| Year |
Citation |
Score |
| 2023 |
Tabatabaee Y, Roch S, Warnow T. QR-STAR: A Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 37902986 DOI: 10.1089/cmb.2023.0185 |
0.365 |
|
| 2023 |
Liu B, Warnow T. Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms For Molecular Biology : Amb. 18: 6. PMID 37468904 DOI: 10.1186/s13015-023-00230-6 |
0.411 |
|
| 2023 |
Tabatabaee Y, Zhang C, Warnow T, Mirarab S. Phylogenomic branch length estimation using quartets. Bioinformatics (Oxford, England). 39: i185-i193. PMID 37387151 DOI: 10.1093/bioinformatics/btad221 |
0.687 |
|
| 2023 |
Park M, Warnow T. HMMerge: an ensemble method for multiple sequence alignment. Bioinformatics Advances. 3: vbad052. PMID 37128578 DOI: 10.1093/bioadv/vbad052 |
0.301 |
|
| 2023 |
Liu B, Warnow T. WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity. Bioinformatics Advances. 3: vbad024. PMID 36970502 DOI: 10.1093/bioadv/vbad024 |
0.361 |
|
| 2023 |
Chu G, Warnow T. SCAMPP+FastTree: improving scalability for likelihood-based phylogenetic placement. Bioinformatics Advances. 3: vbad008. PMID 36818728 DOI: 10.1093/bioadv/vbad008 |
0.455 |
|
| 2023 |
Willson J, Tabatabaee Y, Liu B, Warnow T. DISCO+QR: rooting species trees in the presence of GDL and ILS. Bioinformatics Advances. 3: vbad015. PMID 36789293 DOI: 10.1093/bioadv/vbad015 |
0.366 |
|
| 2023 |
Park M, Ivanovic S, Chu G, Shen C, Warnow T. UPP2: fast and accurate alignment of datasets with fragmentary sequences. Bioinformatics (Oxford, England). 39. PMID 36625535 DOI: 10.1093/bioinformatics/btad007 |
0.345 |
|
| 2022 |
Zaharias P, Warnow T. Recent progress on methods for estimating and updating large phylogenies. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210244. PMID 35989607 DOI: 10.1098/rstb.2021.0244 |
0.483 |
|
| 2022 |
Zaharias P, Smirnov V, Warnow T. Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 35849662 DOI: 10.1109/TCBB.2022.3191848 |
0.369 |
|
| 2022 |
Tabatabaee Y, Sarker K, Warnow T. Quintet Rooting: rooting species trees under the multi-species coalescent model. Bioinformatics (Oxford, England). 38: i109-i117. PMID 35758805 DOI: 10.1093/bioinformatics/btac224 |
0.403 |
|
| 2022 |
Wedell E, Cai Y, Warnow T. SCAMPP: Scaling Alignment-based Phylogenetic Placement to Large Trees. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 35471888 DOI: 10.1109/TCBB.2022.3170386 |
0.448 |
|
| 2022 |
Liu B, Warnow T. Scalable Species Tree Inference with External Constraints. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35196115 DOI: 10.1089/cmb.2021.0543 |
0.416 |
|
| 2022 |
Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, ... ... Warnow T, et al. Why sequence all eukaryotes? Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042801 DOI: 10.1073/pnas.2115636118 |
0.331 |
|
| 2022 |
Zaharias P, Grosshauser M, Warnow T. Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 29: 74-89. PMID 34986031 DOI: 10.1089/cmb.2021.0383 |
0.375 |
|
| 2021 |
Shen C, Zaharias P, Warnow T. MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences. Bioinformatics (Oxford, England). PMID 34791036 DOI: 10.1093/bioinformatics/btab788 |
0.339 |
|
| 2021 |
Willson J, Roddur MS, Liu B, Zaharias P, Warnow T. DISCO: Species Tree Inference using Multi-Copy gene family Tree Decomposition. Systematic Biology. PMID 34450658 DOI: 10.1093/sysbio/syab070 |
0.385 |
|
| 2021 |
Yu X, Le T, Christensen SA, Molloy EK, Warnow T. Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation. Algorithms For Molecular Biology : Amb. 16: 12. PMID 34183037 DOI: 10.1186/s13015-021-00189-2 |
0.412 |
|
| 2021 |
Dibaeinia P, Bordbar ST, Warnow T. FASTRAL: Improving scalability of phylogenomic analysis. Bioinformatics (Oxford, England). PMID 33576396 DOI: 10.1093/bioinformatics/btab093 |
0.362 |
|
| 2021 |
Warnow T. Revisiting Evaluation of Multiple Sequence Alignment Methods. Methods in Molecular Biology (Clifton, N.J.). 2231: 299-317. PMID 33289899 DOI: 10.1007/978-1-0716-1036-7_17 |
0.308 |
|
| 2021 |
Warnow T, Mirarab S. Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. Methods in Molecular Biology (Clifton, N.J.). 2231: 99-119. PMID 33289889 DOI: 10.1007/978-1-0716-1036-7_7 |
0.698 |
|
| 2020 |
Legried B, Molloy EK, Warnow T, Roch S. Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 28: 452-468. PMID 33325781 DOI: 10.1089/cmb.2020.0424 |
0.417 |
|
| 2020 |
Smirnov V, Warnow T. MAGUS: Multiple Sequence Alignment using Graph Clustering. Bioinformatics (Oxford, England). PMID 33252662 DOI: 10.1093/bioinformatics/btaa992 |
0.367 |
|
| 2020 |
Le T, Sy A, Molloy EK, Zhang Q, Rao S, Warnow T. Using Constrained-INC for Large-scale Gene Tree and Species Tree Estimation. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 32750844 DOI: 10.1109/Tcbb.2020.2990867 |
0.56 |
|
| 2020 |
Smirnov V, Warnow T. Phylogeny Estimation Given Sequence Length Heterogeneity. Systematic Biology. PMID 32692823 DOI: 10.1093/Sysbio/Syaa058 |
0.52 |
|
| 2020 |
Molloy EK, Warnow T. FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinformatics (Oxford, England). 36: i57-i65. PMID 32657396 DOI: 10.1093/Bioinformatics/Btaa444 |
0.497 |
|
| 2020 |
Smirnov V, Warnow T. Unblended disjoint tree merging using GTM improves species tree estimation. Bmc Genomics. 21: 235. PMID 32299343 DOI: 10.1186/S12864-020-6605-1 |
0.504 |
|
| 2020 |
Nute M, Chou J, Molloy EK, Warnow T. Correction to: The performance of coalescent-based species tree estimation methods under models of missing data. Bmc Genomics. 21: 133. PMID 32039710 DOI: 10.1186/S12864-020-6540-1 |
0.445 |
|
| 2020 |
Christensen S, Molloy EK, Vachaspati P, Yammanuru A, Warnow T. Non-parametric correction of estimated gene trees using TRACTION. Algorithms For Molecular Biology : Amb. 15: 1. PMID 31911812 DOI: 10.1186/S13015-019-0161-8 |
0.478 |
|
| 2020 |
Molloy EK, Warnow T. TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinformatics (Oxford, England). 35: i417-i426. PMID 31510668 DOI: 10.1093/Bioinformatics/Btz344 |
0.487 |
|
| 2019 |
Pattabiraman S, Warnow T. Profile Hidden Markov Models are Not Identifiable. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 31425043 DOI: 10.1109/Tcbb.2019.2933821 |
0.405 |
|
| 2019 |
Molloy EK, Warnow T. Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms For Molecular Biology : Amb. 14: 14. PMID 31360216 DOI: 10.1186/S13015-019-0151-X |
0.515 |
|
| 2019 |
Zhang Q, Rao S, Warnow T. Constrained incremental tree building: new absolute fast converging phylogeny estimation methods with improved scalability and accuracy. Algorithms For Molecular Biology : Amb. 14: 2. PMID 30839943 DOI: 10.1186/S13015-019-0136-9 |
0.541 |
|
| 2019 |
Roch S, Nute M, Warnow T. Long-Branch Attraction in Species Tree Estimation: Inconsistency of Partitioned Likelihood and Topology-Based Summary Methods. Systematic Biology. 68: 281-297. PMID 30247732 DOI: 10.1093/Sysbio/Syy061 |
0.557 |
|
| 2018 |
Nute M, Saleh E, Warnow T. Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets. Systematic Biology. PMID 30329135 DOI: 10.1093/Sysbio/Syy068 |
0.487 |
|
| 2018 |
Collins K, Warnow T. PASTA for Proteins. Bioinformatics (Oxford, England). PMID 29931282 DOI: 10.1093/Bioinformatics/Bty495 |
0.487 |
|
| 2018 |
Johnson KP, Nguyen NP, Sweet AD, Boyd BM, Warnow T, Allen JM. Simultaneous radiation of bird and mammal lice following the K-Pg boundary. Biology Letters. 14. PMID 29794007 DOI: 10.1098/Rsbl.2018.0141 |
0.338 |
|
| 2018 |
Nute M, Chou J, Molloy EK, Warnow T. The performance of coalescent-based species tree estimation methods under models of missing data. Bmc Genomics. 19: 286. PMID 29745854 DOI: 10.1186/S12864-018-4619-8 |
0.486 |
|
| 2018 |
Vachaspati P, Warnow T. SIESTA: enhancing searches for optimal supertrees and species trees. Bmc Genomics. 19: 252. PMID 29745851 DOI: 10.1186/S12864-018-4621-1 |
0.482 |
|
| 2018 |
Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, ... ... Warnow T, et al. A roadmap for global synthesis of the plant tree of life. American Journal of Botany. PMID 29603138 DOI: 10.1002/Ajb2.1041 |
0.664 |
|
| 2018 |
Christensen S, Molloy EK, Vachaspati P, Warnow T. OCTAL: Optimal Completion of gene trees in polynomial time. Algorithms For Molecular Biology : Amb. 13: 6. PMID 29568323 DOI: 10.1186/S13015-018-0124-5 |
0.413 |
|
| 2018 |
Vachaspati P, Warnow T. SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. Molecular Phylogenetics and Evolution. 124: 122-136. PMID 29530498 DOI: 10.1016/J.Ympev.2018.03.006 |
0.531 |
|
| 2018 |
Bayzid MS, Warnow T. Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms For Molecular Biology : Amb. 13: 1. PMID 29387142 DOI: 10.1186/S13015-017-0120-1 |
0.442 |
|
| 2017 |
Molloy EK, Warnow T. To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods. Systematic Biology. PMID 29029338 DOI: 10.1093/Sysbio/Syx077 |
0.503 |
|
| 2017 |
Allen JM, Boyd B, Nguyen NP, Vachaspati P, Warnow T, Huang DI, Grady PG, Bell KC, Cronk QC, Mugisha L, Pittendrigh BR, Soledad Leonardi M, Reed DL, Johnson KP. Phylogenomics from Whole Genome Sequences Using aTRAM. Systematic Biology. PMID 28123117 DOI: 10.1093/Sysbio/Syw105 |
0.424 |
|
| 2017 |
Boyd BM, Allen JM, Nguyen N, Sweet AD, Warnow T, Shapiro MD, Villa SM, Bush SE, Clayton DH, Johnson KP. Phylogenomics using Target-restricted Assembly Resolves Intra-generic Relationships of Parasitic Lice (Phthiraptera: Columbicola). Systematic Biology. PMID 28108601 DOI: 10.1093/Sysbio/Syx027 |
0.434 |
|
| 2016 |
Nguyen NP, Nute M, Mirarab S, Warnow T. HIPPI: highly accurate protein family classification with ensembles of HMMs. Bmc Genomics. 17: 765. PMID 28185571 DOI: 10.1186/S12864-016-3097-0 |
0.646 |
|
| 2016 |
Uricchio LH, Warnow T, Rosenberg NA. 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 Bioinformatics. 17: 417. PMID 28185570 DOI: 10.1186/S12859-016-1266-4 |
0.521 |
|
| 2016 |
Nute M, Warnow T. Scaling statistical multiple sequence alignment to large datasets. Bmc Genomics. 17: 764. PMID 28185555 DOI: 10.1186/S12864-016-3101-8 |
0.5 |
|
| 2016 |
Vachaspati P, Warnow T. FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization. Bioinformatics (Oxford, England). PMID 27663499 DOI: 10.1093/Bioinformatics/Btw600 |
0.512 |
|
| 2016 |
Hansen TA, Mollerup S, Nguyen NP, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR, Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, et al. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging Microbes & Infections. 5: e90. PMID 27530749 DOI: 10.1038/Emi.2016.90 |
0.338 |
|
| 2016 |
Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PC, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biology and Evolution. PMID 26733575 DOI: 10.1093/Gbe/Evv261 |
0.668 |
|
| 2015 |
Davidson R, Vachaspati P, Mirarab S, Warnow T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. Bmc Genomics. 16: S1. PMID 26450506 DOI: 10.1186/1471-2164-16-S10-S1 |
0.69 |
|
| 2015 |
Mirarab S, Bayzid MS, Boussau B, Warnow T. Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science (New York, N.Y.). 350: 171. PMID 26450204 DOI: 10.1126/Science.Aaa7719 |
0.657 |
|
| 2015 |
Vachaspati P, Warnow T. ASTRID: Accurate Species TRees from Internode Distances. Bmc Genomics. 16: S3. PMID 26449326 DOI: 10.1186/1471-2164-16-S10-S3 |
0.491 |
|
| 2015 |
Chou J, Gupta A, Yaduvanshi S, Davidson R, Nute M, Mirarab S, Warnow T. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. Bmc Genomics. 16: S2. PMID 26449249 DOI: 10.1186/1471-2164-16-S10-S2 |
0.724 |
|
| 2015 |
Cracraft J, Houde P, Ho SY, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MT, Zhang G, Braun EL, Jarvis ED. Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science (New York, N.Y.). 349: 1460. PMID 26404820 DOI: 10.1126/Science.Aab1578 |
0.655 |
|
| 2015 |
Bayzid MS, Mirarab S, Boussau B, Warnow T. Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses. Plos One. 10: e0129183. PMID 26086579 DOI: 10.1371/Journal.Pone.0129183 |
0.745 |
|
| 2015 |
Nguyen NP, Mirarab S, Kumar K, Warnow T. Ultra-large alignments using phylogeny-aware profiles. Genome Biology. 16: 124. PMID 26076734 DOI: 10.1186/S13059-015-0688-Z |
0.695 |
|
| 2015 |
Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics (Oxford, England). 31: i44-52. PMID 26072508 DOI: 10.1093/Bioinformatics/Btv234 |
0.721 |
|
| 2015 |
Warnow T. Concatenation Analyses in the Presence of Incomplete Lineage Sorting. Plos Currents. 7. PMID 26064786 DOI: 10.1371/Currents.Tol.8D41Ac0F13D1Abedf4C4A59F5D17B1F7 |
0.47 |
|
| 2015 |
Roch S, Warnow T. On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods. Systematic Biology. 64: 663-76. PMID 25813358 DOI: 10.1093/Sysbio/Syv016 |
0.519 |
|
| 2015 |
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, ... ... Warnow T, et al. Phylogenomic analyses data of the avian phylogenomics project. Gigascience. 4: 4. PMID 25741440 DOI: 10.1186/S13742-014-0038-1 |
0.667 |
|
| 2015 |
Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 377-86. PMID 25549288 DOI: 10.1089/Cmb.2014.0156 |
0.764 |
|
| 2015 |
Nguyen NP, Mirarab S, Kumar K, Warnow T. Ultra-large alignments using ensembles of hidden Markov models Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 259-260. DOI: 10.1007/978-3-319-16706-0_26 |
0.566 |
|
| 2014 |
Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, et al. Data access for the 1,000 Plants (1KP) project. Gigascience. 3: 17. PMID 25625010 DOI: 10.1186/2047-217X-3-17 |
0.638 |
|
| 2014 |
Bayzid MS, Hunt T, Warnow T. Disk covering methods improve phylogenomic analyses. Bmc Genomics. 15: S7. PMID 25572610 DOI: 10.1186/1471-2164-15-S6-S7 |
0.535 |
|
| 2014 |
Zimmermann T, Mirarab S, Warnow T. BBCA: Improving the scalability of *BEAST using random binning. Bmc Genomics. 15: S11. PMID 25572469 DOI: 10.1186/1471-2164-15-S6-S11 |
0.738 |
|
| 2014 |
Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science (New York, N.Y.). 346: 1250463. PMID 25504728 DOI: 10.1126/Science.1250463 |
0.734 |
|
| 2014 |
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, ... ... Warnow T, et al. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science (New York, N.Y.). 346: 1320-31. PMID 25504713 DOI: 10.1126/Science.1253451 |
0.706 |
|
| 2014 |
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics (Oxford, England). 30: 3548-55. PMID 25359891 DOI: 10.1093/Bioinformatics/Btu721 |
0.646 |
|
| 2014 |
Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences of the United States of America. 111: E4859-68. PMID 25355905 DOI: 10.1073/Pnas.1323926111 |
0.665 |
|
| 2014 |
Mirarab S, Bayzid MS, Warnow T. Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting. Systematic Biology. PMID 25164915 DOI: 10.1093/Sysbio/Syu063 |
0.73 |
|
| 2014 |
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, S. Swenson M, Warnow T. ASTRAL: Genome-scale coalescent-based species tree estimation Bioinformatics. 30. PMID 25161245 DOI: 10.1093/Bioinformatics/Btu462 |
0.733 |
|
| 2014 |
Liu K, Warnow T. Large-scale multiple sequence alignment and tree estimation using SATé. Methods in Molecular Biology (Clifton, N.J.). 1079: 219-44. PMID 24170406 DOI: 10.1007/978-1-62703-646-7_15 |
0.515 |
|
| 2013 |
Bayzid MS, Warnow T. Naive binning improves phylogenomic analyses. Bioinformatics (Oxford, England). 29: 2277-84. PMID 23842808 DOI: 10.1093/Bioinformatics/Btt394 |
0.488 |
|
| 2013 |
Bayzid MS, Mirarab S, Warnow T. Inferring optimal species trees under gene duplication and loss 18th Pacific Symposium On Biocomputing, Psb 2013. 250-261. PMID 23424130 |
0.67 |
|
| 2013 |
Barbancon F, Evans SN, Nakhleh L, Ringe D, Warnow T. An experimental study comparing linguistic phylogenetic reconstruction methods Diachronica. 30: 143-170. DOI: 10.1075/Dia.30.2.01Bar |
0.669 |
|
| 2013 |
Nakhleh LK, Rosenberg NA, Warnow T. Phylogenomics and population genomics: Moddels, algorithms, and analytical tools 18th Pacific Symposium On Biocomputing, Psb 2013. |
0.549 |
|
| 2012 |
Bayzid MS, Warnow T. Estimating optimal species trees from incomplete gene trees under deep coalescence. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 591-605. PMID 22697236 DOI: 10.1089/Cmb.2012.0037 |
0.537 |
|
| 2012 |
Nelesen S, Liu K, Wang LS, Linder CR, Warnow T. DACTAL: divide-and-conquer trees (almost) without alignments. Bioinformatics (Oxford, England). 28: i274-82. PMID 22689772 DOI: 10.1093/Bioinformatics/Bts218 |
0.636 |
|
| 2012 |
Warnow T. Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent. Plos Currents. 4: RRN1308. PMID 22453901 DOI: 10.1371/Currents.Rrn1308 |
0.46 |
|
| 2012 |
Liu K, Warnow T. Treelength optimization for phylogeny estimation. Plos One. 7: e33104. PMID 22442677 DOI: 10.1371/Journal.Pone.0033104 |
0.512 |
|
| 2012 |
Nguyen N, Mirarab S, Warnow T. MRL and SuperFine+MRL: new supertree methods. Algorithms For Molecular Biology : Amb. 7: 3. PMID 22280525 DOI: 10.1186/1748-7188-7-3 |
0.685 |
|
| 2012 |
Mirarab S, Nguyen N, Warnow T. SEPP: SATé-enabled phylogenetic placement 17th Pacific Symposium On Biocomputing, Psb 2012. 247-258. PMID 22174280 |
0.714 |
|
| 2012 |
Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology. 61: 90-106. PMID 22139466 DOI: 10.1093/Sysbio/Syr095 |
0.536 |
|
| 2012 |
Swenson MS, Suri R, Linder CR, Warnow T. SuperFine: fast and accurate supertree estimation. Systematic Biology. 61: 214-27. PMID 21934137 DOI: 10.1093/Sysbio/Syr092 |
0.557 |
|
| 2011 |
Yang J, Warnow T. Fast and accurate methods for phylogenomic analyses. Bmc Bioinformatics. 12: S4. PMID 22152123 DOI: 10.1186/1471-2105-12-S9-S4 |
0.499 |
|
| 2011 |
Liu K, Linder CR, Warnow T. RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation. Plos One. 6: e27731. PMID 22132132 DOI: 10.1371/Journal.Pone.0027731 |
0.523 |
|
| 2011 |
Yu Y, Warnow T, Nakhleh L. Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1543-59. PMID 22035329 DOI: 10.1089/Cmb.2011.0174 |
0.689 |
|
| 2011 |
Mirarab S, Warnow T. FastSP: linear time calculation of alignment accuracy. Bioinformatics (Oxford, England). 27: 3250-8. PMID 21984754 DOI: 10.1093/Bioinformatics/Btr553 |
0.671 |
|
| 2011 |
Wang LS, Leebens-Mack J, Wall PK, Beckmann K, Depamphilis CW, Warnow T. The impact of multiple protein sequence alignment on phylogenetic estimation Ieee/Acm Transactions On Computational Biology and Bioinformatics. 8: 1108-1119. PMID 21566256 DOI: 10.1109/Tcbb.2009.68 |
0.649 |
|
| 2011 |
Swenson MS, Suri R, Linder CR, Warnow T. An experimental study of Quartets MaxCut and other supertree methods. Algorithms For Molecular Biology : Amb. 6: 7. PMID 21504600 DOI: 10.1186/1748-7188-6-7 |
0.417 |
|
| 2010 |
Liu K, Linder CR, Warnow T. Multiple sequence alignment: a major challenge to large-scale phylogenetics. Plos Currents. 2: RRN1198. PMID 21113338 DOI: 10.1371/Currents.Rrn1198 |
0.509 |
|
| 2010 |
Linder CR, Suri R, Liu K, Warnow T. Benchmark datasets and software for developing and testing methods for large-scale multiple sequence alignment and phylogenetic inference. Plos Currents. 2: RRN1195. PMID 21113335 DOI: 10.1371/Currents.Rrn1195 |
0.517 |
|
| 2010 |
Swenson MS, Barbançon F, Warnow T, Linder CR. A simulation study comparing supertree and combined analysis methods using SMIDGen. Algorithms For Molecular Biology : Amb. 5: 8. PMID 20047664 DOI: 10.1186/1748-7188-5-8 |
0.521 |
|
| 2009 |
Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science (New York, N.Y.). 324: 1561-4. PMID 19541996 DOI: 10.1126/Science.1171243 |
0.55 |
|
| 2009 |
Liu K, Nelesen S, Raghavan S, Linder CR, Warnow T. Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 7-21. PMID 19179695 DOI: 10.1109/Tcbb.2008.63 |
0.475 |
|
| 2008 |
Nelesen S, Liu K, Zhao D, Linder CR, Warnow T. The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses Pacific Symposium On Biocomputing 2008, Psb 2008. 25-36. PMID 18229674 |
0.443 |
|
| 2008 |
Snir S, Warnow T, Rao S. Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 91-103. PMID 18199023 DOI: 10.1089/Cmb.2007.0103 |
0.449 |
|
| 2008 |
Nichols J, Warnow T. Tutorial on computational linguistic phylogeny Linguistics and Language Compass. 2: 760-820. DOI: 10.1111/J.1749-818X.2008.00082.X |
0.406 |
|
| 2006 |
Wang LS, Warnow T, Moret BM, Jansen RK, Raubeson LA. Distance-based genome rearrangement phylogeny. Journal of Molecular Evolution. 63: 473-83. PMID 17021931 DOI: 10.1007/S00239-005-0216-Y |
0.648 |
|
| 2006 |
Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, ... ... Warnow T, et al. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics : a Journal of Integrative Biology. 10: 231-7. PMID 16901231 DOI: 10.1089/Omi.2006.10.231 |
0.418 |
|
| 2006 |
Wang LS, Warnow T. Reconstructing chromosomal evolution Siam Journal On Computing. 36: 99-131. DOI: 10.1137/S0097539701397229 |
0.528 |
|
| 2005 |
Nakhleh L, Warnow T, Linder CR, St John K. Reconstructing reticulate evolution in species-theory and practice. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 796-811. PMID 16108717 DOI: 10.1089/Cmb.2005.12.796 |
0.662 |
|
| 2005 |
Moret BM, Warnow T. Advances in phylogeny reconstruction from gene order and content data. Methods in Enzymology. 395: 673-700. PMID 15865990 DOI: 10.1016/S0076-6879(05)95035-0 |
0.407 |
|
| 2005 |
Nakhleh L, Ringe D, Warnow T. Perfect phylogenetic networks: A new methodology for reconstructing the evolutionary history of natural languages Language. 81: 382-420. DOI: 10.1353/Lan.2005.0078 |
0.623 |
|
| 2005 |
Nakhleh L, Warnow T, Ringe D, Evans SN. A comparison of phylogenetic reconstruction methods on an Indo-European dataset Transactions of the Philological Society. 103: 171-192. DOI: 10.1111/J.1467-968X.2005.00149.X |
0.652 |
|
| 2004 |
Moret BM, Nakhleh L, Warnow T, Linder CR, Tholse A, Padolina A, Sun J, Timme R. Phylogenetic networks: modeling, reconstructibility, and accuracy. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 1: 13-23. PMID 17048405 DOI: 10.1109/Tcbb.2004.10 |
0.615 |
|
| 2004 |
Evans SN, Warnow T. Unidentifiable divergence times in rates-across-sites models. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 1: 130-4. PMID 17048388 DOI: 10.1109/Tcbb.2004.34 |
0.345 |
|
| 2004 |
Roshan UW, Moret BM, Warnow T, Williams TL. Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 98-109. PMID 16448004 |
0.797 |
|
| 2004 |
Nakhleh L, Warnow T, Linder CR. Reconstructing reticulate evolution in species - Theory and practice Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 337-346. |
0.56 |
|
| 2004 |
Ganapathy G, Ramachandran V, Warnow T. On Contract-and-Refine Transformations Between Phylogenetic Trees Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 15: 893-902. |
0.35 |
|
| 2004 |
Roshan UW, Warnow T, Moret BME, Williams TL. Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees Proceedings - 2004 Ieee Computational Systems Bioinformatics Conference, Csb 2004. 98-109. |
0.797 |
|
| 2003 |
Nakhleh L, Sun J, Warnow T, Linder CR, Moret BM, Tholse A. Towards the development of computational tools for evaluating phylogenetic network reconstruction methods. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 315-26. PMID 12603038 |
0.612 |
|
| 2003 |
Spencer M, Bordalejo B, Wang LIS, Barbrook AC, Mooney LR, Robinson P, Warnow T, Howe CJ. Analyzing the order of items in manuscripts of the canterbury tales Computers and the Humanities. 37: 97-109. DOI: 10.1023/A:1021818600001 |
0.52 |
|
| 2003 |
Moret BME, Tang J, Wang LS, Warnow T. Steps toward accurate reconstructions of phylogenies from gene-order data Journal of Computer and System Sciences. 65: 508-525. DOI: 10.1016/S0022-0000(02)00007-7 |
0.635 |
|
| 2002 |
Stockham C, Wang LS, Warnow T. Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics (Oxford, England). 18: S285-93. PMID 12169558 |
0.561 |
|
| 2002 |
Wang LS, Jansen RK, Moret BM, Raubeson LA, Warnow T. Fast phylogenetic methods for the analysis of genome rearrangement data: an empirical study. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 524-35. PMID 11928504 |
0.595 |
|
| 2002 |
Nakhleh L, Moret BM, Roshan U, St John K, Sun J, Warnow T. The accuracy of fast phylogenetic methods for large datasets. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 211-22. PMID 11928477 |
0.824 |
|
| 2002 |
Ringe D, Warnow T, Taylor A. Indo‐European and Computational Cladistics Transactions of the Philological Society. 100: 59-129. DOI: 10.1111/1467-968X.00091 |
0.32 |
|
| 2002 |
Moret BME, Wang LS, Warnow T. Toward new software for computational phylogenetics Computer. 35. DOI: 10.1109/Mc.2002.1016902 |
0.634 |
|
| 2002 |
Moret BME, Bader DA, Warnow T. High-performance algorithm engineering for computational phylogenetics Journal of Supercomputing. 22: 99-111. DOI: 10.1023/A:1014362705613 |
0.373 |
|
| 2002 |
Ganapathy G, Warnow T. Approximating the complement of the maximum compatible subset of leaves of k trees Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2462: 122-134. DOI: 10.1007/3-540-45753-4_12 |
0.391 |
|
| 2002 |
Moret BME, Warnow T. Reconstructing optimal phylogenetic trees: a challenge in experimental algorithmics Lecture Notes in Computer Science. 2547: 163-180. DOI: 10.1007/3-540-36383-1_8 |
0.354 |
|
| 2002 |
Moret BME, Roshan U, Warnow T. Sequence-length requirements for phylogenetic methods Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 343-356. |
0.434 |
|
| 2002 |
Nakhleh L, Roshan U, Vawter L, Warnow T. Estimating the deviation from a molecular clock Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 287-299. |
0.659 |
|
| 2001 |
Nakhleh L, Roshan U, St John K, Sun J, Warnow T. Designing fast converging phylogenetic methods. Bioinformatics (Oxford, England). 17: S190-8. PMID 11473009 DOI: 10.1093/Bioinformatics/17.Suppl_1.S190 |
0.805 |
|
| 2001 |
Moret BM, Wang LS, Warnow T, Wyman SK. New approaches for reconstructing phylogenies from gene order data. Bioinformatics (Oxford, England). 17: S165-73. PMID 11473006 DOI: 10.1093/Bioinformatics/17.Suppl_1.S165 |
0.64 |
|
| 2001 |
Nakhleh L, Roshan U, St. John K, Sun J, Warnow T. The performance of phylogenetic methods on trees of bounded diameter Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2149: 214-226. DOI: 10.1007/3-540-44696-6_17 |
0.643 |
|
| 2001 |
Wang LS, Warnow T. Estimating true evolutionary distances between genomes Conference Proceedings of the Annual Acm Symposium On Theory of Computing. 637-646. |
0.598 |
|
| 2001 |
Warnow T, Moret BME, John KS. Absolute convergence: True trees from short sequences Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 186-195. |
0.373 |
|
| 2000 |
Cosner ME, Jansen RK, Moret BM, Raubeson LA, Wang LS, Warnow T, Wyman S. A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 104-15. PMID 10977071 |
0.614 |
|
| 1999 |
Huson DH, Vawter L, Warnow TJ. Solving large scale phylogenetic problems using DCM2. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 118-29. PMID 10786294 |
0.359 |
|
| 1999 |
Huson DH, Nettles SM, Warnow TJ. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 6: 369-86. PMID 10582573 DOI: 10.1089/106652799318337 |
0.561 |
|
| 1999 |
Huson D, Nettles S, Rice K, Warnow T, Yooseph S. Hybrid tree reconstruction methods Journal of Experimental Algorithmics. 4: 5-es. DOI: 10.1145/347792.347812 |
0.531 |
|
| 1999 |
Bonet M, Phillips C, Warnow T, Yooseph S. Constructing evolutionary trees in the presence of polymorphic characters Siam Journal On Computing. 29: 103-131. DOI: 10.1137/S0097539796324636 |
0.431 |
|
| 1999 |
Erdos PL, Steel MA, Székely LA, Warnow TJ. A few logs suffice to build (almost) all trees: Part II Theoretical Computer Science. 221: 77-118. DOI: 10.1016/S0304-3975(99)00028-6 |
0.508 |
|
| 1999 |
Huson DH, Ann Smith K, Warnow TJ. Estimating large distances in phylogenetic reconstruction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1668: 271-285. DOI: 10.1007/3-540-48318-7_22 |
0.528 |
|
| 1998 |
Bonet M, Steel M, Warnow T, Yooseph S. Better methods for solving parsimony and compatibility Journal of Computational Biology. 5: 391-407. PMID 9773340 DOI: 10.1089/Cmb.1998.5.391 |
0.475 |
|
| 1998 |
Kannan S, Warnow T, Yooseph S. Computing the Local Consensus of Trees Siam Journal On Computing. 27: 1695-1724. DOI: 10.1137/S0097539795287642 |
0.393 |
|
| 1997 |
Warnow T. Mathematical approaches to comparative linguistics Proceedings of the National Academy of Sciences of the United States of America. 94: 6585-6590. PMID 11607730 DOI: 10.1073/Pnas.94.13.6585 |
0.303 |
|
| 1997 |
Kannan S, Warnow T. A Fast Algorithm for the Computation and Enumeration of Perfect Phylogenies Siam Journal On Computing. 26: 1749-1763. DOI: 10.1137/S0097539794279067 |
0.362 |
|
| 1997 |
Steel MA, Székely LA, Warnow TJ, Erdös PL. A few logs suffice to build (almost) all trees (l): part I Random Structures and Algorithms. 14: 153-184. DOI: 10.1002/(Sici)1098-2418(199903)14:2<153::Aid-Rsa3>3.0.Co;2-R |
0.502 |
|
| 1997 |
Rice K, Warnow T. Parsimony is hard to beat! Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1276: 124-133. |
0.445 |
|
| 1997 |
Erdős PL, Steel MA, Székely LA, Warnow TJ. Constructing big trees from short sequences Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1256: 827-837. |
0.397 |
|
| 1996 |
Phillips C, Warnow TJ. The asymmetric median tree—a new model for building consensus trees Discrete Applied Mathematics. 71: 311-335. DOI: 10.1016/S0166-218X(96)00071-6 |
0.445 |
|
| 1996 |
Phillips C, Warnow TJ. The asymmetric median tree - A new model for building consensus trees Discrete Applied Mathematics. 71: 311-335. DOI: 10.1007/3-540-61258-0_18 |
0.339 |
|
| 1996 |
Kannan SK, Lawler EL, Warnow T. Determining the Evolutionary Tree Using Experiments Journal of Algorithms. 21: 26-50. DOI: 10.1006/Jagm.1996.0035 |
0.763 |
|
| 1995 |
Benham C, Kannan S, Paterson M, Warnow T. Hen's teeth and whale's feet: generalized characters and their compatibility Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 515-525. PMID 8634903 DOI: 10.1089/Cmb.1995.2.515 |
0.361 |
|
| 1995 |
Kannan SK, Warnow TJ. Tree Reconstruction from Partial Orders Siam Journal On Computing. 24: 511-519. DOI: 10.1137/S0097539793252195 |
0.372 |
|
| 1995 |
Goldberg LA, Goldberg PW, Phillips CA, Sweedyk E, Warnow T. Minimizing phylogenetic number to find good evolutionary trees Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 937: 102-127. DOI: 10.1016/S0166-218X(96)00060-1 |
0.442 |
|
| 1995 |
Farach M, Kannan S, Warnow T. A robust model for finding optimal evolutionary trees Algorithmica. 13: 155-179. DOI: 10.1007/Bf01188585 |
0.426 |
|
| 1994 |
Kannan SK, Warnow TJ. Inferring Evolutionary History From DNA Sequences Siam Journal On Computing. 23: 713-737. DOI: 10.1137/S0097539791222171 |
0.438 |
|
| 1994 |
Gustfield D, Shmoys D, Lenstra JK, Warnow T. In Memoriam Eugene L. Lawler Journal of Computational Biology. 1: 255-256. DOI: 10.1089/Cmb.1994.1.255 |
0.544 |
|
| 1994 |
Warnow TJ. Tree Compatibility and Inferring Evolutionary History Journal of Algorithms. 16: 388-407. DOI: 10.1006/Jagm.1994.1018 |
0.404 |
|
| 1993 |
Warnow TJ. Constructing phylogenetic trees efficiently using compatibility criteria New Zealand Journal of Botany. 31: 239-248. DOI: 10.1080/0028825X.1993.10419501 |
0.337 |
|
| 1993 |
Steel M, Warnow T. Kaikoura tree theorems: Computing the maximum agreement subtree Information Processing Letters. 48: 77-82. DOI: 10.1016/0020-0190(93)90181-8 |
0.37 |
|
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