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Tandy J. Warnow
Person information
- 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
- 2024
- [j90]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 - 2023
- [j89]Baqiao Liu, Tandy J. Warnow:
Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol. Biol. 18(1): 6 (2023) - [j88]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) - [j87]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) - [j86]Yasamin Tabatabaee
, Chao Zhang, Tandy J. Warnow, Siavash Mirarab
:
Phylogenomic branch length estimation using quartets. Bioinform. 39(Supplement-1): 185-193 (2023) - [j85]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) - [j84]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) - [j83]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
- [j82]Chengze Shen
, Paul Zaharias
, Tandy J. Warnow
:
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinform. 38(4): 918-924 (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
![](https://dblp.org/img/cog.dark.24x24.png)
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