Tandy J. Warnow

207 papers A* 18A 4B 12C 17Misc 13Journal 119Unranked 21

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	An agent-based model of citation behavior. Appl. Netw. Sci. George Chacko, Minhyuk Park, Vikram Ramavarapu, Ananth Grama, Pablo Robles-Granda, Tandy J. Warnow
2026	J	`jnl`	Using stochastic block models for community detection. Appl. Netw. Sci. The-Anh Vu-Le, Minhyuk Park, Ian Chen, Tandy J. Warnow
2025	J	`jnl`	Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. J. Comput. Biol. Tandy J. Warnow, Yasamin Tabatabaee, Steven N. Evans
2025	J	`jnl`	An Agent-based Model of Citation Behavior. CoRR George Chacko, Minhyuk Park, Vikram Ramavarapu, Ananth Grama, Pablo Robles-Granda, Tandy J. Warnow
2025	J	`jnl`	BSCAMPP: Batch-Scaled Phylogenetic Placement on Large Trees. IEEE Trans. Comput. Biol. Bioinform. Eleanor Wedell, Chengze Shen, Tandy J. Warnow
2025	J	`jnl`	Dense Subgraph Clustering and a New Cluster Ensemble Method. CoRR The-Anh Vu-Le, João Alfredo Cardoso Lamy, Tomás Alessi, Ian Chen, Minhyuk Park, Elfarouk Harb, George Chacko, Tandy J. Warnow
2025	J	`jnl`	EC-SBM Synthetic Network Generator. CoRR The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow
2025	J	`jnl`	EC-SBM synthetic network generator. Appl. Netw. Sci. The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow
2025	J	`jnl`	Improved Community Detection using Stochastic Block Models. CoRR Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow
2025	J	`jnl`	On the Optimization of Methods for Establishing Well-Connected Communities. CoRR Mohammad Dindoost, Oliver Alvarado Rodriguez, Bartosz Bryg, Minhyuk Park, George Chacko, Tandy J. Warnow, David A. Bader
2025	J	`jnl`	RECCS: Realistic Cluster Connectivity Simulator for Synthetic Network Generation. CoRR Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy J. Warnow, George Chacko
2025	J	`jnl`	Reccs: Realistic Cluster connectivity Simulator for Synthetic Network Generation. Adv. Complex Syst. Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy J. Warnow, George Chacko
2025	—	`conf`	Species detection for microbiomes with TIPP-SD. BCB Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow
2025	J	`jnl`	TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. PLoS Comput. Biol. Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow
2025	J	`jnl`	Using Stochastic Block Models for Community Detection: The issue of edge-connectivity. CoRR The-Anh Vu-Le, Minhyuk Park, Ian Chen, George Chacko, Tandy J. Warnow
2024	J	`jnl`	CM++ - A Meta-method for Well-Connected Community Detection. J. Open Source Softw. Vikram Ramavarapu, Fábio José Ayres, Minhyuk Park, Vidya Kamath Pailodi, João Alfredo Cardoso Lamy, Tandy J. Warnow, George Chacko
2024	J	`jnl`	FastEnsemble: A new scalable ensemble clustering method. CoRR Yasamin Tabatabaee, Eleanor Wedell, Minhyuk Park, Tandy J. Warnow
2024	J	`jnl`	Improved Community Detection using Stochastic Block Models. CoRR Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vu-Le, George Chacko, Tandy J. Warnow
2024	—	`conf`	Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data. RECOMB-CG Tandy J. Warnow, Yasamin Tabatabaee, Steven N. Evans
2024	J	`jnl`	Synthetic Networks That Preserve Edge Connectivity. CoRR Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy J. Warnow, George Chacko
2023	J	`jnl`	Axioms for Distanceless Graph Partitioning. CoRR James Willson, Tandy J. Warnow
2023	C	`conf`	BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). WABI Eleanor Wedell, Chengze Shen, Tandy J. Warnow
2023	C	`conf`	EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). WABI Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow
2023	J	`jnl`	EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. Algorithms Mol. Biol. Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow
2023	—	`conf`	Identifying Well-Connected Communities in Real-World and Synthetic Networks. COMPLEX NETWORKS (2) Minhyuk Park, Yasamin Tabatabaee, Vikram Ramavarapu, Baqiao Liu, Vidya Kamath Pailodi, Rajiv Ramachandran, Dmitriy Korobskiy, Fábio J. Ayres, George Chacko, Tandy J. Warnow
2023	J	`jnl`	Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. IEEE ACM Trans. Comput. Biol. Bioinform. Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow
2023	J	`jnl`	Phylogenomic branch length estimation using quartets. Bioinform. Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab
2023	J	`jnl`	QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. J. Comput. Biol. Yasamin Tabatabaee, Sebastien Roch, Tandy J. Warnow
2023	J	`jnl`	SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. IEEE ACM Trans. Comput. Biol. Bioinform. Eleanor Wedell, Yirong Cai, Tandy J. Warnow
2023	B	`conf`	Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. RECOMB Yasamin Tabatabaee, Sébastien Roch, Tandy J. Warnow
2023	J	`jnl`	UPP2: fast and accurate alignment of datasets with fragmentary sequences. Bioinform. Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, Tandy J. Warnow
2023	J	`jnl`	Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol. Biol. Baqiao Liu, Tandy J. Warnow
2023	J	`jnl`	Well-Connected Communities in Real-World Networks. CoRR Minhyuk Park, Yasamin Tabatabaee, Baqiao Liu, Vidya Kamath Pailodi, Vikram Ramavarapu, Rajiv Ramachandran, Dmitriy Korobskiy, Fábio J. Ayres, George Chacko, Tandy J. Warnow
2022	J	`jnl`	AOC: Assembling overlapping communities. Quant. Sci. Stud. Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko
2022	J	`jnl`	AOC; Assembling Overlapping Communities. CoRR Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko
2022	J	`jnl`	Center-periphery structure in research communities. Quant. Sci. Stud. Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2022	C	`conf`	Fast and Accurate Species Trees from Weighted Internode Distances. WABI Baqiao Liu, Tandy J. Warnow
2022	J	`jnl`	MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinform. Chengze Shen, Paul Zaharias, Tandy J. Warnow
2022	J	`jnl`	Quintet Rooting: rooting species trees under the multi-species coalescent model. Bioinform. Yasamin Tabatabaee, Kowshika Sarker, Tandy J. Warnow
2022	J	`jnl`	Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. J. Comput. Biol. Paul Zaharias, Martin Grosshauser, Tandy J. Warnow
2022	J	`jnl`	Scalable Species Tree Inference with External Constraints. J. Comput. Biol. Baqiao Liu, Tandy J. Warnow
2022	J	`jnl`	WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. J. Comput. Biol. Chengze Shen, Minhyuk Park, Tandy J. Warnow
2021	J	`jnl`	Accurate large-scale phylogeny-aware alignment using BAli-Phy. Bioinform. Maya Gupta, Paul Zaharias, Tandy J. Warnow
2021	J	`jnl`	Center-Periphery Structure in Communities: Extracellular Vesicles. CoRR Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2021	—	`conf`	Comparing Methods for Species Tree Estimation with Gene Duplication and Loss. AlCoB James Willson, Mrinmoy Saha Roddur, Tandy J. Warnow
2021	J	`jnl`	Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. Algorithms Minhyuk Park, Paul Zaharias, Tandy J. Warnow
2021	J	`jnl`	FASTRAL: improving scalability of phylogenomic analysis. Bioinform. Payam Dibaeinia, Shayan Tabe-Bordbar, Tandy J. Warnow
2021	J	`jnl`	Finding scientific communities in citation graphs: Articles and authors. Quant. Sci. Stud. Shreya Chandrasekharan, Mariam Zaka, Stephen A. Gallo, Wenxi Zhao, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2021	J	`jnl`	MAGUS: Multiple sequence Alignment using Graph clUStering. Bioinform. Vladimir Smirnov, Tandy J. Warnow
2021	J	`jnl`	Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. J. Comput. Biol. Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch
2021	J	`jnl`	Profile Hidden Markov Models Are Not Identifiable. IEEE ACM Trans. Comput. Biol. Bioinform. Srilakshmi Pattabiraman, Tandy J. Warnow
2021	—	`conf`	Scalable and Accurate Phylogenetic Placement Using pplacer-XR. AlCoB Eleanor Wedell, Yirong Cai, Tandy J. Warnow
2021	J	`jnl`	TIPP2: metagenomic taxonomic profiling using phylogenetic markers. Bioinform. Nidhi Shah, Erin K. Molloy, Mihai Pop, Tandy J. Warnow
2021	—	`conf`	The Maximum Weight Trace Alignment Merging Problem. AlCoB Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow
2021	J	`jnl`	Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. IEEE ACM Trans. Comput. Biol. Bioinform. Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, Tandy J. Warnow
2021	J	`jnl`	Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. Algorithms Mol. Biol. Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow
2021	—	`conf`	ppIacerDC: a new scalable phylogenetic placement method. BCB Elizabeth R. Koning, Malachi Phillips, Tandy J. Warnow
2020	C	`conf`	Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. WABI Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow
2020	J	`jnl`	Co-citations in context: Disciplinary heterogeneity is relevant. Quant. Sci. Stud. James R. Bradley, Sitaram Devarakonda, Avon Davey, Dmitriy Korobskiy, Siyu Liu, Djamil Lakhdar-Hamina, Tandy J. Warnow, George Chacko
2020	J	`jnl`	FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinform. Erin K. Molloy, Tandy J. Warnow
2020	J	`jnl`	Finding Scientific Communities In Citation Graphs: Convergent Clustering. CoRR Shreya Chandrasekharan, Mariam Zaka, Stephen A. Gallo, Tandy J. Warnow, George Chacko
2020	J	`jnl`	Frequently Co-cited Publications: Features and Kinetics. CoRR Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2020	J	`jnl`	Frequently cocited publications: Features and kinetics. Quant. Sci. Stud. Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2020	J	`jnl`	Non-parametric correction of estimated gene trees using TRACTION. Algorithms Mol. Biol. Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Ananya Yammanuru, Tandy J. Warnow
2020	B	`conf`	Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. RECOMB Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch
2020	J	`jnl`	Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2019	J	`jnl`	Co-citations in context: disciplinary heterogeneity is relevant. CoRR James R. Bradley, Sitaram Devarakonda, Avon Davey, Dmitriy Korobskiy, Siyu Liu, Djamil Lakhdar-Hamina, Tandy J. Warnow, George Chacko
2019	J	`jnl`	Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms Mol. Biol. Qiuyi Zhang, Satish Rao, Tandy J. Warnow
2019	J	`jnl`	Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinform. Nidhi Shah, Michael G. Nute, Tandy J. Warnow, Mihai Pop
2019	—	`conf`	New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. AlCoB Tandy J. Warnow
2019	J	`jnl`	Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms Mol. Biol. Erin K. Molloy, Tandy J. Warnow
2019	C	`conf`	TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. WABI Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow
2019	J	`jnl`	TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinform. Erin K. Molloy, Tandy J. Warnow
2019	—	`conf`	Using INC Within Divide-and-Conquer Phylogeny Estimation. AlCoB Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow
2019	J	`jnl`	Viewing Computer Science through Citation Analysis; Salton and Bergmark Redux. CoRR Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
2018	—	`conf`	Are Profile Hidden Markov Models Identifiable? BCB Srilakshmi Pattabiraman, Tandy J. Warnow
2018	J	`jnl`	Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms Mol. Biol. Md. Shamsuzzoha Bayzid, Tandy J. Warnow
2018	J	`jnl`	Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. CoRR Sebastien Roch, Michael Nute, Tandy J. Warnow
2018	—	`conf`	NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. RECOMB-CG Erin K. Molloy, Tandy J. Warnow
2018	C	`conf`	New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. WABI Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow
2018	J	`jnl`	OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms Mol. Biol. Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow
2018	J	`jnl`	PASTA for proteins. Bioinform. Kodi Collins, Tandy J. Warnow
2018	J	`jnl`	The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput. Biol. 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
2017	A	`conf`	Computational Challenges in Constructing the Tree of Life. IPDPS Tandy J. Warnow
2017	—	`conf`	Enhancing Searches for Optimal Trees Using SIESTA. RECOMB-CG Pranjal Vachaspati, Tandy J. Warnow
2017	J	`jnl`	FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. Bioinform. Pranjal Vachaspati, Tandy J. Warnow
2017	C	`conf`	Gene Tree Parsimony for Incomplete Gene Trees. WABI Md. Shamsuzzoha Bayzid, Tandy J. Warnow
2017	—	`conf`	Genome-scale Estimation of the Tree of Life. BCB Tandy J. Warnow
2017	C	`conf`	Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. WABI Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow
2016	J	`jnl`	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. BMC Bioinform. Lawrence H. Uricchio, Tandy J. Warnow, Noah A. Rosenberg
2016	J	`jnl`	Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput. Biol. 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, Naomi Rosenberg, Anne G. Rosenwald, Gabriella Rustici, Tandy J. Warnow
2016	J	`jnl`	Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports Gene Myers, Mihai Pop, Knut Reinert, Tandy J. Warnow
2015	J	`jnl`	ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. Siavash Mirarab, Tandy J. Warnow
2015	J	`jnl`	PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow
2015	B	`conf`	Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
2015	J	`jnl`	Ultra-large alignments using Phylogeny-aware Profiles. CoRR Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
2014	J	`jnl`	ASTRAL: genome-scale coalescent-based species tree estimation. Bioinform. Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow
2014	B	`conf`	PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow
2014	J	`jnl`	TIPP: taxonomic identification and phylogenetic profiling. Bioinform. Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow
2013	Misc	`conf`	Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow
2013	—	`ch.`	Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. Models and Algorithms for Genome Evolution Tandy J. Warnow
2013	J	`jnl`	Naive binning improves phylogenomic analyses. Bioinform. Md. Shamsuzzoha Bayzid, Tandy J. Warnow
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow
2012	J	`jnl`	DACTAL: divide-and-conquer trees (almost) without alignments. Bioinform. Serita M. Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder, Tandy J. Warnow
2012	J	`jnl`	Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. J. Comput. Biol. Md. Shamsuzzoha Bayzid, Tandy J. Warnow
2012	J	`jnl`	MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow
2012	Misc	`conf`	Parallelizing SuperFine. SAC Diogo Telmo Neves, Tandy J. Warnow, João Luís Sobral, Keshav Pingali
2012	Misc	`conf`	SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing Siavash Mirarab, Nam Nguyen, Tandy J. Warnow
2011	J	`jnl`	Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. J. Comput. Biol. Yun Yu, Tandy J. Warnow, Luay Nakhleh
2011	B	`conf`	Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB Yun Yu, Tandy J. Warnow, Luay Nakhleh
2011	J	`jnl`	An experimental study of Quartets MaxCut and other supertree methods. Algorithms Mol. Biol. M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow
2011	J	`jnl`	FASTSP: linear time calculation of alignment accuracy. Bioinform. Siavash Mirarab, Tandy J. Warnow
2011	J	`jnl`	Fast and accurate methods for phylogenomic analyses. BMC Bioinform. Jimmy Yang, Tandy J. Warnow
2011	J	`jnl`	The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. IEEE ACM Trans. Comput. Biol. Bioinform. Li-San Wang, James H. Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy J. Warnow
2010	J	`jnl`	A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms Mol. Biol. M. Shel Swenson, François Barbançon, Tandy J. Warnow, C. Randal Linder
2010	C	`conf`	An Experimental Study of Quartets MaxCut and Other Supertree Methods. WABI M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow
2009	C	`conf`	A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. WABI M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy J. Warnow
2009	C	`ed.`	Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings WABI Steven Salzberg, Tandy J. Warnow
2009	J	`jnl`	Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. Kevin Liu, Serita M. Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy J. Warnow
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow
2008	J	`jnl`	Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. J. Comput. Biol. Sagi Snir, Tandy J. Warnow, Satish Rao
2008	Misc	`conf`	The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. Pacific Symposium on Biocomputing Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy J. Warnow
2008	J	`jnl`	Tutorial on Computational Linguistic Phylogeny. Lang. Linguistics Compass Johanna Nichols, Tandy J. Warnow
2007	—	`ch.`	Distance-based genome rearrangement phylogeny. Mathematics of Evolution and Phylogeny Li-San Wang, Tandy J. Warnow
2007	—	`ch.`	Reconstructing phylogenies from gene-content and gene-order data. Mathematics of Evolution and Phylogeny Bernard M. E. Moret, Jijun Tang, Tandy J. Warnow
2006	J	`jnl`	Pattern Identification in Biogeography. IEEE ACM Trans. Comput. Biol. Bioinform. Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Hai-Son Le, Vijaya Ramachandran, Tandy J. Warnow
2006	J	`jnl`	Reconstructing Chromosomal Evolution. SIAM J. Comput. Li-San Wang, Tandy J. Warnow
2005	C	`conf`	Pattern Identification in Biogeography. WABI Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow
2005	J	`jnl`	Reconstructing Reticulate Evolution in SpeciesTheory and Practice. J. Comput. Biol. Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John
2004	A*	`conf`	On contract-and-refine transformations between phylogenetic trees. SODA Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow
2004	J	`jnl`	Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme
2004	J	`jnl`	Preface. Theor. Comput. Sci. Tandy J. Warnow, Binhai Zhu
2004	—	`conf`	Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. CSB Usman Roshan, Bernard M. E. Moret, Tandy J. Warnow, Tiffani L. Williams
2004	B	`conf`	Reconstructing reticulate evolution in species: theory and practice. RECOMB Luay Nakhleh, Tandy J. Warnow, C. Randal Linder
2004	J	`jnl`	Unidentifiable Divergence Times in Rates-across-Sites Models. IEEE ACM Trans. Comput. Biol. Bioinform. Steven N. Evans, Tandy J. Warnow
2003	J	`jnl`	Analyzing the Order of Items in Manuscripts of Comput. Humanit. Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy J. Warnow, Christopher J. Howe
2003	C	`conf`	Better Hill-Climbing Searches for Parsimony. WABI Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow
2003	Misc	`ed.`	Computing and Combinatorics, 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003, Proceedings COCOON Tandy J. Warnow, Binhai Zhu
2003	J	`jnl`	Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. J. Algorithms Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter
2003	Misc	`conf`	Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse
2002	—	`conf`	Approximating the Complement of the Maximum Compatible Subset of Leaves of k Trees. APPROX Ganeshkumar Ganapathy, Tandy J. Warnow
2002	C	`conf`	Estimating the Deviation from a Molecular Clock. WABI Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow
2002	Misc	`conf`	Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. Pacific Symposium on Biocomputing Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow
2002	J	`jnl`	High-Performance Algorithm Engineering for Computational Phylogenetics. J. Supercomput. Bernard M. E. Moret, David A. Bader, Tandy J. Warnow
2002	C	`conf`	Sequence-Length Requirements for Phylogenetic Methods. WABI Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow
2002	A	`conf`	Statistically based postprocessing of phylogenetic analysis by clustering. ISMB Cara Stockham, Li-San Wang, Tandy J. Warnow
2002	J	`jnl`	Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. Bernard M. E. Moret, Jijun Tang, Li-San Wang, Tandy J. Warnow
2002	Misc	`conf`	The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
2002	J	`jnl`	Toward New Software for Computational Phylogenetics. Computer Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow
2001	Misc	`conf`	A New Implmentation and Detailed Study of Breakpoint Analysis. Pacific Symposium on Biocomputing Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan
2001	A*	`conf`	Absolute convergence: true trees from short sequences. SODA Tandy J. Warnow, Bernard M. E. Moret, Katherine St. John
2001	—	`conf`	Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
2001	A*	`conf`	Estimating true evolutionary distances between genomes. STOC Li-San Wang, Tandy J. Warnow
2001	C	`conf`	Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time. WABI Ganeshkumar Ganapathysaravanabavan, Tandy J. Warnow
2001	Misc	`conf`	High-Performance Algorithm Engineering for Computational Phylogenetics. International Conference on Computational Science (2) Bernard M. E. Moret, David A. Bader, Tandy J. Warnow
2001	—	`conf`	New approaches for reconstructing phylogenies from gene order data. ISMB (Supplement of Bioinformatics) Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman
2001	A*	`conf`	Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. SODA Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter
2001	C	`conf`	The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
2000	A	`conf`	A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. ISMB Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman
2000	—	`conf`	Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics. Experimental Algorithmics Bernard M. E. Moret, Tandy J. Warnow
2000	J	`jnl`	The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs. Theor. Comput. Sci. Hans L. Bodlaender, Michael R. Fellows, Michael T. Hallett, Todd Wareham, Tandy J. Warnow
1999	J	`jnl`	A Few Logs Suffice to Build (almost) All Trees: Part II. Theor. Comput. Sci. Péter L. Erdös, Michael Anthony Steel, László A. Székely, Tandy J. Warnow
1999	J	`jnl`	A few logs suffice to build (almost) all trees (I). Random Struct. Algorithms Péter L. Erdös, Michael Anthony Steel, László A. Székely, Tandy J. Warnow
1999	J	`jnl`	Constructing Evolutionary Trees in the Presence of Polymorphic Characters. SIAM J. Comput. Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1999	J	`jnl`	Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. Algorithmica Monika Rauch Henzinger, Valerie King, Tandy J. Warnow
1999	J	`jnl`	Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction. J. Comput. Biol. Daniel H. Huson, Scott Nettles, Tandy J. Warnow
1999	—	`conf`	Estimating Large Distances in Phylogenetic Reconstruction. WAE Daniel H. Huson, Kelly Ann Smith, Tandy J. Warnow
1999	J	`jnl`	Hybrid Tree Reconstruction Methods. ACM J. Exp. Algorithmics Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
1999	B	`conf`	Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. RECOMB Daniel H. Huson, Scott Nettles, Tandy J. Warnow
1999	A*	`ed.`	Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 17-19 January 1999, Baltimore, Maryland, USA. SODA Robert Endre Tarjan, Tandy J. Warnow
1999	A	`conf`	Solving Large Scale Phylogenetic Problems using DCM2. ISMB Daniel H. Huson, Lisa Vawter, Tandy J. Warnow
1998	J	`jnl`	Better Methods for Solving Parsimony and Compatibility. J. Comput. Biol. Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
1998	B	`conf`	Better methods for solving parsimony and compatibility. RECOMB Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph
1998	J	`jnl`	Computing the Local Consensus of Trees. SIAM J. Comput. Sampath Kannan, Tandy J. Warnow
1998	—	`conf`	Hybrid Tree Reconstruction Methods. WAE Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph
1997	J	`jnl`	A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies. SIAM J. Comput. Sampath Kannan, Tandy J. Warnow
1997	A*	`conf`	Constructing Big Trees from Short Sequences. ICALP Péter L. Erdös, Mike A. Steel, László A. Székely, Tandy J. Warnow
1997	J	`jnl`	Local Quartet Splits of a Binary Tree Infer All Quartet Splits Via One Dyadic Inference Rule. Comput. Artif. Intell. Péter L. Erdös, Mike A. Steel, László A. Székely, Tandy J. Warnow
1997	Misc	`conf`	Parsimony is Hard to Beat. COCOON Kenneth Rice, Tandy J. Warnow
1996	A*	`conf`	Constructing Evolutionary Trees in the Presence of Polymorphic Characters. STOC Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1996	A*	`conf`	Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. SODA Monika Rauch Henzinger, Valerie King, Tandy J. Warnow
1996	J	`jnl`	Determining the Evolutionary Tree Using Experiments. J. Algorithms Sampath Kannan, Eugene L. Lawler, Tandy J. Warnow
1996	—	`conf`	Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages. Mathematical Hierarchies and Biology Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph
1996	J	`jnl`	Minimizing Phylogenetic Number To Find Good Evolutionary Trees. Discret. Appl. Math. Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy J. Warnow
1996	A*	`conf`	Reconstructing the Evolutionary History of Natural Languages. SODA Tandy J. Warnow, Donald Ringe, Ann Taylor
1996	J	`jnl`	The Asymmetric Median Tree - A New Model for Building Consensus Trees. Discret. Appl. Math. Cynthia A. Phillips, Tandy J. Warnow
1996	B	`conf`	The Asymmetric Median Tree - A New model for Building Consensus Trees. CPM Cynthia A. Phillips, Tandy J. Warnow
1995	A*	`conf`	A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies when the Number of Character States is Fixed. SODA Sampath Kannan, Tandy J. Warnow
1995	J	`jnl`	A Robust Model for Finding Optimal Evolutionary Trees. Algorithmica Martin Farach, Sampath Kannan, Tandy J. Warnow
1995	A*	`conf`	Computing the Local Consensus of Trees. SODA Sampath Kannan, Tandy J. Warnow, Shibu Yooseph
1995	J	`jnl`	Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility. J. Comput. Biol. Craig J. Benham, Sampath Kannan, Michael Paterson, Tandy J. Warnow
1995	B	`conf`	Minimizing Phylogenetic Number to find Good Evolutionary Trees. CPM Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy J. Warnow
1995	B	`conf`	Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility. CPM Craig J. Benham, Sampath Kannan, Tandy J. Warnow
1995	J	`jnl`	Tree Reconstruction from Partial Orders. SIAM J. Comput. Sampath Kannan, Tandy J. Warnow
1994	J	`jnl`	Inferring Evolutionary History from DNA Sequences. SIAM J. Comput. Sampath Kannan, Tandy J. Warnow
1994	J	`jnl`	Tree Compatibility and Inferring Evolutionary History. J. Algorithms Tandy J. Warnow
1994	J	`jnl`	Triangulating Vertex-Colored Graphs. SIAM J. Discret. Math. Fred R. McMorris, Tandy J. Warnow, Thomas Wimer
1993	A*	`conf`	A robust model for finding optimal evolutionary trees. STOC Martin Farach, Sampath Kannan, Tandy J. Warnow
1993	J	`jnl`	Kaikoura Tree Theorems: Computing the Maximum Agreement Subtree. Inf. Process. Lett. Mike A. Steel, Tandy J. Warnow
1993	A*	`conf`	Tree Compatibility and Inferring Evoluationary History. SODA Tandy J. Warnow
1993	B	`conf`	Tree Reconstruction from Partial Orders. WADS Sampath Kannan, Tandy J. Warnow
1993	A*	`conf`	Triangulating Vertex Colored Graphs. SODA Fred R. McMorris, Tandy J. Warnow, Thomas Wimer
1992	J	`jnl`	Triangulating 3-Colored Graphs. SIAM J. Discret. Math. Sampath Kannan, Tandy J. Warnow
1992	A*	`conf`	Two Strikes Against Perfect Phylogeny. ICALP Hans L. Bodlaender, Michael R. Fellows, Tandy J. Warnow
1991	A*	`conf`	Triangulating Three-Colored Graphs. SODA Sampath Kannan, Tandy J. Warnow
1990	A*	`conf`	Determining the Evolutionary Tree. SODA Sampath Kannan, Eugene L. Lawler, Tandy J. Warnow
1990	A*	`conf`	Inferring Evolutionary History from DNA Sequences (Extended Abstract) FOCS Sampath Kannan, Tandy J. Warnow