Tandy J. Warnow

ORCID

Publication Activity (10 Years)

Years Active: 1990-2024
Publications (10 Years): 73

Top Venues

Bioinform.

CoRR

WABI

Algorithms Mol. Biol.

Publications

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)
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) (2024)
Baqiao Liu, Tandy J. Warnow
Weighted ASTRID: fast and accurate species trees from weighted internode distances. Algorithms Mol. Biol. 18 (1) (2023)
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) (2023)
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 (2023)
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)
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)
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) (2023)
Yasamin Tabatabaee, Chao Zhang, Tandy J. Warnow, Siavash Mirarab
Phylogenomic branch length estimation using quartets. Bioinform. 39 (Supplement-1) (2023)
James Willson, Tandy J. Warnow
Axioms for Distanceless Graph Partitioning. CoRR (2023)
Eleanor Wedell, Chengze Shen, Tandy J. Warnow
BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). WABI (2023)
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)
Yasamin Tabatabaee, Sébastien Roch, Tandy J. Warnow
Statistically Consistent Rooting of Species Trees Under the Multispecies Coalescent Model. RECOMB (2023)
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) (2023)
Eleanor Wedell, Yirong Cai, Tandy J. Warnow
SCAMPP: Scaling Alignment-Based Phylogenetic Placement to Large Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (2) (2023)
Chengze Shen, Minhyuk Park, Tandy J. Warnow
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. J. Comput. Biol. 29 (8) (2022)
Chengze Shen, Paul Zaharias, Tandy J. Warnow
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinform. 38 (4) (2022)
Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko
AOC; Assembling Overlapping Communities. CoRR (2022)
Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Center-periphery structure in research communities. Quant. Sci. Stud. 3 (1) (2022)
Baqiao Liu, Tandy J. Warnow
Fast and Accurate Species Trees from Weighted Internode Distances. WABI (2022)
Baqiao Liu, Tandy J. Warnow
Scalable Species Tree Inference with External Constraints. J. Comput. Biol. 29 (7) (2022)
Akhil Jakatdar, Baqiao Liu, Tandy J. Warnow, George Chacko
AOC: Assembling overlapping communities. Quant. Sci. Stud. 3 (4) (2022)
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) (2022)
Elizabeth R. Koning, Malachi Phillips, Tandy J. Warnow
ppIacerDC: a new scalable phylogenetic placement method. BCB (2021)
Minhyuk Park, Paul Zaharias, Tandy J. Warnow
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. Algorithms 14 (5) (2021)
Nidhi Shah, Erin K. Molloy, Mihai Pop, Tandy J. Warnow
TIPP2: metagenomic taxonomic profiling using phylogenetic markers. Bioinform. 37 (13) (2021)
Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi (Richard) 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) (2021)
James Willson, Mrinmoy Saha Roddur, Tandy J. Warnow
Comparing Methods for Species Tree Estimation with Gene Duplication and Loss. AlCoB (2021)
Srilakshmi Pattabiraman, Tandy J. Warnow
Profile Hidden Markov Models Are Not Identifiable. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (1) (2021)
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) (2021)
Paul Zaharias, Vladimir Smirnov, Tandy J. Warnow
The Maximum Weight Trace Alignment Merging Problem. AlCoB (2021)
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) (2021)
Eleanor Wedell, Yirong Cai, Tandy J. Warnow
Scalable and Accurate Phylogenetic Placement Using pplacer-XR. AlCoB (2021)
Maya Gupta, Paul Zaharias, Tandy J. Warnow
Accurate large-scale phylogeny-aware alignment using BAli-Phy. Bioinform. 37 (24) (2021)
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) (2021)
Eleanor Wedell, Minhyuk Park, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Center-Periphery Structure in Communities: Extracellular Vesicles. CoRR (2021)
Payam Dibaeinia, Shayan Tabe-Bordbar, Tandy J. Warnow
FASTRAL: improving scalability of phylogenomic analysis. Bioinform. 37 (16) (2021)
Vladimir Smirnov, Tandy J. Warnow
MAGUS: Multiple sequence Alignment using Graph clUStering. Bioinform. 37 (12) (2021)
Erin K. Molloy, Tandy J. Warnow
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models. Bioinform. 36 (Supplement-1) (2020)
Brandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch
Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss. RECOMB (2020)
Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Viewing computer science through citation analysis: Salton and Bergmark Redux. Scientometrics 125 (1) (2020)
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)
Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Frequently cocited publications: Features and kinetics. Quant. Sci. Stud. 1 (3) (2020)
Sitaram Devarakonda, James R. Bradley, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Frequently Co-cited Publications: Features and Kinetics. CoRR (2020)
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) (2020)
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) (2020)
Shreya Chandrasekharan, Mariam Zaka, Stephen A. Gallo, Tandy J. Warnow, George Chacko
Finding Scientific Communities In Citation Graphs: Convergent Clustering. CoRR (2020)
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)
Tandy J. Warnow
New Divide-and-Conquer Techniques for Large-Scale Phylogenetic Estimation. AlCoB (2019)
Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow
TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. WABI (2019)
Sitaram Devarakonda, Dmitriy Korobskiy, Tandy J. Warnow, George Chacko
Viewing Computer Science through Citation Analysis; Salton and Bergmark Redux. CoRR (2019)
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 (2019)
Erin K. Molloy, Tandy J. Warnow
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge. Algorithms Mol. Biol. 14 (1) (2019)
Qiuyi (Richard) 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) (2019)
Nidhi Shah, Michael G. Nute, Tandy J. Warnow, Mihai Pop
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows. Bioinform. 35 (9) (2019)
Erin K. Molloy, Tandy J. Warnow
TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinform. 35 (14) (2019)
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)
Srilakshmi Pattabiraman, Tandy J. Warnow
Are Profile Hidden Markov Models Identifiable? BCB (2018)
Erin K. Molloy, Tandy J. Warnow
NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. RECOMB-CG (2018)
Qiuyi (Richard) Zhang, Satish Rao, Tandy J. Warnow
New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. WABI (2018)
Sebastien Roch, Michael Nute, Tandy J. Warnow
Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods. CoRR (2018)
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) (2018)
Kodi Collins, Tandy J. Warnow
PASTA for proteins. Bioinform. 34 (22) (2018)
Md. Shamsuzzoha Bayzid, Tandy J. Warnow
Gene tree parsimony for incomplete gene trees: addressing true biological loss. Algorithms Mol. Biol. 13 (1) (2018)
Sarah A. Christensen, Erin K. Molloy, Pranjal Vachaspati, Tandy J. Warnow
Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL. WABI (2017)
Tandy J. Warnow
Genome-scale Estimation of the Tree of Life. BCB (2017)
Tandy J. Warnow
Computational Challenges in Constructing the Tree of Life. IPDPS (2017)
Pranjal Vachaspati, Tandy J. Warnow
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization. Bioinform. 33 (5) (2017)
Pranjal Vachaspati, Tandy J. Warnow
Enhancing Searches for Optimal Trees Using SIESTA. RECOMB-CG (2017)
Md. Shamsuzzoha Bayzid, Tandy J. Warnow
Gene Tree Parsimony for Incomplete Gene Trees. WABI (2017)
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) (2016)
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)
Gene Myers, Mihai Pop, Knut Reinert, Tandy J. Warnow
Next Generation Sequencing (Dagstuhl Seminar 16351). Dagstuhl Reports 6 (8) (2016)
Siavash Mirarab, Tandy J. Warnow
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinform. 31 (12) (2015)
Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
Ultra-large alignments using Phylogeny-aware Profiles. CoRR (2015)
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) (2015)
Nam-phuong Nguyen, Siavash Mirarab, Keerthana Kumar, Tandy J. Warnow
Ultra-Large Alignments Using Ensembles of Hidden Markov Models. RECOMB (2015)
Siavash Mirarab, Nam-phuong Nguyen, Tandy J. Warnow
PASTA: Ultra-Large Multiple Sequence Alignment. RECOMB (2014)
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) (2014)
Nam-phuong Nguyen, Siavash Mirarab, Bo Liu, Mihai Pop, Tandy J. Warnow
TIPP: taxonomic identification and phylogenetic profiling. Bioinform. 30 (24) (2014)
Md. Shamsuzzoha Bayzid, Tandy J. Warnow
Naive binning improves phylogenomic analyses. Bioinform. 29 (18) (2013)
Md. Shamsuzzoha Bayzid, Siavash Mirarab, Tandy J. Warnow
Inferring Optimal Species Trees Under Gene Duplication and Loss. Pacific Symposium on Biocomputing (2013)
Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow
Session introduction. Pacific Symposium on Biocomputing (2013)
Nam-phuong Nguyen, Siavash Mirarab, Tandy J. Warnow
MRL and SuperFine+MRL: new supertree methods. Algorithms Mol. Biol. 7 (2012)
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) (2012)
Diogo Telmo Neves, Tandy J. Warnow, João Luís Sobral, Keshav Pingali
Parallelizing SuperFine. SAC (2012)
Md. Shamsuzzoha Bayzid, Tandy J. Warnow
Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence. J. Comput. Biol. 19 (6) (2012)
Siavash Mirarab, Nam Nguyen, Tandy J. Warnow
SEPP: SATe -Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing (2012)
Yun Yu, Tandy J. Warnow, Luay Nakhleh
Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB (2011)
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) (2011)
Siavash Mirarab, Tandy J. Warnow
FASTSP: linear time calculation of alignment accuracy. Bioinform. 27 (23) (2011)
Jimmy Yang, Tandy J. Warnow
Fast and accurate methods for phylogenomic analyses. BMC Bioinform. 12 (S-9) (2011)
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 (2011)
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) (2011)
M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy J. Warnow
An Experimental Study of Quartets MaxCut and Other Supertree Methods. WABI (2010)
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 (2010)
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) (2009)
M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy J. Warnow
A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen. WABI (2009)
Michael Brudno, Bernard M. E. Moret, C. Randal Linder, Tandy J. Warnow
Session Introduction. Pacific Symposium on Biocomputing (2008)
Johanna Nichols, Tandy J. Warnow
Tutorial on Computational Linguistic Phylogeny. Lang. Linguistics Compass 2 (5) (2008)

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Publication Activity (10 Years)

Top Topics

Top Venues

Tandy J. Warnow