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Research Output 1990 2019

2019
Phylogeny
Joining
Scalability
Large Data Sets
Polynomials

Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets

Nute, M., Saleh, E. & Warnow, T., May 1 2019, In : Systematic biology. 68, 3, p. 396-411 16 p.

Research output: Contribution to journalArticle

Open Access
Sequence Alignment
sequence alignment
Benchmarking
Indonesia
protein

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

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

Shah, N., Nute, M. G., Warnow, T. & Pop, M., May 1 2019, In : Bioinformatics. 35, 9, p. 1613-1614 2 p.

Research output: Contribution to journalLetter

Workflow
Bioinformatics
Computational Biology
Work Flow
Correctness

New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation

Warnow, T., Jan 1 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer-Verlag, p. 3-21 19 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Divide and conquer
Phylogenetics
Scalability
Subset
Large Data Sets

Using INC Within Divide-and-Conquer Phylogeny Estimation

Le, T., Sy, A., Molloy, E. K., Zhang, Q. R., Rao, S. & Warnow, T., Jan 1 2019, Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Proceedings. Vega-Rodríguez, M. A., Holmes, I. & Martín-Vide, C. (eds.). Springer-Verlag, p. 167-178 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11488 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phylogeny
Divide and conquer
Maximum likelihood
Molecular biology
Maximum Likelihood
2018

Are Profile Hidden Markov Models Identifiable?

Pattabiraman, S. & Warnow, T., Aug 15 2018, ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, p. 448-456 9 p. (ACM-BCB 2018 - Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hidden Markov models
Computational Biology
Sequence Alignment
Statistical Models
Bioinformatics

A roadmap for global synthesis of the plant tree of life

Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., Enquist, B. J., Forest, F., Kim, J. T., Kozlov, A. M., Leitch, I. J., Maitner, B. S., Mirarab, S., Piel, W. H., Pérez-Escobar, O. A., Pokorny, L., Rahbek, C., Sandel, B., Smith, S. A., Stamatakis, A. & 3 othersVos, R. A., Warnow, T. & Baker, W. J., Mar 1 2018, In : American journal of botany. 105, 3, p. 614-622 9 p.

Research output: Contribution to journalArticle

synthesis
phylogeny
phylogenetics
informatics
botanists

Gene tree parsimony for incomplete gene trees: Addressing true biological loss

Bayzid, M. S. & Warnow, T., Jan 19 2018, In : Algorithms for Molecular Biology. 13, 1, 1.

Research output: Contribution to journalArticle

Parsimony
Genes
Gene
Incompleteness
Duplication

New absolute fast converging phylogeny estimation methods with improved scalability and accuracy

Zhang, Q., Rao, S. & Warnow, T., Aug 1 2018, 18th International Workshop on Algorithms in Bioinformatics, WABI 2018. Parida, L. & Ukkonen, E. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 8. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 113).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Scalability
Joining
Polynomials
Trees (mathematics)
Maximum likelihood

NJMerge: A Generic technique for scaling phylogeny estimation methods and its application to species trees

Molloy, E. K. & Warnow, T., Jan 1 2018, Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings. Ouangraoua, A. & Blanchette, M. (eds.). Springer-Verlag, p. 260-276 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11183 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phylogeny
Scaling
Scalability
Subset
Divide and conquer

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

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

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

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

Molloy, E. K. & Warnow, T., Nov 13 2018, (In preparation) 30 p.

Research output: Working paper

Joining
Pipelines
Scalability
Polynomials
Phylogeny

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

Vachaspati, P. & Warnow, T., Jul 1 2018, In : Molecular Phylogenetics and Evolution. 124, p. 122-136 15 p.

Research output: Contribution to journalArticle

gene
Genes
genes
methodology
loci

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 1 2018, In : PLoS computational biology. 14, 2, e1005772.

Research output: Contribution to journalArticle

bioinformatics
education and training
Bioinformatics
Computational Biology
education

The performance of coalescent-based species tree estimation methods under models of missing data

Nute, M., Chou, J., Molloy, E. K. & Warnow, T., May 8 2018, In : BMC genomics. 19, 286.

Research output: Contribution to journalArticle

Genes
Horizontal Gene Transfer
Gene Duplication
Expressed Sequence Tags
Gene Deletion

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

Molloy, E. K. & Warnow, T., Mar 1 2018, In : Systematic biology. 67, 2, p. 285-303 19 p.

Research output: Contribution to journalArticle

estimation method
gene
Genes
genes
sorting
2017
Computer science
Students
Computational methods
Statistics
Phylogeny

Enhancing searches for optimal trees using SIESTA

Vachaspati, P. & Warnow, T., Jan 1 2017, Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Proceedings. Nakhleh, L. & Meidanis, J. (eds.). Springer-Verlag, p. 232-255 24 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10562 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Trees (mathematics)
Dynamic programming
Set theory
Data structures
Polynomials

FastRFS: Fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

Vachaspati, P. & Warnow, T., Jan 1 2017, In : Bioinformatics. 33, 5, p. 631-639 9 p.

Research output: Contribution to journalArticle

Constrained optimization
Optimization
Trees (mathematics)
Dynamic programming
Large Data Sets

Gene tree parsimony for incomplete gene trees

Bayzid, M. S. & Warnow, T., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Sampling
Dynamic programming

Optimal completion of incomplete gene trees in polynomial time using OCTAL

Christensen, S., Molloy, E. K., Vachaspati, P. & Warnow, T., Aug 1 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Reinert, K. & Schwartz, R. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 27. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 88).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Polynomials
Binary trees

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

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

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
2016

An analytical upper bound on the number of loci required for all splits of a species tree to appear in a set of gene trees

Uricchio, L. H., Warnow, T. & Rosenberg, N. A., Nov 11 2016, In : BMC bioinformatics. 17, 417.

Research output: Contribution to journalArticle

Locus
Genes
Upper bound
Gene
Topology

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

Nguyen, N. P., Warnow, T., Pop, M. & White, B., Apr 20 2016, In : npj Biofilms and Microbiomes. 2, 16004.

Research output: Contribution to journalReview article

Cluster Analysis
Sequence Alignment
Microbiota

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB’s Education Committee)

Welch, L., Brooksbank, C., Schwartz, R., Morgan, S. L., Gaeta, B., Kilpatrick, A. M., Mietchen, D., Moore, B. L., Mulder, N., Pauley, M., Pearson, W., Radivojac, P., Rosenberg, N., Rosenwald, A., Rustici, G. & Warnow, T., May 1 2016, In : PLoS computational biology. 12, 5, e1004943.

Research output: Contribution to journalArticle

Evaluating summarymethods for multilocus species tree estimation in the presence of incomplete lineage sorting

Mirarab, S., Bayzid, M. S. & Warnow, T., Jan 1 2016, In : Systematic biology. 65, 3, p. 366-380 15 p.

Research output: Contribution to journalArticle

sorting
gene
Genes
genes
estimation method

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

Hansen, T. A., Mollerup, S., Nguyen, N. P., White, N. E., Coghlan, M., Alquezar-Planas, D. E., Joshi, T., Jensen, R. H., Fridholm, H., Kjartansdóttir, K. R., Mourier, T., Warnow, T., Belsham, G. J., Bunce, M., Willerslev, E., Nielsen, L. P., Vinner, L. & Hansen, A. J., Aug 17 2016, In : Emerging microbes & infections. 5, 8, p. e90

Research output: Contribution to journalArticle

Picornaviridae
High-Throughput Nucleotide Sequencing
Zoonoses
Cardiovirus
Arthropod Vectors

HIPPI: Highly accurate protein family classification with ensembles of HMMs

Nguyen, N. P., Nute, M., Mirarab, S. & Warnow, T., Nov 11 2016, In : BMC genomics. 17, 765.

Research output: Contribution to journalArticle

Computational Biology
Sequence Alignment
Proteins
Databases
Metagenomics

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

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
2015

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

Chou, J., Gupta, A., Yaduvanshi, S., Davidson, R., Nute, M., Mirarab, S. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-11 11 p.

Research output: Contribution to journalArticle

Genes
Sequence Alignment
Genetic Recombination

ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

Mirarab, S. & Warnow, T., Jun 15 2015, In : Bioinformatics. 31, 12, p. i44-i52

Research output: Contribution to journalArticle

Genes
Gene
Locus
Sorting
Search Space

ASTRID: Accurate species TRees from internode distances

Vachaspati, P. & Warnow, T., Jan 1 2015, In : BMC genomics. 16, p. 1-13 13 p.

Research output: Contribution to journalArticle

Datasets
Genes

Concatenation analyses in the presence of incomplete lineage sorting

Warnow, T., May 22 2015, In : PLoS Currents. 7, TREEOFLIFE

Research output: Contribution to journalArticle

Steel
Genome
Genes
Surveys and Questionnaires

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

GOBLET Consortium, Apr 1 2015, In : PLoS computational biology. 11, 4, e1004143.

Research output: Contribution to journalArticle

bioinformatics
education and training
Bioinformatics
Computational Biology
education

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

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

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

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

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds"

Cracraft, J., Houde, P., Ho, S. Y. W., Mindell, D. P., Fjeldså, J., Lindow, B., Edwards, S. V., Rahbek, C., Mirarab, S., Warnow, T., Gilbert, M. T. P., Zhang, G., Braun, E. L. & Jarvis, E. D., Sep 25 2015, In : Science. 349, 6255, p. 1460-b

Research output: Contribution to journalComment/debate

Birds
Biological Extinction
Genome
Phylogeny

Ultra-large alignments using ensembles of hidden Markov models

Nguyen, N. P., Mirarab, S., Kumar, K. & Warnow, T., 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Springer Verlag, Vol. 9029. p. 259-260 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hidden Markov models
Markov Model
Alignment
Ensemble

Ultra-large alignments using phylogeny-aware profiles

Nguyen, N. P. D., Mirarab, S., Kumar, K. & Warnow, T., Jun 16 2015, In : Genome biology. 16, 1, 124.

Research output: Contribution to journalArticle

sequence alignment
Phylogeny
Sequence Alignment
phylogeny
amino acid sequences

Weighted statistical binning: Enabling statistically consistent genome-scale phylogenetic analyses

Bayzid, M. S., Mirarab, S., Boussau, B. & Warnow, T., Jun 18 2015, In : PloS one. 10, 6, e0129183.

Research output: Contribution to journalArticle

Genes
Genome
genome
phylogeny
genes