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ORCIDTandy J. Warnow
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- affiliation: University of Illinois at Urbana-Champaign, Department of Computer Science, IL, USA
- affiliation: University of Texas at Austin, Department of Computer Science, TX, USA
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2020 – today
- 2025
[j94]The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow:
EC-SBM synthetic network generator. Appl. Netw. Sci. 10(1): 15 (2025)- [j93]Tandy J. Warnow
, Yasamin Tabatabaee, Steven N. Evans:
Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. J. Comput. Biol. 32(1): 3-27 (2025) - [j92]Chengze Shen, Eleanor Wedell, Mihai Pop, Tandy J. Warnow:
TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics. PLoS Comput. Biol. 21(4): 1012593 (2025) - [i18]Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow:
Improved Community Detection using Stochastic Block Models. CoRR abs/2502.00686 (2025) - [i17]Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy J. Warnow, George Chacko:
RECCS: Realistic Cluster Connectivity Simulator for Synthetic Network Generation. CoRR abs/2502.02050 (2025) - [i16]The-Anh Vu-Le, Lahari Anne, George Chacko, Tandy J. Warnow:
EC-SBM Synthetic Network Generator. CoRR abs/2502.03662 (2025) - [i15]George Chacko, Minhyuk Park, Vikram Ramavarapu, Ananth Grama, Pablo Robles-Granda, Tandy J. Warnow:
An Agent-based Model of Citation Behavior. CoRR abs/2503.06579 (2025) - 2024
- [j91]Vikram Ramavarapu, Fabio Jose Ayres, Minhyuk Park, Vidya Kamath Pailodi, João Alfredo Cardoso Lamy, Tandy J. Warnow, George Chacko:
CM++ - A Meta-method for Well-Connected Community Detection. J. Open Source Softw. 9(94): 6073 (2024) - [c81]Tandy J. Warnow, Yasamin Tabatabaee, Steven N. Evans:
Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data. RECOMB-CG 2024: 3-23 - [i14]Minhyuk Park, Daniel Wang Feng, Siya Digra, The-Anh Vu-Le, George Chacko, Tandy J. Warnow:
Improved Community Detection using Stochastic Block Models. CoRR abs/2408.10464 (2024) - [i13]Lahari Anne, The-Anh Vu-Le, Minhyuk Park, Tandy J. Warnow, George Chacko:
Synthetic Networks That Preserve Edge Connectivity. CoRR abs/2408.13647 (2024) - [i12]Yasamin Tabatabaee, Eleanor Wedell, Minhyuk Park, Tandy J. Warnow:
FastEnsemble: A new scalable ensemble clustering method. CoRR abs/2409.02077 (2024) - 2023
- [j90]Baqiao Liu, Tandy J. Warnow:
Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol. Biol. 18(1): 6 (2023) - [j89]Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow:
EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment. Algorithms Mol. Biol. 18(1): 21 (2023) - [j88]Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, Tandy J. Warnow:
UPP2: fast and accurate alignment of datasets with fragmentary sequences. Bioinform. 39(1) (2023) - [j87]Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab:
Phylogenomic branch length estimation using quartets. Bioinform. 39(Supplement-1): 185-193 (2023) - [j86]Yasamin Tabatabaee, Sebastien Roch, Tandy J. Warnow:
QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. J. Comput. Biol. 30(11): 1146-1181 (2023) - [j85]Eleanor Wedell, Yirong Cai, Tandy J. Warnow:
SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 20(2): 1417-1430 (2023) - [j84]Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow:
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 1700-1712 (2023) - [c80]Minhyuk Park, Yasamin Tabatabaee, Vikram Ramavarapu, Baqiao Liu, Vidya Kamath Pailodi, Rajiv Ramachandran, Dmitriy Korobskiy, Fábio Ayres, George Chacko, Tandy J. Warnow:
Identifying Well-Connected Communities in Real-World and Synthetic Networks. COMPLEX NETWORKS (2) 2023: 3-14 - [c79]Yasamin Tabatabaee, Sébastien Roch, Tandy J. Warnow:
Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. RECOMB 2023: 41-57 - [c78]Chengze Shen, Baqiao Liu, Kelly P. Williams, Tandy J. Warnow:
EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). WABI 2023: 2:1-2:2 - [c77]Eleanor Wedell, Chengze Shen, Tandy J. Warnow:
BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). WABI 2023: 3:1-3:2 - [i11]Minhyuk Park, Yasamin Tabatabaee, Baqiao Liu, Vidya Kamath Pailodi, Vikram Ramavarapu, Rajiv Ramachandran, Dmitriy Korobskiy, Fábio Ayres, George Chacko, Tandy J. Warnow:
Well-Connected Communities in Real-World Networks. CoRR abs/2303.02813 (2023) - [i10]James Willson, Tandy J. Warnow:
Axioms for Distanceless Graph Partitioning. CoRR abs/2309.09386 (2023) - 2022
- [j83]Chengze Shen, Paul Zaharias, Tandy J. Warnow:
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinform. 38(4): 918-924 (2022) - [j82]Yasamin Tabatabaee, Kowshika Sarker, Tandy J. Warnow:
Quintet Rooting: rooting species trees under the multi-species coalescent model. Bioinform. 38(Supplement_1): i109-i117 (2022) - [j81]Paul Zaharias, Martin Grosshauser, Tandy J. Warnow:
Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. J. Comput. Biol. 29(1): 74-89 (2022) - [j80]Baqiao Liu, Tandy J. Warnow:
Scalable Species Tree Inference with External Constraints. J. Comput. Biol. 29(7): 664-678 (2022) - [j79]Chengze Shen, Minhyuk Park, Tandy J. Warnow:
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. J. Comput. Biol. 29(8): 782-801 (2022) - [j78]Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Center-periphery structure in research communities. Quant. Sci. Stud. 3(1): 289-314 (2022) - [j77]Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko:
AOC: Assembling overlapping communities. Quant. Sci. Stud. 3(4): 1079-1096 (2022) - [c76]Baqiao Liu, Tandy J. Warnow:
Fast and Accurate Species Trees from Weighted Internode Distances. WABI 2022: 8:1-8:24 - [i9]Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko:
AOC; Assembling Overlapping Communities. CoRR abs/2208.04842 (2022) - 2021
- [j76]Minhyuk Park, Paul Zaharias, Tandy J. Warnow:
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. Algorithms 14(5): 148 (2021) - [j75]Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow:
Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. Algorithms Mol. Biol. 16(1): 12 (2021) - [j74]Vladimir Smirnov, Tandy J. Warnow:
MAGUS: Multiple sequence Alignment using Graph clUStering. Bioinform. 37(12): 1666-1672 (2021) - [j73]Nidhi Shah, Erin K. Molloy, Mihai Pop, Tandy J. Warnow:
TIPP2: metagenomic taxonomic profiling using phylogenetic markers. Bioinform. 37(13): 1839-1845 (2021) - [j72]Payam Dibaeinia, Shayan Tabe-Bordbar, Tandy J. Warnow:
FASTRAL: improving scalability of phylogenomic analysis. Bioinform. 37(16): 2317-2324 (2021) - [j71]Maya Gupta, Paul Zaharias, Tandy J. Warnow:
Accurate large-scale phylogeny-aware alignment using BAli-Phy. Bioinform. 37(24): 4677-4683 (2021) - [j70]Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch:
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. J. Comput. Biol. 28(5): 452-468 (2021) - [j69]Shreya Chandrasekharan, Mariam Zaka, Stephen A. Gallo, Wenxi Zhao, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Finding scientific communities in citation graphs: Articles and authors. Quant. Sci. Stud. 2(1): 184-203 (2021) - [j68]Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, Tandy J. Warnow:
Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 2-15 (2021) - [j67]Srilakshmi Pattabiraman, Tandy J. Warnow:
Profile Hidden Markov Models Are Not Identifiable. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 162-172 (2021) - [c75]Eleanor Wedell, Yirong Cai, Tandy J. Warnow:
Scalable and Accurate Phylogenetic Placement Using pplacer-XR. AlCoB 2021: 94-105 - [c74]James Willson, Mrinmoy Saha Roddur, Tandy J. Warnow:
Comparing Methods for Species Tree Estimation with Gene Duplication and Loss. AlCoB 2021: 106-117 - [c73]Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow:
The Maximum Weight Trace Alignment Merging Problem. AlCoB 2021: 159-171 - [c72]Elizabeth R. Koning, Malachi Phillips, Tandy J. Warnow:
ppIacerDC: a new scalable phylogenetic placement method. BCB 2021: 3:1-3:9 - [i8]Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Center-Periphery Structure in Communities: Extracellular Vesicles. CoRR abs/2111.07410 (2021) - 2020
- [j66]Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Ananya Yammanuru, Tandy J. Warnow:
Non-parametric correction of estimated gene trees using TRACTION. Algorithms Mol. Biol. 15(1): 1 (2020) - [j65]Erin K. Molloy, Tandy J. Warnow:
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinform. 36(Supplement-1): i57-i65 (2020) - [j64]James R. Bradley, Sitaram Devarakonda, Avon Davey, Dmitriy Korobskiy, Siyu Liu, Djamil Lakhdar-Hamina, Tandy J. Warnow, George Chacko:
Co-citations in context: Disciplinary heterogeneity is relevant. Quant. Sci. Stud. 1(1): 264-276 (2020) - [j63]Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Frequently cocited publications: Features and kinetics. Quant. Sci. Stud. 1(3): 1223-1241 (2020) - [j62]Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics 125(1): 271-287 (2020) - [c71]Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch:
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. RECOMB 2020: 120-135 - [c70]Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy J. Warnow:
Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. WABI 2020: 15:1-15:17 - [i7]Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Frequently Co-cited Publications: Features and Kinetics. CoRR abs/2005.04793 (2020) - [i6]Shreya Chandrasekharan, Mariam Zaka, Stephen A. Gallo, Tandy J. Warnow, George Chacko:
Finding Scientific Communities In Citation Graphs: Convergent Clustering. CoRR abs/2007.14452 (2020)
2010 – 2019
- 2019
- [j61]Qiuyi Zhang, Satish Rao, Tandy J. Warnow:
Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms Mol. Biol. 14(1): 2:1-2:12 (2019) - [j60]Erin K. Molloy, Tandy J. Warnow:
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms Mol. Biol. 14(1): 14:1-14:17 (2019) - [j59]Nidhi Shah, Michael G. Nute, Tandy J. Warnow, Mihai Pop:
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinform. 35(9): 1613-1614 (2019) - [j58]Erin K. Molloy, Tandy J. Warnow:
TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinform. 35(14): i417-i426 (2019) - [c69]Tandy J. Warnow:
New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. AlCoB 2019: 3-21 - [c68]Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow:
Using INC Within Divide-and-Conquer Phylogeny Estimation. AlCoB 2019: 167-178 - [c67]Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow:
TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. WABI 2019: 4:1-4:16 - [i5]James R. Bradley, Sitaram Devarakonda, Avon Davey, Dmitriy Korobskiy, Siyu Liu, Djamil Lakhdar-Hamina, Tandy J. Warnow, George Chacko:
Co-citations in context: disciplinary heterogeneity is relevant. CoRR abs/1909.08738 (2019) - [i4]Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko:
Viewing Computer Science through Citation Analysis; Salton and Bergmark Redux. CoRR abs/1912.10521 (2019) - 2018
- [j57]Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms Mol. Biol. 13(1): 1:1-1:12 (2018) - [j56]Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow:
OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms Mol. Biol. 13(1): 6:1-6:18 (2018) - [j55]Kodi Collins, Tandy J. Warnow:
PASTA for proteins. Bioinform. 34(22): 3939-3941 (2018) - [j54]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:
The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput. Biol. 14(2) (2018) - [c66]Srilakshmi Pattabiraman, Tandy J. Warnow:
Are Profile Hidden Markov Models Identifiable? BCB 2018: 448-456 - [c65]Erin K. Molloy, Tandy J. Warnow:
NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. RECOMB-CG 2018: 260-276 - [c64]Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow:
New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. WABI 2018: 8:1-8:12 - [i3]Sebastien Roch, Michael Nute, Tandy J. Warnow:
Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. CoRR abs/1803.02800 (2018) - 2017
- [j53]Pranjal Vachaspati, Tandy J. Warnow:
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. Bioinform. 33(5): 631-639 (2017) - [c63]Tandy J. Warnow:
Genome-scale Estimation of the Tree of Life. BCB 2017: 634 - [c62]Tandy J. Warnow:
Computational Challenges in Constructing the Tree of Life. IPDPS 2017: 1 - [c61]Pranjal Vachaspati, Tandy J. Warnow:
Enhancing Searches for Optimal Trees Using SIESTA. RECOMB-CG 2017: 232-255 - [c60]Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
Gene Tree Parsimony for Incomplete Gene Trees. WABI 2017: 2:1-2:13 - [c59]Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow:
Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. WABI 2017: 27:1-27:14 - 2016
- [j52]Lawrence H. Uricchio, Tandy J. Warnow, Noah A. Rosenberg:
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. 17(S-14): 241-250 (2016) - [j51]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:
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput. Biol. 12(5) (2016) - [i2]Gene Myers, Mihai Pop, Knut Reinert, Tandy J. Warnow:
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6(8): 91-130 (2016) - 2015
- [j50]Siavash Mirarab, Tandy J. Warnow:
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. 31(12): 44-52 (2015) - [j49]Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow:
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. 22(5): 377-386 (2015) - [c58]Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow:
Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB 2015: 259-260 - [i1]Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow:
Ultra-large alignments using Phylogeny-aware Profiles. CoRR abs/1504.01142 (2015) - 2014
- [j48]Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow:
ASTRAL: genome-scale coalescent-based species tree estimation. Bioinform. 30(17): 541-548 (2014) - [j47]Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow:
TIPP: taxonomic identification and phylogenetic profiling. Bioinform. 30(24): 3548-3555 (2014) - [c57]Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow:
PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB 2014: 177-191 - 2013
- [j46]Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
Naive binning improves phylogenomic analyses. Bioinform. 29(18): 2277-2284 (2013) - [c56]Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow:
Session introduction. Pacific Symposium on Biocomputing 2013: 247-249 - [c55]Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow:
Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing 2013: 250-261 - [p3]Tandy J. Warnow:
Large-Scale Multiple Sequence Alignment and Phylogeny Estimation. Models and Algorithms for Genome Evolution 2013: 85-146 - 2012
- [j45]Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow:
MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. 7: 3 (2012) - [j44]Serita M. Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder, Tandy J. Warnow:
DACTAL: divide-and-conquer trees (almost) without alignments. Bioinform. 28(12): 274-282 (2012) - [j43]Md. Shamsuzzoha Bayzid, Tandy J. Warnow:
Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. J. Comput. Biol. 19(6): 591-605 (2012) - [c54]Siavash Mirarab, Nam Nguyen, Tandy J. Warnow:
SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing 2012: 247-258 - [c53]Diogo Telmo Neves, Tandy J. Warnow, João Luís Sobral, Keshav Pingali:
Parallelizing SuperFine. SAC 2012: 1361-1367 - 2011
- [j42]M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow:
An experimental study of Quartets MaxCut and other supertree methods. Algorithms Mol. Biol. 6: 7 (2011) - [j41]Siavash Mirarab, Tandy J. Warnow:
FASTSP: linear time calculation of alignment accuracy. Bioinform. 27(23): 3250-3258 (2011) - [j40]Jimmy Yang, Tandy J. Warnow:
Fast and accurate methods for phylogenomic analyses. BMC Bioinform. 12(S-9): S4 (2011) - [j39]Yun Yu, Tandy J. Warnow, Luay Nakhleh:
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. J. Comput. Biol. 18(11): 1543-1559 (2011) - [j38]Li-San Wang, James H. Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy J. Warnow:
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 1108-1119 (2011) - [c52]Yun Yu, Tandy J. Warnow, Luay Nakhleh:
Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB 2011: 531-545 - 2010
- [j37]M. Shel Swenson, François Barbançon, Tandy J. Warnow, C. Randal Linder:
A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms Mol. Biol. 5: 8 (2010) - [c51]M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow:
An Experimental Study of Quartets MaxCut and Other Supertree Methods. WABI 2010: 288-299
2000 – 2009
- 2009
- [j36]Kevin Liu, Serita M. Nelesen, Sindhu Raghavan, C. Randal Linder, Tandy J. Warnow:
Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 6(1): 7-21 (2009) - [c50]M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy J. Warnow:
A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. WABI 2009: 333-344 - [e3]Steven Salzberg, Tandy J. Warnow:
Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings. Lecture Notes in Computer Science 5724, Springer 2009, ISBN 978-3-642-04240-9 [contents] - 2008
- [j35]Sagi Snir, Tandy J. Warnow, Satish Rao:
Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. J. Comput. Biol. 15(1): 91-103 (2008) - [j34]Johanna Nichols, Tandy J. Warnow:
Tutorial on Computational Linguistic Phylogeny. Lang. Linguistics Compass 2(5): 760-820 (2008) - [c49]Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow:
Session Introduction. Pacific Symposium on Biocomputing 2008: 1-2 - [c48]Serita M. Nelesen, Kevin Liu, D. Zhao, C. Randal Linder, Tandy J. Warnow:
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis. Pacific Symposium on Biocomputing 2008: 25-36 - 2007
- [p2]Bernard M. E. Moret, Jijun Tang, Tandy J. Warnow:
Reconstructing phylogenies from gene-content and gene-order data. Mathematics of Evolution and Phylogeny 2007 - [p1]Li-San Wang, Tandy J. Warnow:
Distance-based genome rearrangement phylogeny. Mathematics of Evolution and Phylogeny 2007 - 2006
- [j33]Li-San Wang, Tandy J. Warnow:
Reconstructing Chromosomal Evolution. SIAM J. Comput. 36(1): 99-131 (2006) - [j32]Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Hai-Son Le, Vijaya Ramachandran, Tandy J. Warnow:
Pattern Identification in Biogeography. IEEE ACM Trans. Comput. Biol. Bioinform. 3(4): 334-346 (2006) - 2005
- [j31]Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John:
Reconstructing Reticulate Evolution in SpeciesTheory and Practice. J. Comput. Biol. 12(6): 796-811 (2005) - [c47]Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy J. Warnow:
Pattern Identification in Biogeography. WABI 2005: 116-127 - 2004
- [j30]Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme:
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 1(1): 13-23 (2004) - [j29]Steven N. Evans, Tandy J. Warnow:
Unidentifiable Divergence Times in Rates-across-Sites Models. IEEE ACM Trans. Comput. Biol. Bioinform. 1(3): 130-134 (2004) - [j28]Tandy J. Warnow, Binhai Zhu:
Preface. Theor. Comput. Sci. 325(3): 345-346 (2004) - [c46]Usman Roshan, Bernard M. E. Moret, Tandy J. Warnow, Tiffani L. Williams:
Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees. CSB 2004: 98-109 - [c45]Luay Nakhleh, Tandy J. Warnow, C. Randal Linder:
Reconstructing reticulate evolution in species: theory and practice. RECOMB 2004: 337-346 - [c44]Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow:
On contract-and-refine transformations between phylogenetic trees. SODA 2004: 900-909 - 2003
- [j27]Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter:
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. J. Algorithms 48(1): 173-193 (2003) - [j26]Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy J. Warnow, Christopher J. Howe:
Analyzing the Order of Items in Manuscripts of The Canterbury Tales. Comput. Humanit. 37(1): 97-109 (2003) - [c43]Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse:
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing 2003: 315-326 - [c42]Ganeshkumar Ganapathy, Vijaya Ramachandran, Tandy J. Warnow:
Better Hill-Climbing Searches for Parsimony. WABI 2003: 245-258 - [e2]Tandy J. Warnow, Binhai Zhu:
Computing and Combinatorics, 9th Annual International Conference, COCOON 2003, Big Sky, MT, USA, July 25-28, 2003, Proceedings. Lecture Notes in Computer Science 2697, Springer 2003, ISBN 3-540-40534-8 [contents] - 2002
- [j25]Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow:
Toward New Software for Computational Phylogenetics. Computer 35(7): 55-64 (2002) - [j24]Bernard M. E. Moret, Jijun Tang, Li-San Wang, Tandy J. Warnow:
Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65(3): 508-525 (2002) - [j23]Bernard M. E. Moret, David A. Bader, Tandy J. Warnow:
High-Performance Algorithm Engineering for Computational Phylogenetics. J. Supercomput. 22(1): 99-111 (2002) - [c41]Ganeshkumar Ganapathy, Tandy J. Warnow:
Approximating the Complement of the Maximum Compatible Subset of Leaves of k Trees. APPROX 2002: 122-134 - [c40]Cara Stockham, Li-San Wang, Tandy J. Warnow:
Statistically based postprocessing of phylogenetic analysis by clustering. ISMB 2002: 285-293 - [c39]Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow:
The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing 2002: 211-222 - [c38]Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow:
Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. Pacific Symposium on Biocomputing 2002: 524-535 - [c37]Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow:
Estimating the Deviation from a Molecular Clock. WABI 2002: 287-299 - [c36]Bernard M. E. Moret, Usman Roshan, Tandy J. Warnow:
Sequence-Length Requirements for Phylogenetic Methods. WABI 2002: 343-356 - 2001
- [c35]Bernard M. E. Moret, David A. Bader, Tandy J. Warnow:
High-Performance Algorithm Engineering for Computational Phylogenetics. International Conference on Computational Science (2) 2001: 1012-1021 - [c34]Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman:
New approaches for reconstructing phylogenies from gene order data. ISMB (Supplement of Bioinformatics) 2001: 165-173 - [c33]Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow:
Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) 2001: 190-198 - [c32]Bernard M. E. Moret, Stacia K. Wyman, David A. Bader, Tandy J. Warnow, Mi Yan:
A New Implmentation and Detailed Study of Breakpoint Analysis. Pacific Symposium on Biocomputing 2001: 583-594 - [c31]Tandy J. Warnow, Bernard M. E. Moret, Katherine St. John:
Absolute convergence: true trees from short sequences. SODA 2001: 186-195 - [c30]Katherine St. John, Tandy J. Warnow, Bernard M. E. Moret, Lisa Vawter:
Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. SODA 2001: 196-205 - [c29]Li-San Wang, Tandy J. Warnow:
Estimating true evolutionary distances between genomes. STOC 2001: 637-646 - [c28]Ganeshkumar Ganapathysaravanabavan, Tandy J. Warnow:
Finding a Maximum Compatible Tree for a Bounded Number of Trees with Bounded Degree Is Solvable in Polynomial Time. WABI 2001: 156-163 - [c27]Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow:
The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI 2001: 214-226 - 2000
- [j22]Hans L. Bodlaender, Michael R. Fellows, Michael T. Hallett, Todd Wareham, Tandy J. Warnow:
The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs. Theor. Comput. Sci. 244(1-2): 167-188 (2000) - [c26]Bernard M. E. Moret, Tandy J. Warnow:
Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics. Experimental Algorithmics 2000: 163-180 - [c25]Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman:
A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. ISMB 2000: 104-115
1990 – 1999
- 1999
- [j21]Monika Rauch Henzinger, Valerie King, Tandy J. Warnow:
Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. Algorithmica 24(1): 1-13 (1999) - [j20]Daniel H. Huson, Scott Nettles, Tandy J. Warnow:
Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction. J. Comput. Biol. 6(3/4): 369-386 (1999) - [j19]Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph:
Hybrid Tree Reconstruction Methods. ACM J. Exp. Algorithmics 4: 5 (1999) - [j18]Péter L. Erdös, Michael Anthony Steel, László A. Székely, Tandy J. Warnow:
A few logs suffice to build (almost) all trees (I). Random Struct. Algorithms 14(2): 153-184 (1999) - [j17]Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph:
Constructing Evolutionary Trees in the Presence of Polymorphic Characters. SIAM J. Comput. 29(1): 103-131 (1999) - [j16]Péter L. Erdös, Michael Anthony Steel, László A. Székely, Tandy J. Warnow:
A Few Logs Suffice to Build (almost) All Trees: Part II. Theor. Comput. Sci. 221(1-2): 77-118 (1999) - [c24]Daniel H. Huson, Lisa Vawter, Tandy J. Warnow:
Solving Large Scale Phylogenetic Problems using DCM2. ISMB 1999: 118-129 - [c23]Daniel H. Huson, Scott Nettles, Tandy J. Warnow:
Obtaining highly accurate topology estimates of evolutionary trees from very short sequences. RECOMB 1999: 198-207 - [c22]Daniel H. Huson, Kelly Ann Smith, Tandy J. Warnow:
Estimating Large Distances in Phylogenetic Reconstruction. WAE 1999: 272-286 - [e1]Robert Endre Tarjan, Tandy J. Warnow:
Proceedings of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, 17-19 January 1999, Baltimore, Maryland, USA. ACM/SIAM 1999, ISBN 0-89871-434-6 [contents] - 1998
- [j15]Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph:
Better Methods for Solving Parsimony and Compatibility. J. Comput. Biol. 5(3): 391-407 (1998) - [j14]Sampath Kannan, Tandy J. Warnow:
Computing the Local Consensus of Trees. SIAM J. Comput. 27(6): 1695-1724 (1998) - [c21]Maria Luisa Bonet, Mike A. Steel, Tandy J. Warnow, Shibu Yooseph:
Better methods for solving parsimony and compatibility. RECOMB 1998: 40-49 - [c20]Daniel H. Huson, Scott Nettles, Kenneth Rice, Tandy J. Warnow, Shibu Yooseph:
Hybrid Tree Reconstruction Methods. WAE 1998: 179-192 - 1997
- [j13]Péter L. Erdös, Mike A. Steel, László A. Székely, Tandy J. Warnow:
Local Quartet Splits of a Binary Tree Infer All Quartet Splits Via One Dyadic Inference Rule. Comput. Artif. Intell. 16(2): 217-227 (1997) - [j12]Sampath Kannan, Tandy J. Warnow:
A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies. SIAM J. Comput. 26(6): 1749-1763 (1997) - [c19]Kenneth Rice, Tandy J. Warnow:
Parsimony is Hard to Beat. COCOON 1997: 124-133 - [c18]Péter L. Erdös, Mike A. Steel, László A. Székely, Tandy J. Warnow:
Constructing Big Trees from Short Sequences. ICALP 1997: 827-837 - 1996
- [j11]Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy J. Warnow:
Minimizing Phylogenetic Number To Find Good Evolutionary Trees. Discret. Appl. Math. 71(1-3): 111-136 (1996) - [j10]Cynthia A. Phillips, Tandy J. Warnow:
The Asymmetric Median Tree - A New Model for Building Consensus Trees. Discret. Appl. Math. 71(1-3): 311-335 (1996) - [j9]Sampath Kannan, Eugene L. Lawler, Tandy J. Warnow:
Determining the Evolutionary Tree Using Experiments. J. Algorithms 21(1): 26-50 (1996) - [c17]Cynthia A. Phillips, Tandy J. Warnow:
The Asymmetric Median Tree - A New model for Building Consensus Trees. CPM 1996: 234-252 - [c16]Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph:
Inferring evolutionary trees from polymorphic characters, and an analysis of the Indo-European family of languages. Mathematical Hierarchies and Biology 1996: 43-56 - [c15]Tandy J. Warnow, Donald Ringe, Ann Taylor:
Reconstructing the Evolutionary History of Natural Languages. SODA 1996: 314-322 - [c14]Monika Rauch Henzinger, Valerie King, Tandy J. Warnow:
Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology. SODA 1996: 333-340 - [c13]Maria Luisa Bonet, Cynthia A. Phillips, Tandy J. Warnow, Shibu Yooseph:
Constructing Evolutionary Trees in the Presence of Polymorphic Characters. STOC 1996: 220-229 - 1995
- [j8]Martin Farach, Sampath Kannan, Tandy J. Warnow:
A Robust Model for Finding Optimal Evolutionary Trees. Algorithmica 13(1/2): 155-179 (1995) - [j7]Craig J. Benham, Sampath Kannan, Michael Paterson, Tandy J. Warnow:
Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility. J. Comput. Biol. 2(4): 515-525 (1995) - [j6]Sampath Kannan, Tandy J. Warnow:
Tree Reconstruction from Partial Orders. SIAM J. Comput. 24(3): 511-519 (1995) - [c12]Craig J. Benham, Sampath Kannan, Tandy J. Warnow:
Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility. CPM 1995: 17-26 - [c11]Leslie Ann Goldberg, Paul W. Goldberg, Cynthia A. Phillips, Elizabeth Sweedyk, Tandy J. Warnow:
Minimizing Phylogenetic Number to find Good Evolutionary Trees. CPM 1995: 102-127 - [c10]Sampath Kannan, Tandy J. Warnow, Shibu Yooseph:
Computing the Local Consensus of Trees. SODA 1995: 68-77 - [c9]Sampath Kannan, Tandy J. Warnow:
A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies when the Number of Character States is Fixed. SODA 1995: 595-603 - 1994
- [j5]Tandy J. Warnow:
Tree Compatibility and Inferring Evolutionary History. J. Algorithms 16(3): 388-407 (1994) - [j4]Sampath Kannan, Tandy J. Warnow:
Inferring Evolutionary History from DNA Sequences. SIAM J. Comput. 23(4): 713-737 (1994) - [j3]Fred R. McMorris, Tandy J. Warnow, Thomas Wimer:
Triangulating Vertex-Colored Graphs. SIAM J. Discret. Math. 7(2): 296-306 (1994) - 1993
- [j2]Mike A. Steel, Tandy J. Warnow:
Kaikoura Tree Theorems: Computing the Maximum Agreement Subtree. Inf. Process. Lett. 48(2): 77-82 (1993) - [c8]Fred R. McMorris, Tandy J. Warnow, Thomas Wimer:
Triangulating Vertex Colored Graphs. SODA 1993: 120-127 - [c7]Tandy J. Warnow:
Tree Compatibility and Inferring Evoluationary History. SODA 1993: 382-391 - [c6]Martin Farach, Sampath Kannan, Tandy J. Warnow:
A robust model for finding optimal evolutionary trees. STOC 1993: 137-145 - [c5]Sampath Kannan, Tandy J. Warnow:
Tree Reconstruction from Partial Orders. WADS 1993: 397-408 - 1992
- [j1]Sampath Kannan, Tandy J. Warnow:
Triangulating 3-Colored Graphs. SIAM J. Discret. Math. 5(2): 249-258 (1992) - [c4]Hans L. Bodlaender, Michael R. Fellows, Tandy J. Warnow:
Two Strikes Against Perfect Phylogeny. ICALP 1992: 273-283 - 1991
- [c3]Sampath Kannan, Tandy J. Warnow:
Triangulating Three-Colored Graphs. SODA 1991: 337-343 - 1990
- [c2]Sampath Kannan, Tandy J. Warnow:
Inferring Evolutionary History from DNA Sequences (Extended Abstract). FOCS 1990: 362-371 - [c1]Sampath Kannan, Eugene L. Lawler, Tandy J. Warnow:
Determining the Evolutionary Tree. SODA 1990: 475-484
Coauthor Index
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