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Tandy Warnow

University of Illinois at Urbana-Champaign

Biological Sciences

2018

Molloy, E.K. and T. Warnow (2018): TERADACTAL: A scalable Divide-And-Conquer approach for constructing large phylogenetic Trees (almost) without Alignments, (in progress)
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
Michael G Nute, Ehsan Saleh, and Tandy Warnow (2018): Benchmarking Statistical Multiple Sequence Alignment , High Energy Density Physics, Cold Spring Harbor Laboratory, Vol 17, pp157-161
Collins, Kodi and Warnow, Tandy (2018): PASTA For Proteins Data (BALiBASE), Illinois Data Bank, University of Illinois at Urbana-Champaign
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
Christensen, Sarah, Molloy, Erin K., Vachaspati, Pranjal, and Warnow, Tandy (2018): Datasets from the study OCTAL: Optimal Completion of Gene Trees in Polynomial Time, Illinois Data Bank, University of Illinois at Urbana-Champaign

2017

Molloy, Erin K. and Warnow, Tandy (2017): To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods, Systematic Biology, Oxford University Press
Nute, Michael, Jed, Chou, Molloy, Erin K., and Warnow, Tandy (2017): Data from: The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data, Illinois Data Bank, University of Illinois at Urbana-Champaign
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
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
P. Vachaspati and T. 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

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

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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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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