T. Warnow

Most-cited papers

Towards complete and error-free genome assemblies of all vertebrate species
A. Rhie, Shane A. McCarthy, O. Fedrigo, Joana Damas +123 more
2020Nature2,918 citations Open access
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One thousand plant transcriptomes and the phylogenomics of green plants
J. Leebens-Mack, M. Barker, E. Carpenter, M. Deyholos +190 more
2019Nature1,374 citations Open access
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Long‐Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology‐Based Summary Methods
S. Roch, Michael G. Nute, T. Warnow
2018Systematic Biology90 citations Open access
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Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows
Nidhi Shah, Michael G. Nute, T. Warnow, Mihai Pop
2018Bioinform.84 citations
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Why sequence all eukaryotes?
M. Blaxter, J. Archibald, Anna K. Childers, J. Coddington +23 more
2022Proceedings of the National Academy of Sciences of the United States of America80 citations Open access
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The performance of coalescent-based species tree estimation methods under models of missing data
Michael G. Nute, Jed Chou, E. Molloy, T. Warnow
2018BMC Genomics75 citations Open access
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Multispecies Coalescent: Theory and Applications in Phylogenetics
S. Mirarab, L. Nakhleh, T. Warnow
2021Annual Review of Ecology, Evolution and Systematics70 citations
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MAGUS: Multiple sequence Alignment using Graph clUStering
Vladimir Smirnov, T. Warnow
2020Bioinform.69 citations Open access
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Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
Brandon Legried, E. Molloy, T. Warnow, S. Roch
2019bioRxiv45 citations Open access
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DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition
J. Willson, M. Roddur, Ba-Qiao Liu, P. Zaharias +1 more
2021Systematic Biology40 citations Open access
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FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
E. Molloy, T. Warnow
2019bioRxiv37 citations Open access
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Phylogeny Estimation Given Sequence Length Heterogeneity
Vladimir Smirnov, T. Warnow
2020Systematic Biology34 citations Open access
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A roadmap for global synthesis of the plant tree of life.
W. L. Eiserhardt, A. Antonelli, Dominic J. Bennett, Laura R. Botigué +19 more
2018American-Eurasian journal of botany33 citations Open access
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Phylogenomic branch length estimation using quartets
Yasamin Tabatabaee, Chao Zhang, T. Warnow, S. Mirarab
2023Bioinform.27 citations Open access
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TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Nidhi Shah, E. Molloy, Mihai Pop, T. Warnow
2021Bioinform.25 citations Open access
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Center–periphery structure in research communities
E. Wedell, Minhyuk Park, Dmitriy Korobskiy, T. Warnow +1 more
2021Quantitative Science Studies22 citations Open access
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MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences
Cheng-guo Shen, P. Zaharias, T. Warnow
2021Bioinform.22 citations Open access
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TreeMerge: a new method for improving the scalability of species tree estimation methods
E. Molloy, T. Warnow
2019Bioinform.22 citations Open access
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Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling
P. Zaharias, M. Grosshauser, T. Warnow
2022J. Comput. Biol.21 citations
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Co-citations in context: Disciplinary heterogeneity is relevant
James Bradley, Sitaram Devarakonda, Avon Davey, Dmitriy Korobskiy +4 more
2019Quantitative Science Studies19 citations Open access
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NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees
E. Molloy, T. Warnow
2018RECOMB Comparative Genomics Satellite Conference17 citations
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SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees
E. Wedell, Y. Cai, T. Warnow
2022IEEE/ACM Transactions on Computational Biology & Bioinformatics16 citations Open access
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Recent progress on methods for estimating and updating large phylogenies
P. Zaharias, T. Warnow
2021Philosophical Transactions of the Royal Society of London. Biological Sciences16 citations Open access
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WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment
Cheng Shen, Minhyuk Park, T. Warnow
2022J. Comput. Biol.15 citations
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UPP2: fast and accurate alignment of datasets with fragmentary sequences
Minhyuk Park, Stefan Ivanovic, Gillian Chu, Cheng-guo Shen +1 more
2023Bioinform.14 citations Open access
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Revisiting Evaluation of Multiple Sequence Alignment Methods.
T. Warnow
2021Methods in molecular biology13 citations
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FASTRAL: improving scalability of phylogenomic analysis
Payam Dibaeinia, Shayan Tabe-Bordbar, T. Warnow
2021Bioinform.12 citations Open access
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Divide-and-Conquer Tree Estimation: Opportunities and Challenges
T. Warnow
2019Bioinformatics and Phylogenetics12 citations
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Profile Hidden Markov Models Are Not Identifiable
Srilakshmi Pattabiraman, T. Warnow
2019IEEE/ACM Transactions on Computational Biology & Bioinformatics12 citations Open access
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Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation
Minhyuk Park, P. Zaharias, T. Warnow
2021Algorithms11 citations Open access
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ppIacerDC: a new scalable phylogenetic placement method
Elizabeth R. Koning, Malachi Phillips, T. Warnow
2021ACM International Conference on Bioinformatics, Computational Biology and Biomedicine11 citations Open access
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Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy
Qiuyi Zhang, Satish B. Rao, T. Warnow
2019Algorithms for Molecular Biology11 citations Open access
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Unblended disjoint tree merging using GTM improves species tree estimation
Vladimir Smirnov, T. Warnow
2019BMC Genomics11 citations Open access
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Viewing Computer Science through Citation Analysis
Sitaram Devarakonda, Dmitriy Korobskiy, T. Warnow, George Chacko
2019Scientometrics10 citations Open access
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SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement
Gillian Chu, T. Warnow
2022bioRxiv9 citations Open access
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Scalable and Accurate Phylogenetic Placement Using pplacer-XR
E. Wedell, Y. Cai, T. Warnow
2021International Conference on Algorithms for Computational Biology9 citations
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Finding scientific communities in citation graphs: Articles and authors
Shreya Chandrasekharan, M. Zaka, Stephen A. Gallo, Wenxi Zhao +3 more
2020Quantitative Science Studies9 citations Open access
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NJst and ASTRID are not statistically consistent under a random model of missing data
J. Rhodes, Michael G. Nute, T. Warnow
20209 citations
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Non-parametric correction of estimated gene trees using TRACTION
Sarah A. Christensen, E. Molloy, P. Vachaspati, Ananya Yammanuru +1 more
2020Algorithms for Molecular Biology8 citations Open access
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Weighted ASTRID: fast and accurate species trees from weighted internode distances
Ba-Qiao Liu, T. Warnow
2023Algorithms for Molecular Biology6 citations Open access
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Using INC Within Divide-and-Conquer Phylogeny Estimation
Thien Le, Aaron Sy, E. Molloy, Qiuyi Zhang +2 more
2019International Conference on Algorithms for Computational Biology6 citations
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CM++ - A Meta-method for Well-Connected Community Detection
V. Ramavarapu, F. Ayres, Minhyuk Park, Vidya Kamath Pailodi +3 more
2024Journal of Open Source Software5 citations Open access
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HMMerge: an ensemble method for multiple sequence alignment
Minhyuk Park, T. Warnow
2023Bioinformatics Advances5 citations Open access
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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
Cheng-guo Shen, Ba-Qiao Liu, K. Williams, T. Warnow
2023bioRxiv5 citations Open access
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Quintet Rooting: rooting species trees under the multi-species coalescent model
Yasamin Tabatabaee, Kowshika Sarker, T. Warnow
2022Bioinform.5 citations Open access
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WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity
Ba-Qiao Liu, T. Warnow
2022bioRxiv5 citations Open access
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AOC: Assembling overlapping communities
Akhil Jakatdar, Ba-Qiao Liu, T. Warnow, George Chacko
2022Quantitative Science Studies5 citations Open access
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TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees
Sarah A. Christensen, E. Molloy, P. Vachaspati, T. Warnow
2019Workshop on Algorithms in Bioinformatics5 citations
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Large-scale Species Tree Estimation
E. Molloy, T. Warnow
20195 citations
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BSCAMPP: Batch Scaled Phylogenetic Placement on Large Trees
E. Wedell, Cheng-guo Shen, T. Warnow
2024bioRxiv4 citations Open access
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