Tandy Warnow

2023

Minhyuk Park, and Tandy Warnow (2023): HMMerge: An Ensemble Method for Multiple Sequence Alignment, Bioinformatics Advances, Oxford University Press (OUP)

2022

Paul Zaharias, Martin Grosshauser, and Tandy Warnow (2022): Re-Evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling, Journal of Computational Biology, Mary Ann Liebert Inc, Vol 29, Num 1, pp74--89

2021

Nidhi Shah, Erin K Molloy, Mihai Pop, and Tandy Warnow (2021): TIPP2: Metagenomic Taxonomic Profiling Using Phylogenetic Markers, Bioinformatics, Oxford University Press (OUP), Vol 37, Num 13, pp1839--1845
Minhyuk Park, Paul Zaharias, and Tandy Warnow (2021): Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation, Algorithms, MDPI AG, Vol 14, Num 5, pp148
Chengze Shen, Paul Zaharias, and Tandy Warnow (2021): MAGUS+eHMMs: Improved Multiple Sequence Alignment Accuracy for Fragmentary Sequences, Bioinformatics, Oxford University Press (OUP), Vol 38, Num 4, pp918--924

2020

Brandon Legried, Erin K. Molloy, Tandy Warnow, and Sébastien Roch (2020): Data from: Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss, University of Illinois at Urbana-Champaign, Illinois Data Bank
Brandon Legried, Erin K. Molloy, Tandy Warnow, and Sébastien Roch (2020): Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss, Springer International Publishing, Lecture Notes in Computer Science: Research in Computational Molecular Biology 24th Annual International Conference (RECOMB 2020), pp120-135, Padua, Italy
Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, Ananya Yammanuru, and Tandy Warnow (2020): Non-parametric correction of estimated gene trees using TRACTION, Algorithms for Molecular Biology, Springer Nature Switzerland AG, Vol 15, Num 1, pp1
Erin K. Molloy and Tandy Warnow (2020): FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models, Bioinformatics, Oxford University Press, Vol 36, Num Supplement 1, ppi57-i65
Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, and Tandy Warnow (2020): Advancing Divide-and-Conquer Phylogeny Estimation using Robinson-Foulds Supertrees, Schloss Dagstuhl – Leibniz Center for Informatics, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020), Vol 172, pp15:1-15:17, Pisa, Italy

2019

Erin K. Molloy and Tandy Warnow (2019): Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge, Algorithms for Molecular Biology, Springer Nature, Vol 14, Num 1, pp14
Michael Nute, Ehsan Saleh, and Tandy Warnow (2019): Evaluating Statistical Multiple Sequence Alignment in Comparison to Other Alignment Methods on Protein Data Sets, Systematic Biology, Society of Systematic Biologists, Vol 68, Num 3, pp396-411
Erin K. Molloy and Tandy Warnow (2019): TreeMerge: a new method for improving the scalability of species tree estimation methods, Bioinformatics, Oxford University Press, Vol 35, Num 14, ppi417–i426
Thien Le, Aaron Sy, Erin K. Molloy, Qiuyi Zhang, Satish Rao, and Tandy Warnow (2019): Using INC Within Divide-and-Conquer Phylogeny Estimation, Springer International Publishing, Algorithms for Computational Biology (International Conference on Algorithms for Computational Biology, AlCoB 2019), Vol 11488, pp167-178, Berkeley, California, U.S.A.,

2018

Molloy, Erin K. and Warnow, Tandy (2018): NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees, University of Illinois at Urbana-Champaign, Illinois Data Bank
Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, and Tandy Warnow (2018): OCTAL: Optimal Completion of Gene Trees in Polynomial Time, Algorithms for Molecular Biology, Springer Nature, Vol 13, Num 1, pp6
Molloy, Erin K. and Warnow, Tandy (2018): To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods, Systematic Biology, Oxford University Press, Vol 67, Num 2, pp285-303
Kodi Collins and Tandy Warnow (2018): PASTA for proteins, Bioinformatics, Oxford University Press, Vol 34, Num 22, pp3939-3941
Michael Nute, Jed Chou, Erin K. Molloy, and Tandy Warnow (2018): The Performance of Coalescent-Based Species Tree Estimation Methods Under Models of Missing Data, BMC Genomics, Springer Nature, Vol 19, Num S5, pp80
Kodi Collins and Tandy Warnow (2018): PASTA For Proteins Data (BALiBASE), University of Illinois at Urbana-Champaign, Illinois Data Bank
Erin K. Molloy and Tandy Warnow (2018): NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees, Springer International Publishing, Lecture Notes in Computer Science: Comparative Genomics (RECOMB International conference on Comparative Genomics, RECOMB-CG 2018), Vol 11183, pp260-276, Magog-Orford, Quebec City, Canada
Christensen, Sarah, Molloy, Erin K., Vachaspati, Pranjal, and Warnow, Tandy (2018): Datasets from the study OCTAL: Optimal Completion of Gene Trees in Polynomial Time, University of Illinois at Urbana-Champaign, Illinois Data Bank

2017

Julie M. Allen, Bret Boyd, Nam-Phuong Nguyen, Pranjal Vachaspati, Tandy Warnow, Daisie I. Huang, Patrick G. S. Grady, Kayce C. Bell, Quentin C. B. Cronk, Lawrence Mugisha, Barry R. Pittendrigh, M. Soledad Leonardi, David L. Reed, Kevin P. Johnson (2017): Phylogenomics from Whole Genome Sequences Using aTRAM, Systematic Biology, Oxford University Press, Vol 66, Num 5, pp786–798
Michael Nute, Chou Jed, Erin K. Molloy, and Tandy Warnow (2017): Data from: The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data, University of Illinois at Urbana-Champaign, Illinois Data Bank
Bret M. Boyd, Julie M. Allen, Nam-Phuong Nguyen, Andrew D. Sweet, Tandy Warnow, Michael D. Shapiro, Scott M. Villa, Sarah E. Bush, Dale H. Clayton, Kevin P. Johnson (2017): Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola), Systematic Biology, Oxford University Press, Vol 66, Num 6, pp896–911
Pranjal Vachaspati and Tandy Warnow (2017): FastRFS: Fast and Accurate Robinson-Foulds Supertrees using Constrained Exact Optimization, Bioinformatics, Oxford University Press, Vol 33, Num 5, pp631-639

2016

Michael Nute and Tandy Warnow (2016): Scaling Statistical Multiple Sequence Alignment to Large Datasets, BMC Genomics, Springer Nature, Vol 17, Num S10, pp764
Nam-phuong Nguyen, Michael Nute, Siavash Mirarab, and Tandy Warnow (2016): HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs, BMC Genomics, Springer Nature, Vol 17, Num S10, pp765
Nam-Phuong Nguyen, Tandy Warnow, Mihai Pop, and Bryan White (2016): A Perspective on 16S rRNA Operational Taxonomic Unit Clustering Using Sequence Similarity, npj Biofilms and Microbiomes, Nature Publishing Group, Vol 2, pp16004

2019

Tandy Warnow, William Gropp, Erin Molloy, Pranjal Vachaspati (2019): Algorithms for Large-Scale Evolutionary Tree Construction: Improving Scalability and Accuracy through Divide-and-Conquer, 2019 Blue Waters Annual Report, pp232-233

2018

William Gropp, Erin Molloy, Tandy Warnow (2018): Constructing Large Evolutionary Trees on Supercomputers, 2018 Blue Waters Annual Report, pp226-227
Tandy Warnow, Erin Molloy, Michael Nute, Ehsan Saleh, Kodi Collins (2018): Improving Accuracy and Scalability for Core Bioinformatics Analyses, 2018 Blue Waters Annual Report, pp260-261

2017

Tandy Warnow (2017): Parallel Algorithms for Big-data Phylogenomics, Proteomics, and Metagenomics, 2017 Blue Waters Annual Report, pp184-185

2016

Tandy Warnow (2016): Advancing genome-scale phylogenomic analysis, 2016 Blue Waters Annual Report, pp242-243

Tandy Warnow: Computational Challenges in Constructing the Tree of Life (conference keynote)


31st IEEE International Parallel and Distributed Processing Symposium (IPDPS 2017); Orlando, Florida, U.S.A., May 30, 2017

Tandy Warnow: Advancing Genome-scale Phylogenomic Analysis


Blue Waters Symposium 2016, Jun 14, 2016

Study Provides Framework for 1 Billion Years of Green Plant Evolution


Oct 23, 2019

Gene sequences for more than 1100 plant species have been released by an international consortium of nearly 200 plant scientists, the culmination of a nine-year research project.


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NCSA releases 2017 Blue Waters Project Annual Report Detailing Innovative Research and Scientific Breakthroughs


Sep 1, 2017

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign released today the 2017 Blue Waters Project Annual Report. For the project’s fourth annual report, research teams were invited to present highlights from their research that leveraged Blue Waters, the National Science Foundation’s (NSF) most powerful system for sustained computation and data analysis. Spanning economics to engineering, geoscience to space science, Blue Waters has accelerated research and impact across an enormous range of science and engineering disciplines throughout its more than 4-year history covered by the report series. This year is no different.


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NCSA Grants $2.6M in Blue Waters Awards to Illinois Researchers


Jul 6, 2017

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign has awarded 3,697,000 node hours (NH) of time on the Blue Waters supercomputer to Illinois researchers from Spring 2017 proposal submissions. The combined value of these awards is over $2.6 million dollars, and through the life of the Blue Waters program, NCSA has awarded over 43 million node hours to UI researchers—a value of nearly $27 million. Some of the time allocated for Blue Waters will go to projects that focus on HIV research, Laser Interferometer Gravitational-Wave Observatory (LIGO) simulations, genomics and global warming research.


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17 campus teams to accelerate their research with Blue Waters


Jun 10, 2015

Seventeen U of I research teams from a wide range of disciplines have been awarded computational and data resources on the sustained-petascale Blue Waters supercomputer at NCSA. “These diverse projects highlight the breadth of computational research at the University of Illinois,” said Athol Kemball, associate professor of Astronomy and chair of the Illinois allocation review committee. “Illinois has a tremendous pool of talented researchers in fields from political science to chemistry to engineering who can harness the power of Blue Waters to discover and innovate.”


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