. & Warnow, T., Dec 1 2006, In : SIAM Journal on Computing. 36, 1, p. 99-131 33 p.

Research output: Contribution to journalArticle

Chromosomes
Chromosome
Transposition
Genes
Genome Rearrangement

Reconstructing reticulate evolution in species - Theory and practice

Nakhleh, L., Warnow, T., Linder, C. R. & St. John, K., Jul 1 2005, In : Journal of Computational Biology. 12, 6, p. 796-811 16 p.

Research output: Contribution to journalArticle

Genes
Polynomials
Polynomial-time Algorithm
Phylogenetic Network
Gene

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree"

Mirarab, S., Bayzid, M. S., Boussau, B. & Warnow, T., Oct 9 2015, In : Science. 350, 6257, 171.

Research output: Contribution to journalArticle

SATé-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S. M., Yu, J., Stamatakis, A. P. & Randal Linder, C., Jan 1 2012, In : Systematic biology. 61, 1, p. 90-106 17 p.

Research output: Contribution to journalArticle

Sequence Alignment
sequence alignment
phylogenetics
phylogeny
alignment

Scaling statistical multiple sequence alignment to large datasets

Nute, M. & Warnow, T., Nov 11 2016, In : BMC genomics. 17, 764.

Research output: Contribution to journalArticle

Sequence Alignment
Bayes Theorem
Statistical Models
Datasets
Computational Biology

Short Quartet Puzzling: A new quartet-based phylogeny reconstruction algorithm

Snir, S., Warnow, T. & Rao, S., Jan 1 2008, In : Journal of Computational Biology. 15, 1, p. 91-103 13 p.

Research output: Contribution to journalArticle

Phylogeny
Reconstruction Algorithm
Joining
Maximum likelihood
Maximum Parsimony

SIESTA: Enhancing searches for optimal supertrees and species trees

Vachaspati, P. & Warnow, T., May 8 2018, In : BMC genomics. 19, 252.

Research output: Contribution to journalArticle

Simultaneous radiation of bird and mammal lice following the K-Pg boundary

Johnson, K. P., Nguyen, N. P., Sweet, A. D., Boyd, B. M., Warnow, T. & Allen, J. M., Jan 1 2018, In : Biology Letters. 14, 5, 20180141.

Research output: Contribution to journalArticle

Phthiraptera
lice
Birds
Mammals
mammals

Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent

Warnow, T., Oct 19 2012, In : PLoS Currents. ecurrents.RRN1308.

Research output: Contribution to journalArticle

Phylogeny
Sequence Alignment
Research

Statistical binning enables an accurate coalescent-based estimation of the avian tree

Mirarab, S., Bayzid, M. S., Boussau, B. & Warnow, T., Dec 12 2014, In : Science. 346, 6215, 1250463.

Research output: Contribution to journalArticle

Genes
Expressed Sequence Tags
Genome

Statistically based postprocessing of phylogenetic analysis by clustering

Stockham, C., Wang, L. S. & Warnow, T., Jan 1 2002, In : Bioinformatics. 18, SUPPL. 1, p. S285-S293

Research output: Contribution to journalArticle

Phylogenetic Analysis
Post-processing
Cluster Analysis
Clustering
Clustering algorithms

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge

Molloy, E. K. & Warnow, T., Jul 19 2019, In : Algorithms for Molecular Biology. 14, 1, 30 p., 14.

Research output: Contribution to journalArticle

Open Access
Phylogeny
Divide and conquer
Joining
Pipelines
Scalability

Steps toward accurate reconstructions of phylogenies from gene-order data

Moret, B. M. E., Tang, J., Wang, L. S. & Warnow, T., Nov 2002, In : Journal of Computer and System Sciences. 65, 3, p. 508-525 18 p.

Research output: Contribution to journalArticle

Phylogeny
Speedup
Genes
Gene
Joining

SuperFine: Fast and accurate supertree estimation

Swenson, M. S., Suri, R., Linder, C. R. & Warnow, T., Mar 1 2012, In : Systematic biology. 61, 2, p. 214-227 14 p.

Research output: Contribution to journalArticle

phylogenetics
phylogeny
estimation method
methodology
method

SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space

Vachaspati, P. & Warnow, T., Jul 2018, In : Molecular Phylogenetics and Evolution. 124, p. 122-136 15 p.

Research output: Contribution to journalArticle

gene
Genes
genes
methodology
loci

The asymmetric median tree - A new model for building consensus trees

Phillips, C. & Warnow, T., Dec 5 1996, In : Discrete Applied Mathematics. 71, 1-3, p. 311-335 25 p.

Research output: Contribution to journalArticle

Trees (mathematics)
Approximation algorithms
Computational complexity
Polynomials
Model

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Mulder, N., Schwartz, R., Brazas, M. D., Brooksbank, C., Gaeta, B., Morgan, S. L., Pauley, M. A., Rosenwald, A., Rustici, G., Sierk, M., Warnow, T. & Welch, L., Feb 2018, In : PLoS computational biology. 14, 2, e1005772.

Research output: Contribution to journalArticle

bioinformatics
education and training
Bioinformatics
Computational Biology
education

The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs

Bodlaender, H. L., Fellows, M. R., Hallett, M. T., Wareham, H. T. & Warnow, T. J., Aug 6 2000, In : Theoretical Computer Science. 244, 1-2, p. 167-188 22 p.

Research output: Contribution to journalArticle

Colored Graph
Phylogeny
Coloring
Hardness
DNA

The impact of multiple protein sequence alignment on phylogenetic estimation

Wang, L. S., Leebens-Mack, J., Wall, P. K., Beckmann, K., Depamphilis, C. W. & Warnow, T., Mar 22 2011, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 8, 4, p. 1108-1119 12 p., 5235137.

Research output: Contribution to journalArticle

Sequence Alignment
Phylogenetics
Protein Sequence
Alignment
Proteins

The interrelationships of placental mammals and the limits of phylogenetic inference

Tarver, J. E., Dos Reis, M., Mirarab, S., Moran, R. J., Parker, S., O'Reilly, J. E., King, B. L., O'Connell, M. J., Asher, R. J., Warnow, T., Peterson, K. J., Donoghue, P. C. J. & Pisani, D., Jan 1 2016, In : Genome biology and evolution. 8, 2, p. 330-344 15 p.

Research output: Contribution to journalArticle

sorting
Mammals
mammal
mammals
phylogenetics