Tandy Warnow

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Frequently cocited publications: Features and kinetics

James Bradley, Sitaram Devarakonda, Dmitriy Korobskiy, 2020, Quantitative Science Studies.

Binning Code for Mirarab et. al.

Tandy Warnow, Siavash Mirarab, Shamsuzzoha Bayzid, 2014 .

Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees

Tandy Warnow, Erin K. Molloy, Xilin Yu, 2020, bioRxiv.

Faculty of 1000 evaluation for Phase transition in the sample complexity of likelihood-based phylogeny inference.

Tandy Warnow, 2018 .

Data from: SuperFine: fast and accurate supertree estimation

C. Randal Linder, Tandy Warnow, M. Shel Swenson, 2011 .

Faculty Opinions recommendation of Reversible polymorphism-aware phylogenetic models and their application to tree inference.

Tandy Warnow, 2017 .

Non-parametric correction of estimated gene trees using TRACTION

Tandy Warnow, Erin K. Molloy, Sarah Christensen, 2020, Algorithms for Molecular Biology.

Concatenation Analyses in the Presence of Incomplete Lineage Sorting

Tandy Warnow, T. Warnow, 2015, PLoS currents.

Proceedings of the 9th international conference on Algorithms in bioinformatics

Tandy Warnow, Steven L. Salzberg, 2009 .

FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models

Tandy Warnow, Erin K. Molloy, 2020, Bioinform..

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

Tandy Warnow, Erin K. Molloy, T. Warnow, 2018, Algorithms for Molecular Biology.

Faculty Opinions recommendation of Accurate inference of tree topologies from multiple sequence alignments using deep learning.

Tandy Warnow, 2019 .

An Overview of Phylogeny Reconstruction

C. Randal Linder, Tandy Warnow, 2005 .

Data access for the 1,000 Plants (1KP) project

Xiao Sun, Ram Samudrala, Ling-Hong Hung, 2014, GigaScience.

Tree Alignment

Tandy Warnow, 2008, Encyclopedia of Algorithms.

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

Tandy Warnow, Erin K. Molloy, 2019 .

Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation

Satish Rao, Tandy Warnow, Erin K. Molloy, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Inferring Evolutionary History from DNA Sequences (Extended Abstract)

Sampath Kannan, Tandy Warnow, Sampath Kannan, 1990, IEEE Annual Symposium on Foundations of Computer Science.

Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 17-19 January 1999, Baltimore, Maryland, USA

Robert E. Tarjan, Tandy Warnow, R. Tarjan, 1999, SODA.

Faculty Opinions recommendation of Skmer: assembly-free and alignment-free sample identification using genome skims.

Tandy Warnow, 2019 .

Reconstructing phylogenies from gene-content and gene-order data

Jijun Tang, Bernard M. E. Moret, Tandy Warnow, 2007, Mathematics of Evolution and Phylogeny.

Computing and Combinatorics: 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003, Proceedings

Binhai Zhu, Tandy Warnow, 2003 .

Divide-and-Conquer Tree Estimation: Opportunities and Challenges

Tandy Warnow, T. Warnow, 2019, Bioinformatics and Phylogenetics.

Viewing computer science through citation analysis: Salton and Bergmark Redux

Sitaram Devarakonda, Dmitriy Korobskiy, Tandy Warnow, 2020, Scientometrics.

Character-Based Reconstruction of a Linguistic Cladogram

Tandy Warnow, Ann Taylor, Don Ringe, 2000 .

Distance-based Tree Estimation Methods

Tandy Warnow, 2017 .

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

Mihai Pop, Tandy Warnow, Bryan White, 2016, npj Biofilms and Microbiomes.

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

Tandy Warnow, Kevin Liu, Sindhu Raghavan, 2009, TCBB.

Supertree Construction: Opportunities and Challenges

Tandy Warnow, T. Warnow, 2018, 1805.03530.

ASTRID: Accurate Species TRees from Internode Distances

Tandy Warnow, Pranjal Vachaspati, 2015 .

Profile Hidden Markov Models are Not Identifiable.

Tandy Warnow, Srilakshmi Pattabiraman, 2019, IEEE/ACM transactions on computational biology and bioinformatics.

Faculty of 1000 evaluation for Efficient exploration of the space of reconciled gene trees.

Tandy Warnow, 2018 .

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models

Tandy Warnow, Erin K Molloy, 2020, Bioinformatics.

Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss

Tandy Warnow, Erin K. Molloy, Sebastien Roch, 2019, bioRxiv.

Algorithmic techniques for improving the speed and accuracy of phylogenetic methods

Tandy Warnow, Usman Roshan, T. Warnow, 2004 .

In Memoriam: Eugene L. Lawler

Jan Karel Lenstra, David B. Shmoys, Tandy Warnow, 1994, J. Comput. Biol..

Multiple Sequence Alignment

Tandy Warnow, T. Warnow, 2017 .

SATe-Enabled Phylogenetic Placement

Tandy Warnow, 2013 .

Finding scientific communities in citation graphs: Articles and authors

Dmitriy Korobskiy, Tandy Warnow, Wenxi Zhao, 2020, Quantitative Science Studies.

Indo‐European and Computational Cladistics

Tandy Warnow, Ann Taylor, Don Ringe, 2002 .

Phylogenomics and population genomics: Moddels, algorithms, and analytical tools

Noah A. Rosenberg, Luay Nakhleh, Tandy Warnow, 2012, PSB 2012.

Supplementary Online Material, PASTA: ultra-large multiple sequence alignment

Tandy Warnow, Nam Nguyen, Siavash Mirarab, 2014 .

Some combinatorial optimization problems in phylogenetics

Tandy Warnow, T. Warnow, 1999 .

A detailed study of breakpoint analysis

David A. Bader, Bernard M. E. Moret, Tandy Warnow, 2001 .

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

Gad M. Landau, Steven Skiena, Roded Sharan, 2006, WABI 2012.

Absolute phylogeny: true trees from short sequences

Bernard M. E. Moret, Tandy Warnow, Bernard M. E. Moret, 2001, ACM-SIAM Symposium on Discrete Algorithms.

Finding scientific communities in citation graphs: Articles and authors pdf

Tandy Warnow, George Chacko, Shreya Chandrasekharan, 2020, Quantitative Science Studies.

Computing and Combinatorics

Kyung-Yong Chwa, J. van Leeuwen, Bernard Chazelle, 2001, Lecture Notes in Computer Science.

MAGUS: Multiple sequence Alignment using Graph clUStering

Tandy Warnow, Vladimir Smirnov, T. Warnow, 2020, Bioinform..

Unblended disjoint tree merging using GTM improves species tree estimation

Tandy Warnow, Vladimir Smirnov, T. Warnow, 2019, BMC Genomics.

Performance of Supertree Methods on Various Data Set Decompositions

Bernard M. E. Moret, Tandy Warnow, Tiffani L. Williams, 2004 .

Beyond gap models: Reconstructing alignments and phylogenies under genomic-scale events

Bernard M. E. Moret, Michael Brudno, Tandy Warnow, 2007 .

Benchmarking Statistical Multiple Sequence Alignment

Tandy Warnow, Michael G. Nute, Michael Nute, 2018, bioRxiv.

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

C. Randal Linder, Tandy Warnow, Kevin Liu, 2011, PLoS currents.

Running Head: SUPERFINE Title: SuperFine: Fast and Accurate Supertree Estimation

C. Randal Linder, Tandy Warnow, M. Shel Swenson, 2011 .

Using INC within Divide-and-Conquer Phylogeny Estimation - Datasets

Satish Rao, Tandy Warnow, Erin K. Molloy, 2019 .

Co-citations in context: Disciplinary heterogeneity is relevant

Sitaram Devarakonda, Dmitriy Korobskiy, Tandy Warnow, 2019, Quantitative Science Studies.

Introduction to Computational Phylogenetics

Tandy Warnow, T. Warnow, 2013 .

New Software for Computational Phylogenetics

Bernard M. E. Moret, Tandy Warnow, Li-San Wang, 2002 .

Phylogenetic networks

Luay Nakhleh, Tandy Warnow, T. Warnow, 2004 .

Faculty Opinions recommendation of Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

Tandy Warnow, 2017 .

Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings

Tandy Warnow, Steven L. Salzberg, S. Salzberg, 2009, WABI.

Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference

C. Randal Linder, Tandy Warnow, Kevin Liu, 2010, PLoS currents.

Revisiting Evaluation of Multiple Sequence Alignment Methods.

Tandy Warnow, T. Warnow, 2021, Methods in molecular biology.

Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP.

Tandy Warnow, Siavash Mirarab, T. Warnow, 2021, Methods in molecular biology.

Fragmentary Sequences for Variable-Sized RNAsim Datasets

Tandy Warnow, Eleanor Wedell, 2021 .

Multispecies Coalescent: Theory and Applications in Phylogenetics

Luay Nakhleh, Tandy Warnow, Siavash Mirarab, 2021, Annual Review of Ecology, Evolution, and Systematics.

MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences

Tandy Warnow, Chengze Shen, Paul Zaharias, 2021 .

Data from: Accurate Large-scale Phylogeny-Aware Alignment using BAli-Phy

Tandy Warnow, Paul Zaharias, Maya Gupta, 2021 .

Data from "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The issue of taxon sampling"

Tandy Warnow, Paul Zaharias, Martin Grosshauser, 2021 .

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

Tandy Warnow, Siavash Mirarab, Pranjal Vachaspati, 2015, bioRxiv.

Data from: FastMulRFS: Statistically consistent polynomial time species tree estimation under gene duplication

Tandy Warnow, Erin K. Molloy, 2019 .

An experimental study comparing linguistic phylogenetic reconstruction methods

Luay Nakhleh, Tandy Warnow, Steven N. Evans, 2013 .

Network (Reticulated) Evolution: Biology, Models, and Algorithms

Bernard M. E. Moret, Tandy Warnow, T. Warnow, 2004 .

Algorithms and heuristics for combinatorial optimization in phylogeny

Vijaya Ramachandran, Tandy Warnow, Ganeshkumar Ganapathysaravanabavan, 2006 .

One thousand plant transcriptomes and the phylogenomics of green plants

Xun Xu, Fan Yang, Ivo Grosse, 2019, Nature.

High-Performance Algorithm Engineering for Gene-Order Phylogenies

David A. Bader, Bernard M. E. Moret, Tandy Warnow, .

Chemical Phylogenetics of Histone Deacetylases

James E. Bradner, Tandy Warnow, Stephen J. Haggarty, 2010, Nature chemical biology.

Large-scale multiple sequence alignment and tree estimation using SATé.

Tandy Warnow, Kevin J. Liu, Kevin Liu, 2014, Methods in molecular biology.

New approaches for reconstructing phylogenies based on gene order

Bernard M. E. Moret, Tandy Warnow, Stacia K. Wyman, 2001 .

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting.

Tandy Warnow, Md. Shamsuzzoha Bayzid, Siavash Mirarab, 2016, Systematic biology.

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

Tandy Warnow, Pranjal Vachaspati, T. Warnow, 2018, Molecular phylogenetics and evolution.

Treelength Optimization for Phylogeny Estimation

Tandy Warnow, Kevin Liu, Kevin J. Liu, 2012, PloS one.

A comparison of phylogenetic reconstruction methods on an Indo‐European dataset

Luay Nakhleh, Tandy Warnow, Steven N. Evans, 2005 .

Data from TRACTION: Fast non-parametric improvement of estimated gene trees

Tandy Warnow, Erin K. Molloy, Pranjal Vachaspati, 2019 .

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

Tandy Warnow, Siavash Mirarab, Pranjal Vachaspati, 2015 .

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

Tandy Warnow, Sebastien Roch, T. Warnow, 2015, Systematic biology.

Advances in phylogeny reconstruction from gene order and content data.

Bernard M. E. Moret, Tandy Warnow, Bernard M E Moret, 2005, Methods in enzymology.

Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets

Tandy Warnow, Michael G. Nute, Michael Nute, 2018, Systematic biology.

Large-scale Species Tree Estimation

Tandy Warnow, Erin K. Molloy, T. Warnow, 2019, 1904.02600.

To include or not to include: The impact of gene filtering on species tree estimation methods

Tandy Warnow, Erin K. Molloy, Erin K Molloy, 2017, bioRxiv.

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

Sergey Koren, Adam M. Phillippy, Eugene W. Myers, 2020, Nature.

ASTRID: Accurate Species TRees from Internode Distances

Tandy Warnow, Pranjal Vachaspati, T. Warnow, 2015, bioRxiv.

Computational Phylogenetics: An Introduction to Designing Methods for Phylogeny Estimation

Tandy Warnow, T. Warnow, 2017 .

To include or not to include: The impact of gene filtering on species tree estimation methods

Tandy Warnow, Erin K. Molloy, T. Warnow, 2017 .

Constructing phylogenetic trees efficiently using compatibility criteria

Tandy Warnow, T. Warnow, 1993 .

Multiple sequence alignment: a major challenge to large-scale phylogenetics.

Tandy Warnow, Kevin Liu, C Randal Linder, 2010, PLoS currents.

Phylogeny Estimation Given Sequence Length Heterogeneity

Tandy Warnow, Vladimir Smirnov, T. Warnow, 2020, Systematic biology.

The Short Quartet Method

László A. Székely, Péter L. Erdös, Mike Steel, 1998 .

SuperFine: fast and accurate supertree estimation.

Tandy Warnow, Rahul Suri, C Randal Linder, 2012, Systematic biology.

Disk covering methods improve phylogenomic analyses

Tandy Warnow, Md. Shamsuzzoha Bayzid, Md Shamsuzzoha Bayzid, 2014, BMC Genomics.

BBCA: Improving the scalability of *BEAST using random binning

Tandy Warnow, Siavash Mirarab, T. Warnow, 2014, BMC Genomics.