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Bioinformatics (Oxford, England)|November 18, 2021
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequencesChengze Shen, Paul Zaharias, Tandy WarnowPhilosophical Transactions of the Royal Society of London. Series B, Biological Sciences|August 22, 2022
Recent progress on methods for estimating and updating large phylogeniesPaul Zaharias, Tandy WarnowJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|January 5, 2022
Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon SamplingPaul Zaharias, Martin Grosshauser, Tandy WarnowBioinformatics (Oxford, England)|July 28, 2021
Accurate large-scale phylogeny-aware alignment using BAli-PhyMaya Gupta, Paul Zaharias, Tandy WarnowIEEE/ACM Transactions on Computational Biology and Bioinformatics|July 18, 2022
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging ProblemPaul Zaharias, Vladimir Smirnov, Tandy WarnowMethods in Molecular Biology (Clifton, N.J.)|April 29, 2026
Phylogenetic Placement Using SCAMPP and Batch-SCAMPPEleanor Wedell, Chengze Shen, Tandy WarnowIEEE Transactions on Computational Biology and Bioinformatics|August 14, 2025
BSCAMPP: Batch-Scaled Phylogenetic Placement on Large TreesEleanor Wedell, Chengze Shen, Tandy WarnowJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|May 16, 2022
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model AlignmentChengze Shen, Minhyuk Park, Tandy WarnowPlos Computational Biology|May 28, 2026
TIPP-SD: A new method for species detection in microbiomesChengze Shen, Eleanor Wedell, Mihai Pop, et al.Plos Computational Biology|April 4, 2025
TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomicsChengze Shen, Eleanor Wedell, Mihai Pop, et al.Pageof 14