Inferring Evolutionary History from DNA Sequences (Extended Abstract) - Sampath Kannan; Tandy J. Warnow (FOCS, 1990)

Determining the Evolutionary Tree. - Sampath Kannan; Eugene L. Lawler; Tandy J. Warnow (SODA, 1990)

Triangulating Three-Colored Graphs. - Sampath Kannan; Tandy J. Warnow (SODA, 1991)

Two Strikes Against Perfect Phylogeny. - Hans L. Bodlaender; Michael R. Fellows; Tandy J. Warnow (ICALP, 1992)

Triangulating 3-Colored Graphs. - Sampath Kannan; Tandy J. Warnow (SIAM J. Discret. Math., 1992)

Tree Compatibility and Inferring Evoluationary History. - Tandy J. Warnow (SODA, 1993)

Kaikoura Tree Theorems: Computing the Maximum Agreement Subtree. - Mike A. Steel; Tandy J. Warnow (Inf. Process. Lett., 1993)

Tree Compatibility and Inferring Evolutionary History. - Tandy J. Warnow (J. Algorithms, 1994)

Inferring Evolutionary History from DNA Sequences. - Sampath Kannan; Tandy J. Warnow (SIAM J. Comput., 1994)

Triangulating Vertex-Colored Graphs. - Fred R. McMorris; Tandy J. Warnow; Thomas Wimer (SIAM J. Discret. Math., 1994)

Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility. - Craig J. Benham; Sampath Kannan; Tandy J. Warnow (CPM, 1995)

A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies when the Number of Character States is Fixed. - Sampath Kannan; Tandy J. Warnow (SODA, 1995)

Computing the Local Consensus of Trees. - Sampath Kannan; Tandy J. Warnow; Shibu Yooseph (SODA, 1995)

A Robust Model for Finding Optimal Evolutionary Trees. - Martin Farach; Sampath Kannan; Tandy J. Warnow (Algorithmica, 1995)

Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility. - Craig J. Benham; Sampath Kannan; Michael Paterson; Tandy J. Warnow (J. Comput. Biol., 1995)

Tree Reconstruction from Partial Orders. - Sampath Kannan; Tandy J. Warnow (SIAM J. Comput., 1995)

Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages. - Maria Luisa Bonet; Cynthia A. Phillips; Tandy J. Warnow; Shibu Yooseph (Mathematical Hierarchies and Biology, 1996)

Reconstructing the Evolutionary History of Natural Languages. - Tandy J. Warnow; Donald Ringe; Ann Taylor (SODA, 1996)

Minimizing Phylogenetic Number To Find Good Evolutionary Trees. - Leslie Ann Goldberg; Paul W. Goldberg; Cynthia A. Phillips; Elizabeth Sweedyk; Tandy J. Warnow (Discret. Appl. Math., 1996)

The Asymmetric Median Tree - A New Model for Building Consensus Trees. - Cynthia A. Phillips; Tandy J. Warnow (Discret. Appl. Math., 1996)

Determining the Evolutionary Tree Using Experiments. - Sampath Kannan; Eugene L. Lawler; Tandy J. Warnow (J. Algorithms, 1996)

Parsimony is Hard to Beat. - Kenneth Rice; Tandy J. Warnow (COCOON, 1997)

Constructing Big Trees from Short Sequences. - Péter L. Erdös; Mike A. Steel; László A. Székely; Tandy J. Warnow (ICALP, 1997)

Local Quartet Splits of a Binary Tree Infer All Quartet Splits Via One Dyadic Inference Rule. - Péter L. Erdös; Mike A. Steel; László A. Székely; Tandy J. Warnow (Comput. Artif. Intell., 1997)

A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies. - Sampath Kannan; Tandy J. Warnow (SIAM J. Comput., 1997)

Better Methods for Solving Parsimony and Compatibility. - Maria Luisa Bonet; Mike A. Steel; Tandy J. Warnow; Shibu Yooseph (J. Comput. Biol., 1998)

Computing the Local Consensus of Trees. - Sampath Kannan; Tandy J. Warnow (SIAM J. Comput., 1998)

Solving Large Scale Phylogenetic Problems using DCM2. - Daniel H. Huson; Lisa Vawter; Tandy J. Warnow (ISMB, 1999)

Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. - Daniel H. Huson; Scott Nettles; Tandy J. Warnow (RECOMB, 1999)

Estimating Large Distances in Phylogenetic Reconstruction. - Daniel H. Huson; Kelly Ann Smith; Tandy J. Warnow (WAE, 1999)

Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. - Monika Rauch Henzinger; Valerie King; Tandy J. Warnow (Algorithmica, 1999)

Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction. - Daniel H. Huson; Scott Nettles; Tandy J. Warnow (J. Comput. Biol., 1999)

Hybrid Tree Reconstruction Methods. - Daniel H. Huson; Scott Nettles; Kenneth Rice; Tandy J. Warnow; Shibu Yooseph (ACM J. Exp. Algorithmics, 1999)

A few logs suffice to build (almost) all trees (I). - Péter L. Erdös; Michael Anthony Steel; László A. Székely; Tandy J. Warnow (Random Struct. Algorithms, 1999)

Constructing Evolutionary Trees in the Presence of Polymorphic Characters. - Maria Luisa Bonet; Cynthia A. Phillips; Tandy J. Warnow; Shibu Yooseph (SIAM J. Comput., 1999)

A Few Logs Suffice to Build (almost) All Trees: Part II. - Péter L. Erdös; Michael Anthony Steel; László A. Székely; Tandy J. Warnow (Theor. Comput. Sci., 1999)

Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics. - Bernard M. E. Moret; Tandy J. Warnow (Experimental Algorithmics, 2000)

A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. - Mary E. Cosner; Robert K. Jansen; Bernard M. E. Moret; Linda A. Raubeson; Li-San Wang; Tandy J. Warnow; Stacia K. Wyman (ISMB, 2000)

The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs. - Hans L. Bodlaender; Michael R. Fellows; Michael T. Hallett; Todd Wareham; Tandy J. Warnow (Theor. Comput. Sci., 2000)

New approaches for reconstructing phylogenies from gene order data. - Bernard M. E. Moret; Li-San Wang; Tandy J. Warnow; Stacia K. Wyman (ISMB (Supplement of Bioinformatics), 2001)

Designing fast converging phylogenetic methods. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (ISMB (Supplement of Bioinformatics), 2001)

A New Implmentation and Detailed Study of Breakpoint Analysis. - Bernard M. E. Moret; Stacia K. Wyman; David A. Bader; Tandy J. Warnow; Mi Yan (Pacific Symposium on Biocomputing, 2001)

Absolute convergence: true trees from short sequences. - Tandy J. Warnow; Bernard M. E. Moret; Katherine St. John (SODA, 2001)

Estimating true evolutionary distances between genomes. - Li-San Wang; Tandy J. Warnow (STOC, 2001)

Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time. - Ganeshkumar Ganapathysaravanabavan; Tandy J. Warnow (WABI, 2001)

The Performance of Phylogenetic Methods on Trees of Bounded Diameter. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (WABI, 2001)

Approximating the Complement of the Maximum Compatible Subset of Leaves of k Trees. - Ganeshkumar Ganapathy; Tandy J. Warnow (APPROX, 2002)

Statistically based postprocessing of phylogenetic analysis by clustering. - Cara Stockham; Li-San Wang; Tandy J. Warnow (ISMB, 2002)

The Accuracy of Fast Phylogenetic Methods for Large Datasets. - Luay Nakhleh; Bernard M. E. Moret; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2002)

Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. - Li-San Wang; Robert K. Jansen; Bernard M. E. Moret; Linda A. Raubeson; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2002)

Sequence-Length Requirements for Phylogenetic Methods. - Bernard M. E. Moret; Usman Roshan; Tandy J. Warnow (WABI, 2002)

Estimating the Deviation from a Molecular Clock. - Luay Nakhleh; Usman Roshan; Lisa Vawter; Tandy J. Warnow (WABI, 2002)

Toward New Software for Computational Phylogenetics. - Bernard M. E. Moret; Li-San Wang; Tandy J. Warnow (Computer, 2002)

Steps toward accurate reconstructions of phylogenies from gene-order data. - Bernard M. E. Moret; Jijun Tang; Li-San Wang; Tandy J. Warnow (J. Comput. Syst. Sci., 2002)

High-Performance Algorithm Engineering for Computational Phylogenetics. - Bernard M. E. Moret; David A. Bader; Tandy J. Warnow (J. Supercomput., 2002)

Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. - Luay Nakhleh; Jerry Sun 001; Tandy J. Warnow; C. Randal Linder; Bernard M. E. Moret; Anna Tholse (Pacific Symposium on Biocomputing, 2003)

Better Hill-Climbing Searches for Parsimony. - Ganeshkumar Ganapathy; Vijaya Ramachandran; Tandy J. Warnow (WABI, 2003)

Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. - Katherine St. John; Tandy J. Warnow; Bernard M. E. Moret; Lisa Vawter (J. Algorithms, 2003)

Analyzing the Order of Items in Manuscripts of The Canterbury Tales. - Matthew Spencer; Barbara Bordalejo; Li-San Wang; Adrian C. Barbrook; Linne R. Mooney; Peter Robinson 003; Tandy J. Warnow; Christopher J. Howe (Comput. Humanit., 2003)

Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. - Usman Roshan; Bernard M. E. Moret; Tandy J. Warnow; Tiffani L. Williams (CSB, 2004)

Reconstructing reticulate evolution in species: theory and practice. - Luay Nakhleh; Tandy J. Warnow; C. Randal Linder (RECOMB, 2004)

On contract-and-refine transformations between phylogenetic trees. - Ganeshkumar Ganapathy; Vijaya Ramachandran; Tandy J. Warnow (SODA, 2004)

Unidentifiable Divergence Times in Rates-across-Sites Models. - Steven N. Evans; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. - Bernard M. E. Moret; Luay Nakhleh; Tandy J. Warnow; C. Randal Linder; Anna Tholse; Anneke Padolina; Jerry Sun 001; Ruth E. Timme (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

Preface. - Tandy J. Warnow; Binhai Zhu (Theor. Comput. Sci., 2004)

Pattern Identification in Biogeography. - Ganeshkumar Ganapathy; Barbara Goodson; Robert K. Jansen; Vijaya Ramachandran; Tandy J. Warnow (WABI, 2005)

Reconstructing Reticulate Evolution in SpeciesTheory and Practice. - Luay Nakhleh; Tandy J. Warnow; C. Randal Linder; Katherine St. John (J. Comput. Biol., 2005)

Reconstructing Chromosomal Evolution. - Li-San Wang; Tandy J. Warnow (SIAM J. Comput., 2006)

Pattern Identification in Biogeography. - Ganeshkumar Ganapathy; Barbara Goodson; Robert K. Jansen; Hai-Son Le; Vijaya Ramachandran; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Reconstructing phylogenies from gene-content and gene-order data. - Bernard M. E. Moret; Jijun Tang; Tandy J. Warnow (Mathematics of Evolution and Phylogeny, 2007)

Distance-based genome rearrangement phylogeny. - Li-San Wang; Tandy J. Warnow (Mathematics of Evolution and Phylogeny, 2007)

Session Introduction. - Michael Brudno; Bernard M. E. Moret; C. Randal Linder; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2008)

The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. - Serita M. Nelesen; Kevin Liu; D. Zhao; C. Randal Linder; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2008)

Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. - Sagi Snir; Tandy J. Warnow; Satish Rao (J. Comput. Biol., 2008)

Tutorial on Computational Linguistic Phylogeny. - Johanna Nichols; Tandy J. Warnow (Lang. Linguistics Compass, 2008)

Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy. - Kevin Liu; Serita M. Nelesen; Sindhu Raghavan; C. Randal Linder; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

A simulation study comparing supertree and combined analysis methods using SMIDGen. - M. Shel Swenson; François Barbançon; Tandy J. Warnow; C. Randal Linder (Algorithms Mol. Biol., 2010)

Algorithms for MDC-Based Multi-locus Phylogeny Inference. - Yun Yu; Tandy J. Warnow; Luay Nakhleh (RECOMB, 2011)

An experimental study of Quartets MaxCut and other supertree methods. - M. Shel Swenson; Rahul Suri; C. Randal Linder; Tandy J. Warnow (Algorithms Mol. Biol., 2011)

FASTSP: linear time calculation of alignment accuracy. - Siavash Mirarab; Tandy J. Warnow (Bioinform., 2011)

Fast and accurate methods for phylogenomic analyses. - Jimmy Yang; Tandy J. Warnow (BMC Bioinform., 2011)

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. - Yun Yu; Tandy J. Warnow; Luay Nakhleh (J. Comput. Biol., 2011)

The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. - Li-San Wang; James H. Leebens-Mack; P. Kerr Wall; Kevin Beckmann; Claude W. dePamphilis; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

SEPP: SATe -Enabled Phylogenetic Placement. - Siavash Mirarab; Nam Nguyen; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2012)

Parallelizing SuperFine. - Diogo Telmo Neves; Tandy J. Warnow; João Luís Sobral; Keshav Pingali (SAC, 2012)

MRL and SuperFine+MRL: new supertree methods. - Nam-phuong Nguyen; Siavash Mirarab; Tandy J. Warnow (Algorithms Mol. Biol., 2012)

DACTAL: divide-and-conquer trees (almost) without alignments. - Serita M. Nelesen; Kevin Liu; Li-San Wang; C. Randal Linder; Tandy J. Warnow (Bioinform., 2012)

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (J. Comput. Biol., 2012)

Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. - Tandy J. Warnow (Models and Algorithms for Genome Evolution, 2013)

Inferring Optimal Species Trees Under Gene Duplication and Loss. - Md. Shamsuzzoha Bayzid; Siavash Mirarab; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2013)

Session introduction. - Luay Nakhleh; Noah A. Rosenberg; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2013)

Naive binning improves phylogenomic analyses. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (Bioinform., 2013)

PASTA: Ultra-Large Multiple Sequence Alignment. - Siavash Mirarab; Nam-phuong Nguyen; Tandy J. Warnow (RECOMB, 2014)

ASTRAL: genome-scale coalescent-based species tree estimation. - Siavash Mirarab; Rezwana Reaz; Md. Shamsuzzoha Bayzid; Théo Zimmermann; M. Shel Swenson; Tandy J. Warnow (Bioinform., 2014)

TIPP: taxonomic identification and phylogenetic profiling. - Nam-phuong Nguyen; Siavash Mirarab; Bo Liu 021; Mihai Pop; Tandy J. Warnow (Bioinform., 2014)

Ultra-Large Alignments Using Ensembles of Hidden Markov Models. - Nam-phuong Nguyen; Siavash Mirarab; Keerthana Kumar; Tandy J. Warnow (RECOMB, 2015)

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. - Siavash Mirarab; Tandy J. Warnow (Bioinform., 2015)

Ultra-large alignments using Phylogeny-aware Profiles. - Nam-phuong Nguyen; Siavash Mirarab; Keerthana Kumar; Tandy J. Warnow (CoRR, 2015)

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. - Siavash Mirarab; Nam Nguyen; Sheng Guo; Li-San Wang; Junhyong Kim; Tandy J. Warnow (J. Comput. Biol., 2015)

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. - Lawrence H. Uricchio; Tandy J. Warnow; Noah A. Rosenberg (BMC Bioinform., 2016)

Next Generation Sequencing (Dagstuhl Seminar 16351). - Gene Myers; Mihai Pop; Knut Reinert; Tandy J. Warnow (Dagstuhl Reports, 2016)

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). - Lonnie R. Welch; Cath Brooksbank; Russell Schwartz; Sarah L. Morgan; Bruno A. Gaëta; Alastair M. Kilpatrick; Daniel Mietchen; Benjamin L. Moore; Nicola J. Mulder; Mark A. Pauley; William R. Pearson; Predrag Radivojac; et al. (PLoS Comput. Biol., 2016)

Genome-scale Estimation of the Tree of Life. - Tandy J. Warnow (BCB, 2017)

Computational Challenges in Constructing the Tree of Life. - Tandy J. Warnow (IPDPS, 2017)

Enhancing Searches for Optimal Trees Using SIESTA. - Pranjal Vachaspati; Tandy J. Warnow (RECOMB-CG, 2017)

Gene Tree Parsimony for Incomplete Gene Trees. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (WABI, 2017)

Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (WABI, 2017)

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. - Pranjal Vachaspati; Tandy J. Warnow (Bioinform., 2017)

Are Profile Hidden Markov Models Identifiable? - Srilakshmi Pattabiraman; Tandy J. Warnow (BCB, 2018)

NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. - Erin K. Molloy; Tandy J. Warnow (RECOMB-CG, 2018)

New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. - Qiuyi (Richard) Zhang; Satish Rao; Tandy J. Warnow (WABI, 2018)

Gene tree parsimony for incomplete gene trees: addressing true biological loss. - Md. Shamsuzzoha Bayzid; Tandy J. Warnow (Algorithms Mol. Biol., 2018)

OCTAL: Optimal Completion of gene trees in polynomial time. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (Algorithms Mol. Biol., 2018)

PASTA for proteins. - Kodi Collins; Tandy J. Warnow (Bioinform., 2018)

Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. - Sebastien Roch; Michael Nute; Tandy J. Warnow (CoRR, 2018)

The development and application of bioinformatics core competencies to improve bioinformatics training and education. - Nicola J. Mulder; Russell Schwartz; Michelle D. Brazas; Cath Brooksbank; Bruno A. Gaëta; Sarah L. Morgan; Mark A. Pauley; Anne G. Rosenwald; Gabriella Rustici; Michael L. Sierk; Tandy J. Warnow; Lonnie R. Welch (PLoS Comput. Biol., 2018)

Using INC Within Divide-and-Conquer Phylogeny Estimation. - Thien Le; Aaron Sy; Erin K. Molloy; Qiuyi (Richard) Zhang; Satish Rao; Tandy J. Warnow (AlCoB, 2019)

New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. - Tandy J. Warnow (AlCoB, 2019)

TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Tandy J. Warnow (WABI, 2019)

Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. - Erin K. Molloy; Tandy J. Warnow (Algorithms Mol. Biol., 2019)

Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy. - Qiuyi Zhang 001; Satish Rao; Tandy J. Warnow (Algorithms Mol. Biol., 2019)

TreeMerge: a new method for improving the scalability of species tree estimation methods. - Erin K. Molloy; Tandy J. Warnow (Bioinform., 2019)

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. - Nidhi Shah; Michael G. Nute; Tandy J. Warnow; Mihai Pop (Bioinform., 2019)

Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. - Xilin Yu; Thien Le; Sarah A. Christensen; Erin K. Molloy; Tandy J. Warnow (WABI, 2020)

Non-parametric correction of estimated gene trees using TRACTION. - Sarah A. Christensen; Erin K. Molloy; Pranjal Vachaspati; Ananya Yammanuru; Tandy J. Warnow (Algorithms Mol. Biol., 2020)

FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. - Erin K. Molloy; Tandy J. Warnow (Bioinform., 2020)

Frequently Co-cited Publications: Features and Kinetics. - Sitaram Devarakonda; James R. Bradley; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (CoRR, 2020)

Finding Scientific Communities In Citation Graphs: Convergent Clustering. - Shreya Chandrasekharan; Mariam Zaka; Stephen A. Gallo; Tandy J. Warnow; George Chacko (CoRR, 2020)

Co-citations in context: Disciplinary heterogeneity is relevant. - James R. Bradley; Sitaram Devarakonda; Avon Davey; Dmitriy Korobskiy; Siyu Liu 006; Djamil Lakhdar-Hamina; Tandy J. Warnow; George Chacko (Quant. Sci. Stud., 2020)

Frequently cocited publications: Features and kinetics. - Sitaram Devarakonda; James R. Bradley; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (Quant. Sci. Stud., 2020)

Viewing computer science through citation analysis: Salton and Bergmark Redux. - Sitaram Devarakonda; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (Scientometrics, 2020)

Scalable and Accurate Phylogenetic Placement Using pplacer-XR. - Eleanor Wedell; Yirong Cai; Tandy J. Warnow (AlCoB, 2021)

Comparing Methods for Species Tree Estimation with Gene Duplication and Loss. - James Willson; Mrinmoy Saha Roddur; Tandy J. Warnow (AlCoB, 2021)

The Maximum Weight Trace Alignment Merging Problem. - Paul Zaharias; Vladimir Smirnov; Tandy J. Warnow (AlCoB, 2021)

ppIacerDC: a new scalable phylogenetic placement method. - Elizabeth R. Koning; Malachi Phillips; Tandy J. Warnow (BCB, 2021)

Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. - Minhyuk Park; Paul Zaharias; Tandy J. Warnow (Algorithms, 2021)

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. - Xilin Yu; Thien Le; Sarah A. Christensen; Erin K. Molloy; Tandy J. Warnow (Algorithms Mol. Biol., 2021)

FASTRAL: improving scalability of phylogenomic analysis. - Payam Dibaeinia; Shayan Tabe-Bordbar; Tandy J. Warnow (Bioinform., 2021)

Accurate large-scale phylogeny-aware alignment using BAli-Phy. - Maya Gupta; Paul Zaharias; Tandy J. Warnow (Bioinform., 2021)

TIPP2: metagenomic taxonomic profiling using phylogenetic markers. - Nidhi Shah; Erin K. Molloy; Mihai Pop; Tandy J. Warnow (Bioinform., 2021)

MAGUS: Multiple sequence Alignment using Graph clUStering. - Vladimir Smirnov; Tandy J. Warnow (Bioinform., 2021)

Center-Periphery Structure in Communities: Extracellular Vesicles. - Eleanor Wedell; Minhyuk Park; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (CoRR, 2021)

Finding scientific communities in citation graphs: Articles and authors. - Shreya Chandrasekharan; Mariam Zaka; Stephen A. Gallo; Wenxi Zhao; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (Quant. Sci. Stud., 2021)

Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. - Thien Le; Aaron Sy; Erin K. Molloy; Qiuyi Zhang 001; Satish Rao; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Profile Hidden Markov Models Are Not Identifiable. - Srilakshmi Pattabiraman; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. - Brandon Legried; Erin K. Molloy; Tandy J. Warnow; Sébastien Roch (J. Comput. Biol., 2021)

Fast and Accurate Species Trees from Weighted Internode Distances. - Baqiao Liu; Tandy J. Warnow (WABI, 2022)

MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. - Chengze Shen; Paul Zaharias; Tandy J. Warnow (Bioinform., 2022)

Quintet Rooting: rooting species trees under the multi-species coalescent model. - Yasamin Tabatabaee; Kowshika Sarker; Tandy J. Warnow (Bioinform., 2022)

Scalable Species Tree Inference with External Constraints. - Baqiao Liu; Tandy J. Warnow (J. Comput. Biol., 2022)

WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. - Chengze Shen; Minhyuk Park; Tandy J. Warnow (J. Comput. Biol., 2022)

Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. - Paul Zaharias; Martin Grosshauser; Tandy J. Warnow (J. Comput. Biol., 2022)

AOC: Assembling overlapping communities. - Akhil Jakatdar; Baqiao Liu; Tandy J. Warnow; George Chacko (Quant. Sci. Stud., 2022)

Center-periphery structure in research communities. - Eleanor Wedell; Minhyuk Park; Dmitriy Korobskiy; Tandy J. Warnow; George Chacko (Quant. Sci. Stud., 2022)

Identifying Well-Connected Communities in Real-World and Synthetic Networks. - Minhyuk Park; Yasamin Tabatabaee; Vikram Ramavarapu; Baqiao Liu; Vidya Kamath Pailodi; Rajiv Ramachandran; Dmitriy Korobskiy; Fábio Ayres; George Chacko; Tandy J. Warnow (COMPLEX NETWORKS (2), 2023)

Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. - Yasamin Tabatabaee; Sébastien Roch; Tandy J. Warnow (RECOMB, 2023)

EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). - Chengze Shen; Baqiao Liu; Kelly P. Williams; Tandy J. Warnow (WABI, 2023)

BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). - Eleanor Wedell; Chengze Shen; Tandy J. Warnow (WABI, 2023)

Phylogenomic branch length estimation using quartets. - Yasamin Tabatabaee; Chao Zhang 055; Tandy J. Warnow; Siavash Mirarab (Bioinform., 2023)

Well-Connected Communities in Real-World Networks. - Minhyuk Park; Yasamin Tabatabaee; Baqiao Liu; Vidya Kamath Pailodi; Vikram Ramavarapu; Rajiv Ramachandran; Dmitriy Korobskiy; Fábio Ayres; George Chacko; Tandy J. Warnow (CoRR, 2023)

Axioms for Distanceless Graph Partitioning. - James Willson; Tandy J. Warnow (CoRR, 2023)

SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. - Eleanor Wedell; Yirong Cai; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. - Paul Zaharias; Vladimir Smirnov; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

UPP2: fast and accurate alignment of datasets with fragmentary sequences. - Minhyuk Park; Stefan Ivanovic; Gillian Chu; Chengze Shen; Tandy J. Warnow (Bioinform., 2023)

QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. - Yasamin Tabatabaee; Sebastien Roch; Tandy J. Warnow (J. Comput. Biol., 2023)

Weighted ASTRID: fast and accurate species trees from weighted internode distances. - Baqiao Liu; Tandy J. Warnow (Algorithms Mol. Biol., 2023)

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. - Chengze Shen; Baqiao Liu; Kelly P. Williams; Tandy J. Warnow (Algorithms Mol. Biol., 2023)

Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data. - Tandy J. Warnow; Yasamin Tabatabaee; Steven N. Evans (RECOMB-CG, 2024)

Improved Community Detection using Stochastic Block Models. - Minhyuk Park; Daniel Wang Feng; Siya Digra; The-Anh Vu-Le; George Chacko; Tandy J. Warnow (CoRR, 2024)

Synthetic Networks That Preserve Edge Connectivity. - Lahari Anne; The-Anh Vu-Le; Minhyuk Park; Tandy J. Warnow; George Chacko (CoRR, 2024)

FastEnsemble: A new scalable ensemble clustering method. - Yasamin Tabatabaee; Eleanor Wedell; Minhyuk Park; Tandy J. Warnow (CoRR, 2024)

CM++ - A Meta-method for Well-Connected Community Detection. - Vikram Ramavarapu; Fabio Jose Ayres; Minhyuk Park; Vidya Kamath Pailodi; João Alfredo Cardoso Lamy; Tandy J. Warnow; George Chacko (J. Open Source Softw., 2024)

Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. - Tandy J. Warnow; Yasamin Tabatabaee; Steven N. Evans (J. Comput. Biol., 2025)

TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. - Chengze Shen; Eleanor Wedell; Mihai Pop; Tandy J. Warnow (PLoS Comput. Biol., 2025)

Improved Community Detection using Stochastic Block Models. - Minhyuk Park; Daniel Wang Feng; Siya Digra; The-Anh Vu-Le; Lahari Anne; George Chacko; Tandy J. Warnow (CoRR, 2025)

An Agent-based Model of Citation Behavior. - George Chacko; Minhyuk Park; Vikram Ramavarapu; Ananth Grama; Pablo Robles-Granda; Tandy J. Warnow (CoRR, 2025)

Reccs: Realistic Cluster connectivity Simulator for Synthetic Network Generation. - Lahari Anne; The-Anh Vu-Le; Minhyuk Park; Tandy J. Warnow; George Chacko (Adv. Complex Syst., 2025)

Using Stochastic Block Models for Community Detection: The issue of edge-connectivity. - The-Anh Vu-Le; Minhyuk Park; Ian Chen; George Chacko; Tandy J. Warnow (CoRR, 2025)

EC-SBM synthetic network generator. - The-Anh Vu-Le; Lahari Anne; George Chacko; Tandy J. Warnow (Appl. Netw. Sci., 2025)