publications

2024

1. PreK-12 school and citywide wastewater monitoring of the enteric viruses astrovirus, rotavirus, and sapovirus

   Madeline Wolken, Michael Wang, Julia Schedler, and 5 more authors

   Science of The Total Environment, 2024
2. Rapid Genomic Characterization of High-Risk, Antibiotic Resistant Pathogens Using Long-Read Sequencing to Identify Nosocomial

   Chin-Ting Wu, Amy Spallone, Sherry Cantu, and 7 more authors

   Antimicrobial Stewardship & Healthcare Epidemiology, 2024
3. Unveiling microbial diversity: harnessing long-read sequencing technology

   Daniel P Agustinho, Yilei Fu, Vipin K Menon, and 3 more authors

   Nature Methods, 2024

   Bib

   

   @article{agustinho2024unveiling,
     title = {Unveiling microbial diversity: harnessing long-read sequencing technology},
     author = {Agustinho, Daniel P and Fu, Yilei and Menon, Vipin K and Metcalf, Ginger A and Treangen, Todd J and Sedlazeck, Fritz J},
     year = {2024},
     journal = {Nature Methods},
     publisher = {Nature Publishing Group US New York},
     pages = {1--13}
   }

4. Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury

   Wellington Z Amaral, Natalie Kokroko, Todd J Treangen, and 2 more authors

   Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 2024
5. Graph-based self-supervised learning for repeat detection in metagenomic assembly

   Ali Azizpour, Advait Balaji, Todd J Treangen, and 1 more author

   Genome Research, 2024

   Bib

   @article{azizpour2024graph,
     title = {Graph-based self-supervised learning for repeat detection in metagenomic assembly},
     author = {Azizpour, Ali and Balaji, Advait and Treangen, Todd J and Segarra, Santiago},
     year = {2024},
     journal = {Genome Research},
     publisher = {Cold Spring Harbor Lab},
     pages = {gr--279136}
   }

6. GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly

   Ali Azizpour, Advait Balaji, Todd J Treangen, and 1 more author

   In International Conference on Research in Computational Molecular Biology, 2024

   Bib

   @inproceedings{azizpour2024grassrep,
     title = {GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly},
     author = {Azizpour, Ali and Balaji, Advait and Treangen, Todd J and Segarra, Santiago},
     year = {2024},
     booktitle = {International Conference on Research in Computational Molecular Biology},
     pages = {372--376},
     organization = {Springer Nature Switzerland Cham}
   }

7. Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu

   Kristen D Curry, Sirena Soriano, Michael G Nute, and 3 more authors

   Current Protocols, 2024

   Bib

   @article{curry2024microbial,
     title = {Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu},
     author = {Curry, Kristen D and Soriano, Sirena and Nute, Michael G and Villapol, Sonia and Dilthey, Alexander and Treangen, Todd J},
     year = {2024},
     journal = {Current Protocols},
     volume = {4},
     number = {3},
     pages = {e978}
   }

8. Reference-free structural variant detection in microbiomes via long-read coassembly graphs

   Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, and 5 more authors

   bioRxiv, 2024

   Bib

   @article{curry2024reference,
     title = {Reference-free structural variant detection in microbiomes via long-read coassembly graphs},
     author = {Curry, Kristen D and Yu, Feiqiao Brian and Vance, Summer E and Segarra, Santiago and Bhaya, Devaki and Chikhi, Rayan and Rocha, Eduardo PC and Treangen, Todd J},
     year = {2024},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory Preprints}
   }

9. Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice.

   Hannah Flinn, Austin Marshall, Morgan Holcomb, and 4 more authors

   bioRxiv, 2024

   Bib

   

   @article{flinn2024antibiotic,
     title = {Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice.},
     author = {Flinn, Hannah and Marshall, Austin and Holcomb, Morgan and Cruz-Pineda, Leonardo and Soriano, Sirena and Treangen, Todd and Villapol, Sonia},
     year = {2024},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {2024--05}
   }

10. MethPhaser: methylation-based long-read haplotype phasing of human genomes

    Yilei Fu, Sergey Aganezov, Medhat Mahmoud, and 4 more authors

    Nature Communications, 2024

    Bib

    @article{fu2024methphaser,
      title = {MethPhaser: methylation-based long-read haplotype phasing of human genomes},
      author = {Fu, Yilei and Aganezov, Sergey and Mahmoud, Medhat and Beaulaurier, John and Juul, Sissel and Treangen, Todd J and Sedlazeck, Fritz J},
      year = {2024},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {15},
      number = {1},
      pages = {5327}
    }

11. Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice

    Morgan Holcomb, Austin Marshall, Hannah Flinn, and 5 more authors

    Research Square, 2024

    Bib

    

    @article{holcomb2024probiotic,
      title = {Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice},
      author = {Holcomb, Morgan and Marshall, Austin and Flinn, Hannah and Lozano, Mariana and Soriano, Sirena and Gomez-Pinilla, Fernando and Treangen, Todd J and Villapol, Sonia},
      year = {2024},
      journal = {Research Square},
      publisher = {American Journal Experts}
    }

12. Parsnp 2.0: scalable core-genome alignment for massive microbial datasets

    Bryce Kille, Michael G Nute, Victor Huang, and 3 more authors

    Bioinformatics, 2024

    Bib

    

    @article{kille2024parsnp,
      title = {Parsnp 2.0: scalable core-genome alignment for massive microbial datasets},
      author = {Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J},
      year = {2024},
      journal = {Bioinformatics},
      publisher = {Oxford University Press},
      volume = {40},
      number = {5},
      pages = {btae311}
    }

13. Crykey: rapid identification of SARS-CoV-2 cryptic mutations in wastewater

    Yunxi Liu, Nicolae Sapoval, Pilar Gallego-Garcı́a, and 4 more authors

    Nature Communications, 2024

    Bib

    @article{liu2024crykey,
      title = {Crykey: rapid identification of SARS-CoV-2 cryptic mutations in wastewater},
      author = {Liu, Yunxi and Sapoval, Nicolae and Gallego-Garc{\'\i}a, Pilar and Tom{\'a}s, Laura and Posada, David and Treangen, Todd J and Stadler, Lauren B},
      year = {2024},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {15},
      number = {1},
      pages = {4545}
    }

14. Sensitivity and consistency of long-and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater

    Esther G Lou, Yilei Fu, Qi Wang, and 2 more authors

    Journal of Hazardous Materials, 2024

    Bib

    @article{lou2024sensitivity,
      title = {Sensitivity and consistency of long-and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater},
      author = {Lou, Esther G and Fu, Yilei and Wang, Qi and Treangen, Todd J and Stadler, Lauren B},
      year = {2024},
      journal = {Journal of Hazardous Materials},
      publisher = {Elsevier},
      volume = {469},
      pages = {133939}
    }

15. MetaCompass: Reference-guided Assembly of Metagenomes

    Tu Luan, Victoria Cepeda, Bo Liu, and 8 more authors

    arXiv preprint arXiv:2403.01578, 2024

    Bib

    @article{luan2024metacompass,
      title = {MetaCompass: Reference-guided Assembly of Metagenomes},
      author = {Luan, Tu and Cepeda, Victoria and Liu, Bo and Bowen, Zac and Ayyangar, Ujjwal and Almeida, Mathieu and Hill, Christopher M and Koren, Sergey and Treangen, Todd J and Porter, Adam and others},
      year = {2024},
      journal = {arXiv preprint arXiv:2403.01578}
    }

16. Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies

    Austin Marshall, Daniel T. Fuller, Paul Dougall, and 3 more authors

    Environ. Sci.: Atmos., 2024

    Bib

    

    @article{marshall2024aerobiome,
      title = {Application of nanopore sequencing for accurate identification of bioaerosol-derived bacterial colonies},
      author = {Marshall, Austin and Fuller, Daniel T. and Dougall, Paul and Kumaragama, Kavindra and Dhaniyala, Suresh and Sur, Shantanu},
      year = {2024},
      journal = {Environ. Sci.: Atmos.},
      publisher = {RSC},
      volume = {4},
      pages = {754--766}
    }

17. Graph-based variant discovery reveals novel dynamics in the human microbiome

    Harihara Subrahmaniam Muralidharan, Jacquelyn S Michaelis, Jay Ghurye, and 4 more authors

    arXiv preprint arXiv:2403.01610, 2024

    Bib

    @article{muralidharan2024graph,
      title = {Graph-based variant discovery reveals novel dynamics in the human microbiome},
      author = {Muralidharan, Harihara Subrahmaniam and Michaelis, Jacquelyn S and Ghurye, Jay and Treangen, Todd and Koren, Sergey and Fedarko, Marcus and Pop, Mihai},
      year = {2024},
      journal = {arXiv preprint arXiv:2403.01610}
    }

18. Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet

    Nicolae Sapoval, Yunxi Liu, Kristen Curry, and 8 more authors

    bioRxiv, 2024

    Bib

    

    @article{sapoval2024lightweight,
      title = {Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet},
      author = {Sapoval, Nicolae and Liu, Yunxi and Curry, Kristen and Kille, Bryce and Huang, Wenyu and Kokroko, Natalie and Nute, Michael G and Tyshaieva, Alona and Dilthey, Alexander T and Molloy, Erin and others},
      year = {2024},
      journal = {bioRxiv},
      publisher = {Cold Spring Harbor Laboratory},
      pages = {2024--06}
    }

19. Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

    Selvalakshmi Selvaraj Anand, Chin-Ting Wu, Jordan Bremer, and 5 more authors

    Microbial genomics, 2024

    Bib

    @article{selvaraj2024identification,
      title = {Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA},
      author = {Selvaraj Anand, Selvalakshmi and Wu, Chin-Ting and Bremer, Jordan and Bhatti, Micah and Treangen, Todd J and Kalia, Awdhesh and Shelburne, Samuel A and Shropshire, William C},
      year = {2024},
      journal = {Microbial genomics},
      publisher = {Microbiology Society},
      volume = {10},
      number = {2},
      pages = {001201}
    }

20. Graph-based variant discovery reveals novel dynamics in the human microbiome

    Harihara Subrahmaniam Muralidharan, Jacquelyn S Michaelis, Jay Ghurye, and 4 more authors

    arXiv e-prints, 2024

    Bib

    @article{subrahmaniam2024graph,
      title = {Graph-based variant discovery reveals novel dynamics in the human microbiome},
      author = {Subrahmaniam Muralidharan, Harihara and Michaelis, Jacquelyn S and Ghurye, Jay and Treangen, Todd and Koren, Sergey and Fedarko, Marcus and Pop, Mihai},
      year = {2024},
      journal = {arXiv e-prints},
      pages = {arXiv--2403}
    }

21. Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

    Michael X Wang, Esther G Lou, Nicolae Sapoval, and 8 more authors

    Nature Communications, 2024

    Bib

    

    @article{wang2024olivar,
      title = {Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens},
      author = {Wang, Michael X and Lou, Esther G and Sapoval, Nicolae and Kim, Eddie and Kalvapalle, Prashant and Kille, Bryce and Elworth, RA Leo and Liu, Yunxi and Fu, Yilei and Stadler, Lauren B and others},
      year = {2024},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {15},
      number = {1},
      pages = {6306}
    }

22. PreK-12 school and citywide wastewater monitoring of the enteric viruses astrovirus, rotavirus, and sapovirus

    Madeline Wolken, Michael Wang, Julia Schedler, and 5 more authors

    Science of The Total Environment, 2024

    Bib

    

    @article{wolken2024prel,
      title = {PreK-12 school and citywide wastewater monitoring of the enteric viruses astrovirus, rotavirus, and sapovirus},
      author = {Wolken, Madeline and Wang, Michael and Schedler, Julia and Campos Jr, Roberto H and Ensor, Katherine and Hopkins, Loren and Treangen, Todd and Stadler, Lauren B},
      year = {2024},
      journal = {Science of The Total Environment},
      publisher = {Elsevier},
      volume = {931},
      pages = {172683}
    }

23. Multiplexed detection, partitioning, and persistence of wild type and vaccine strains of measles, mumps, and rubella viruses in wastewater

    Jingjing Wu, Michael X Wang, Prashant Kalvapalle, and 6 more authors

    medRxiv, 2024

    Bib

    

    @article{wu2024multiplexed,
      title = {Multiplexed detection, partitioning, and persistence of wild type and vaccine strains of measles, mumps, and rubella viruses in wastewater},
      author = {Wu, Jingjing and Wang, Michael X and Kalvapalle, Prashant and Nute, Michael and Treangen, Todd J and Ensor, Katherine and Hopkins, Loren and Poretsky, Rachel and Stadler, Lauren B},
      year = {2024},
      journal = {medRxiv},
      publisher = {Cold Spring Harbor Laboratory Press},
      pages = {2024--05}
    }

24. The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease

    Qinglong Wu, Shyam Badu, Sik Yu So, and 3 more authors

    The Journal of Clinical Investigation, 2024

    Bib

    @article{wu2024pan,
      title = {The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease},
      author = {Wu, Qinglong and Badu, Shyam and So, Sik Yu and Treangen, Todd J and Savidge, Tor C and others},
      year = {2024},
      journal = {The Journal of Clinical Investigation},
      publisher = {American Society for Clinical Investigation},
      volume = {134},
      number = {2}
    }

2023

1. SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens

   Advait Balaji, Yunxi Liu, Michael G Nute, and 6 more authors

   In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2023

   Bib

   @inproceedings{balaji2023seqscreen,
     title = {SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens},
     author = {Balaji, Advait and Liu, Yunxi and Nute, Michael G and Hu, Bingbing and D. Kappell, Anthony and S. Lesassier, Danielle and D. Godbold, Gene and Ternus, Krista and Treangen, Todd},
     year = {2023},
     booktitle = {Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
     pages = {1--10}
   }

2. 2164. Resistome patterns associated with vancomycin non-susceptibility in clinical Clostridioides difficile isolates

   Taryn A Eubank, Anne J Gonzales-Luna, Blake M Hanson, and 3 more authors

   In Open Forum Infectious Diseases, 2023

   Bib

   @inproceedings{eubank20232164,
     title = {2164. Resistome patterns associated with vancomycin non-susceptibility in clinical Clostridioides difficile isolates},
     author = {Eubank, Taryn A and Gonzales-Luna, Anne J and Hanson, Blake M and Treangen, Todd and Earl, Ashlee and Garey, Kevin W},
     year = {2023},
     booktitle = {Open Forum Infectious Diseases},
     volume = {10},
     number = {Supplement\_2},
     pages = {ofad500--1787},
     organization = {Oxford University Press US}
   }

3. MethPhaser: methylation-based haplotype phasing of human genomes

   Yilei Fu, Sergey Aganezov, Medhat Mahmoud, and 4 more authors

   bioRxiv, 2023

   Bib

   @article{fu2023methphaser,
     title = {MethPhaser: methylation-based haplotype phasing of human genomes},
     author = {Fu, Yilei and Aganezov, Sergey and Mahmoud, Medhat and Beaulaurier, John and Juul, Sissel and Treangen, Todd J and Sedlazeck, Fritz J},
     year = {2023},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {2023--05}
   }

4. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern

   Gene D Godbold, F Curtis Hewitt, Anthony D Kappell, and 6 more authors

   Frontiers in Bioengineering and Biotechnology, 2023

   Bib

   @article{godbold2023improved,
     title = {Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern},
     author = {Godbold, Gene D and Hewitt, F Curtis and Kappell, Anthony D and Scholz, Matthew B and Agar, Stacy L and Treangen, Todd J and Ternus, Krista L and Sandbrink, Jonas B and Koblentz, Gregory D},
     year = {2023},
     journal = {Frontiers in Bioengineering and Biotechnology},
     publisher = {Frontiers Media SA},
     volume = {11},
     pages = {1124100}
   }

5. The GIAB genomic stratifications resource for human reference genomes

   Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, and 11 more authors

   bioRxiv, 2023

   Bib

   

   @article{huang2023giab,
     title = {The GIAB genomic stratifications resource for human reference genomes},
     author = {Dwarshuis, Nathan and Kalra, Divya and McDaniel, Jennifer and Sanio, Philippe and Soriano, Jerez and Pilar A, Jadhav and Huang, Wenyu and Mondal, Rajarshi and Busby, Ben and Olson, Nathanael D and Sedlazeck, Fritz J and Wagner, Justin and Majidian, Sina and Zook, Justin M},
     year = {2023},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory}
   }

6. Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation

   Bryce Kille, Erik Garrison, Todd J Treangen, and 1 more author

   Bioinformatics, 2023

   Bib

   

   @article{kille2023minmers,
     title = {Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation},
     author = {Kille, Bryce and Garrison, Erik and Treangen, Todd J and Phillippy, Adam M},
     year = {2023},
     journal = {Bioinformatics},
     publisher = {Oxford University Press},
     volume = {39},
     number = {9},
     pages = {btad512}
   }

7. Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

   Camille McCall, Ryan A Leo Elworth, Kristine M Wylie, and 7 more authors

   ACS ES&T Water, 2023

   Bib

   

   @article{mccall2023targeted,
     title = {Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance},
     author = {McCall, Camille and Leo Elworth, Ryan A and Wylie, Kristine M and Wylie, Todd N and Dyson, Katherine and Doughty, Ryan and Treangen, Todd J and Hopkins, Loren and Ensor, Katherine and Stadler, Lauren B},
     year = {2023},
     journal = {ACS ES\&T Water},
     publisher = {American Chemical Society},
     volume = {3},
     number = {9},
     pages = {2955--2965}
   }

8. Ultra-high throughput mapping of genetic design space

   Ronan W O’Connell, Kshitij Rai, Trenton C Piepergerdes, and 8 more authors

   BioRxiv, 2023

   Bib

   @article{o2023ultra,
     title = {Ultra-high throughput mapping of genetic design space},
     author = {O’Connell, Ronan W and Rai, Kshitij and Piepergerdes, Trenton C and Wang, Yiduo and Samra, Kian D and Wilson, Jack A and Lin, Shujian and Zhang, Thomas H and Ramos, Eduardo M and Sun, Andrew and others},
     year = {2023},
     journal = {BioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {2023--03}
   }

9. Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence

   Felix Quintana, Todd Treangen, and Lydia Kavraki

   In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2023

   Bib

   @inproceedings{quintana2023leveraging,
     title = {Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence},
     author = {Quintana, Felix and Treangen, Todd and Kavraki, Lydia},
     year = {2023},
     booktitle = {Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
     pages = {1--6}
   }

10. Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

    Nicolae Sapoval, Yunxi Liu, Esther G Lou, and 5 more authors

    Nature Communications, 2023

    Bib

    @article{sapoval2023enabling,
      title = {Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater},
      author = {Sapoval, Nicolae and Liu, Yunxi and Lou, Esther G and Hopkins, Loren and Ensor, Katherine B and Schneider, Rebecca and Stadler, Lauren B and Treangen, Todd J},
      year = {2023},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {14},
      number = {1},
      pages = {2834}
    }

11. KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome

    Nicolae Sapoval, Marko Tanevski, and Todd J Treangen

    In Pacific Symposium on Biocomputing 2024, 2023

    Bib

    @inproceedings{sapoval2023kombover,
      title = {KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome},
      author = {Sapoval, Nicolae and Tanevski, Marko and Treangen, Todd J},
      year = {2023},
      booktitle = {Pacific Symposium on Biocomputing 2024},
      pages = {506--520}
    }

12. The long game of tenure

    Todd J Treangen, and Moshe Y Vardi

    Nature Biotechnology, 2023

    Bib

    @article{treangen2023long,
      title = {The long game of tenure},
      author = {Treangen, Todd J and Vardi, Moshe Y},
      year = {2023},
      journal = {Nature Biotechnology},
      publisher = {Nature Publishing Group US New York},
      volume = {41},
      number = {10},
      pages = {1373--1374}
    }

13. Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta

    Nidia S Trovao, Vincent Pan, Chirag Goel, and 8 more authors

    Microbiology Spectrum, 2023

    Bib

    @article{trovao2023evolutionary,
      title = {Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta},
      author = {Trovao, Nidia S and Pan, Vincent and Goel, Chirag and Gallego-Garc{\'\i}a, Pilar and Liu, Yunxi and Barbara, Christopher and Borg, Rebecca and Briffa, Mark and Cilia, Chanelle and Grech, Laura and others},
      year = {2023},
      journal = {Microbiology Spectrum},
      publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
      volume = {11},
      number = {6},
      pages = {e01539--23}
    }

14. Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities

    Qi Wang, Michael Nute, and Todd J Treangen

    Bioinformatics, 2023

    Bib

    @article{wang2023bakdrive,
      title = {Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities},
      author = {Wang, Qi and Nute, Michael and Treangen, Todd J},
      year = {2023},
      journal = {Bioinformatics},
      publisher = {Oxford University Press},
      volume = {39},
      number = {Supplement\_1},
      pages = {i47--i56}
    }

2022

1. Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled aerosols and efficacy of masks during early mild infection

   Oluwasanmi O Adenaiye, Jianyu Lai, P Jacob Mesquita, and 8 more authors

   Clinical Infectious Diseases, 2022

   Bib

   @article{adenaiye2022infectious,
     title = {Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled aerosols and efficacy of masks during early mild infection},
     author = {Adenaiye, Oluwasanmi O and Lai, Jianyu and Bueno de Mesquita, P Jacob and Hong, Filbert and Youssefi, Somayeh and German, Jennifer and Tai, SH Sheldon and Albert, Barbara and Schanz, Maria and Weston, Stuart and others},
     year = {2022},
     journal = {Clinical Infectious Diseases},
     publisher = {Oxford University Press US},
     volume = {75},
     number = {1},
     pages = {e241--e248}
   }

2. KOMB: K-core based de novo characterization of copy number variation in microbiomes

   Advait Balaji, Nicolae Sapoval, Charlie Seto, and 6 more authors

   Computational and Structural Biotechnology Journal, 2022

   Bib

   @article{balaji2022komb,
     title = {KOMB: K-core based de novo characterization of copy number variation in microbiomes},
     author = {Balaji, Advait and Sapoval, Nicolae and Seto, Charlie and Elworth, RA Leo and Fu, Yilei and Nute, Michael G and Savidge, Tor and Segarra, Santiago and Treangen, Todd J},
     year = {2022},
     journal = {Computational and Structural Biotechnology Journal},
     publisher = {Elsevier},
     volume = {20},
     pages = {3208--3222}
   }

3. SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning

   Advait Balaji, Bryce Kille, Anthony D Kappell, and 8 more authors

   Genome biology, 2022

   Bib

   

   @article{balaji2022seqscreen,
     title = {SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning},
     author = {Balaji, Advait and Kille, Bryce and Kappell, Anthony D and Godbold, Gene D and Diep, Madeline and Elworth, RA Leo and Qian, Zhiqin and Albin, Dreycey and Nasko, Daniel J and Shah, Nidhi and others},
     year = {2022},
     journal = {Genome biology},
     publisher = {BioMed Central London},
     volume = {23},
     number = {1},
     pages = {133}
   }

4. One-pass diversified sampling with application to terabyte-scale genomic sequence streams

   Benjamin Coleman, Benito Geordie, Li Chou, and 3 more authors

   In International Conference on Machine Learning, 2022

   Bib

   @inproceedings{coleman2022one,
     title = {One-pass diversified sampling with application to terabyte-scale genomic sequence streams},
     author = {Coleman, Benjamin and Geordie, Benito and Chou, Li and Elworth, RA Leo and Treangen, Todd and Shrivastava, Anshumali},
     year = {2022},
     booktitle = {International Conference on Machine Learning},
     pages = {4202--4218},
     organization = {PMLR}
   }

5. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data

   Kristen D Curry, Qi Wang, Michael G Nute, and 8 more authors

   Nature methods, 2022

   Bib

   

   @article{curry2022emu,
     title = {Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data},
     author = {Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others},
     year = {2022},
     journal = {Nature methods},
     publisher = {Nature Publishing Group US New York},
     volume = {19},
     number = {7},
     pages = {845--853}
   }

6. Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters

   Pilar Gallego-Garcı́a, Nair Varela, Nuria Estévez-Gómez, and 8 more authors

   Virus Evolution, 2022

   Bib

   @article{gallego2022limited,
     title = {Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters},
     author = {Gallego-Garc{\'\i}a, Pilar and Varela, Nair and Est{\'e}vez-G{\'o}mez, Nuria and De Chiara, Loretta and Fern{\'a}ndez-Silva, Iria and Valverde, Diana and Sapoval, Nicolae and Treangen, Todd J and Regueiro, Benito and Cabrera-Alvargonz{\'a}lez, Jorge Julio and others},
     year = {2022},
     journal = {Virus Evolution},
     publisher = {Oxford University Press UK},
     volume = {8},
     number = {1},
     pages = {veac008}
   }

7. Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis

   Gene D Godbold, Anthony D Kappell, Danielle S LeSassier, and 2 more authors

   Infection and immunity, 2022

   Bib

   @article{godbold2022categorizing,
     title = {Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis},
     author = {Godbold, Gene D and Kappell, Anthony D and LeSassier, Danielle S and Treangen, Todd J and Ternus, Krista L},
     year = {2022},
     journal = {Infection and immunity},
     publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
     volume = {90},
     number = {5},
     pages = {e00334--21}
   }

8. Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease

   Michael Jochum, Michael D Lee, Kristen Curry, and 5 more authors

   Scientific Reports, 2022

   Bib

   @article{jochum2022analysis,
     title = {Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease},
     author = {Jochum, Michael and Lee, Michael D and Curry, Kristen and Zaksas, Victoria and Vitalis, Elizabeth and Treangen, Todd and Aagaard, Kjersti and Ternus, Krista L},
     year = {2022},
     journal = {Scientific Reports},
     publisher = {Nature Publishing Group UK London},
     volume = {12},
     number = {1},
     pages = {21125}
   }

9. Multiple genome alignment in the telomere-to-telomere assembly era

   Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and 2 more authors

   Genome Biology, 2022

   Bib

   

   @article{kille2022multiple,
     title = {Multiple genome alignment in the telomere-to-telomere assembly era},
     author = {Kille, Bryce and Balaji, Advait and Sedlazeck, Fritz J and Nute, Michael and Treangen, Todd J},
     year = {2022},
     journal = {Genome Biology},
     publisher = {BioMed Central London},
     volume = {23},
     number = {1},
     pages = {182}
   }

10. Notes from the field: early evidence of the SARS-CoV-2 B. 1.1. 529 (Omicron) variant in community wastewater—United States, November–December 2021

    Amy E Kirby

    MMWR. Morbidity and Mortality Weekly Report, 2022

    Bib

    @article{kirby2022notes,
      title = {Notes from the field: early evidence of the SARS-CoV-2 B. 1.1. 529 (Omicron) variant in community wastewater—United States, November--December 2021},
      author = {Kirby, Amy E},
      year = {2022},
      journal = {MMWR. Morbidity and Mortality Weekly Report},
      volume = {71}
    }

11. De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

    Yunxi Liu, RA Leo Elworth, Michael D Jochum, and 2 more authors

    Nature Communications, 2022

    Bib

    @article{liu2022novo,
      title = {De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee},
      author = {Liu, Yunxi and Elworth, RA Leo and Jochum, Michael D and Aagaard, Kjersti M and Treangen, Todd J},
      year = {2022},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {13},
      number = {1},
      pages = {6799}
    }

12. Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data

    Yunxi Liu, Joshua Kearney, Medhat Mahmoud, and 3 more authors

    Nature communications, 2022

    Bib

    @article{liu2022rescuing,
      title = {Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data},
      author = {Liu, Yunxi and Kearney, Joshua and Mahmoud, Medhat and Kille, Bryce and Sedlazeck, Fritz J and Treangen, Todd J},
      year = {2022},
      journal = {Nature communications},
      publisher = {Nature Publishing Group UK London},
      volume = {13},
      number = {1},
      pages = {1321}
    }

13. Direct Comparison of Rt-Ddpcr and Targeted Amplicon Sequencing for Sars-Cov-2 Mutation Monitoring in Wastewater

    Esther Lou, Nicolae Sapoval, Camille McCall, and 8 more authors

    SSRN Preprint, 2022

    Bib

    @article{lou2022direct,
      title = {Direct Comparison of Rt-Ddpcr and Targeted Amplicon Sequencing for Sars-Cov-2 Mutation Monitoring in Wastewater},
      author = {Lou, Esther and Sapoval, Nicolae and McCall, Camille and Bauhs, Lauren and Carlson-Stadler, Russell and Kalvapalle, Prashant and Lai, Yanlai and Palmer, Kyle and Penn, Ryker and Rich, Whitney and others},
      year = {2022},
      journal = {SSRN Preprint},
      publisher = {https://ssrn.com/abstract=4022373},
      volume = {4022373}
    }

14. Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing

    So Hyun Park, Mingming Cao, Yidan Pan, and 7 more authors

    Science Advances, 2022

    Bib

    @article{park2022comprehensive,
      title = {Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing},
      author = {Park, So Hyun and Cao, Mingming and Pan, Yidan and Davis, Timothy H and Saxena, Lavanya and Deshmukh, Harshavardhan and Fu, Yilei and Treangen, Todd and Sheehan, Vivien A and Bao, Gang},
      year = {2022},
      journal = {Science Advances},
      publisher = {American Association for the Advancement of Science},
      volume = {8},
      number = {42},
      pages = {eabo7676}
    }

15. Current progress and open challenges for applying deep learning across the biosciences

    Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and 8 more authors

    Nature Communications, 2022

    Bib

    

    @article{sapoval2022current,
      title = {Current progress and open challenges for applying deep learning across the biosciences},
      author = {Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others},
      year = {2022},
      journal = {Nature Communications},
      publisher = {Nature Publishing Group UK London},
      volume = {13},
      number = {1},
      pages = {1728}
    }

16. Systematic analysis of mobile genetic elements mediating β-lactamase gene amplification in noncarbapenemase-producing carbapenem-resistant Enterobacterales bloodstream infections

    WC Shropshire, A Konovalova, P McDaneld, and 8 more authors

    Msystems, 2022

    Bib

    @article{shropshire2022systematic,
      title = {Systematic analysis of mobile genetic elements mediating $\beta$-lactamase gene amplification in noncarbapenemase-producing carbapenem-resistant Enterobacterales bloodstream infections},
      author = {Shropshire, WC and Konovalova, A and McDaneld, P and Gohel, M and Strope, B and Sahasrabhojane, P and Tran, CN and Greenberg, D and Kim, J and Zhan, X and others},
      year = {2022},
      journal = {Msystems},
      publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
      volume = {7},
      number = {5},
      pages = {e00476--22}
    }

17. Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study

    Sirena Soriano, Kristen Curry, Saeed S Sadrameli, and 8 more authors

    Brain, Behavior, & Immunity-Health, 2022

    Bib

    @article{soriano2022alterations,
      title = {Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study},
      author = {Soriano, Sirena and Curry, Kristen and Sadrameli, Saeed S and Wang, Qi and Nute, Michael and Reeves, Elizabeth and Kabir, Rasadul and Wiese, Jonathan and Criswell, Amber and Schodrof, Sarah and others},
      year = {2022},
      journal = {Brain, Behavior, \& Immunity-Health},
      publisher = {Elsevier},
      volume = {21},
      pages = {100438}
    }

18. Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls

    Sirena Soriano, Kristen Curry, Qi Wang, and 3 more authors

    International Journal of Molecular Sciences, 2022

    Bib

    @article{soriano2022fecal,
      title = {Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls},
      author = {Soriano, Sirena and Curry, Kristen and Wang, Qi and Chow, Elsbeth and Treangen, Todd J and Villapol, Sonia},
      year = {2022},
      journal = {International Journal of Molecular Sciences},
      publisher = {MDPI},
      volume = {23},
      number = {9},
      pages = {4476}
    }

19. Designing highly multiplex PCR primer sets with simulated annealing design using dimer likelihood estimation (SADDLE)

    Nina G Xie, Michael X Wang, Ping Song, and 6 more authors

    Nature communications, 2022

    Bib

    

    @article{xie2022designing,
      title = {Designing highly multiplex PCR primer sets with simulated annealing design using dimer likelihood estimation (SADDLE)},
      author = {Xie, Nina G and Wang, Michael X and Song, Ping and Mao, Shiqi and Wang, Yifan and Yang, Yuxia and Luo, Junfeng and Ren, Shengxiang and Yu, Zhang David},
      journal = {Nature communications},
      volume = {13},
      number = {1},
      pages = {1881},
      year = {2022},
      publisher = {Nature Publishing Group UK London}
    }

20. Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling

    Lucia Ruojia Wu, Peng Dai, Michael Xiangjiang Wang, and 8 more authors

    Nature communications, 2022

    Bib

    

    @article{wu2022ensemble,
      title = {Ensemble of nucleic acid absolute quantitation modules for copy number variation detection and RNA profiling},
      author = {Wu, Lucia Ruojia and Dai, Peng and Wang, Michael Xiangjiang and Chen, Sherry Xi and Cohen, Evan N and Jayachandran, Gitanjali and Zhang, Jinn Xuemeng and Serrano, Angela V and Xie, Nina Guanyi and Ueno, Naoto T and others},
      journal = {Nature communications},
      volume = {13},
      number = {1},
      pages = {1791},
      year = {2022},
      publisher = {Nature Publishing Group UK London}
    }

21. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms

    Kimberly Walker, Divya Kalra, Rebecca Lowdon, and 8 more authors

    F1000Research, 2022

    Bib

    @article{walker2022third,
      title = {The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms},
      author = {Walker, Kimberly and Kalra, Divya and Lowdon, Rebecca and Chen, Guangyi and Molik, David and Soto, Daniela C and Dabbaghie, Fawaz and Al Khleifat, Ahmad and Mahmoud, Medhat and Paulin, Luis F and others},
      year = {2022},
      journal = {F1000Research},
      publisher = {Faculty of 1000 Ltd},
      volume = {11}
    }

2021

1. High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings

   Irina Maljkovic Berry, Todd Treangen, Christian Fung, and 8 more authors

   bioRxiv, 2021

   Bib

   @article{berry2021high,
     title = {High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings},
     author = {Berry, Irina Maljkovic and Treangen, Todd and Fung, Christian and Tai, Sheldon and Pollett, Simon and Hong, Filbert and Li, Tao and Pireku, Papa and Thomanna, Ashley and German, Jennifer and others},
     year = {2021},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {2021--07}
   }

2. It takes guts to learn: machine learning techniques for disease detection from the gut microbiome

   Kristen D Curry, Michael G Nute, and Todd J Treangen

   Emerging Topics in Life Sciences, 2021

   Bib

   @article{curry2021takes,
     title = {It takes guts to learn: machine learning techniques for disease detection from the gut microbiome},
     author = {Curry, Kristen D and Nute, Michael G and Treangen, Todd J},
     year = {2021},
     journal = {Emerging Topics in Life Sciences},
     publisher = {Portland Press Ltd.},
     volume = {5},
     number = {6},
     pages = {815--827}
   }

3. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment

   Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, and 2 more authors

   GigaScience, 2021

   Bib

   @article{fu2021vulcan,
     title = {Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment},
     author = {Fu, Yilei and Mahmoud, Medhat and Muraliraman, Viginesh Vaibhav and Sedlazeck, Fritz J and Treangen, Todd J},
     year = {2021},
     journal = {GigaScience},
     publisher = {Oxford University Press},
     volume = {10},
     number = {9},
     pages = {giab063}
   }

4. Fast processing and querying of 170tb of genomics data via a repeated and merged bloom filter (rambo)

   Gaurav Gupta, Minghao Yan, Benjamin Coleman, and 5 more authors

   In Proceedings of the 2021 International Conference on Management of Data, 2021

   Bib

   @inproceedings{gupta2021fast,
     title = {Fast processing and querying of 170tb of genomics data via a repeated and merged bloom filter (rambo)},
     author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Kille, Bryce and Elworth, RA Leo and Medini, Tharun and Treangen, Todd and Shrivastava, Anshumali},
     year = {2021},
     booktitle = {Proceedings of the 2021 International Conference on Management of Data},
     pages = {2226--2234}
   }

5. Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets

   Bryce Kille, Yunxi Liu, Nicolae Sapoval, and 4 more authors

   In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), 2021

   Bib

   

   @inproceedings{kille2021accelerating,
     title = {Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets},
     author = {Kille, Bryce and Liu, Yunxi and Sapoval, Nicolae and Nute, Michael and Rauchwerger, Lawrence and Amato, Nancy and Treangen, Todd J},
     year = {2021},
     booktitle = {2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
     pages = {204--208},
     organization = {IEEE}
   }

6. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

   Ann M Mc Cartney, Medhat Mahmoud, Michael Jochum, and 8 more authors

   F1000Research, 2021

   Bib

   @article{mc2021international,
     title = {An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates},
     author = {Mc Cartney, Ann M and Mahmoud, Medhat and Jochum, Michael and Agustinho, Daniel Paiva and Zorman, Barry and Al Khleifat, Ahmad and Dabbaghie, Fawaz and Kesharwani, Rupesh K and Smolka, Moritz and Dawood, Moez and others},
     year = {2021},
     journal = {F1000Research},
     publisher = {Faculty of 1000 Ltd},
     volume = {10}
   }

7. Role of miR-2392 in driving SARS-CoV-2 infection

   J Tyson McDonald, Francisco J Enguita, Deanne Taylor, and 8 more authors

   Cell reports, 2021

   Bib

   @article{mcdonald2021role,
     title = {Role of miR-2392 in driving SARS-CoV-2 infection},
     author = {McDonald, J Tyson and Enguita, Francisco J and Taylor, Deanne and Griffin, Robert J and Priebe, Waldemar and Emmett, Mark R and Sajadi, Mohammad M and Harris, Anthony D and Clement, Jean and Dybas, Joseph M and others},
     year = {2021},
     journal = {Cell reports},
     publisher = {Elsevier},
     volume = {37},
     number = {3}
   }

8. Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial

   Silvia Molino, Andrea Pisarevsky, Fabiana Lopez Mingorance, and 8 more authors

   Trials, 2021

   Bib

   @article{molino2021natural,
     title = {Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial},
     author = {Molino, Silvia and Pisarevsky, Andrea and Mingorance, Fabiana Lopez and Vega, Patricia and Stefanolo, Juan Pablo and Repetti, Julieta and Ludue{\~n}a, Guillermina and Pepa, Pablo and Olmos, Juan Ignacio and Fermepin, Marcelo Rodriguez and others},
     year = {2021},
     journal = {Trials},
     publisher = {BioMed Central London},
     volume = {22},
     number = {1},
     pages = {310}
   }

9. Fr578 ORAL TANNINS REDUCE PROINFLAMMATORY CYTOKINES ASSOCIATED WITH DIARRHEA AND PNEUMONIA IN HOSPITALIZED COVID-19 PATIENTS.

   Ana A Pisarevsky, Fabiana Lopez Mingorance, Patrica Vega, and 8 more authors

   Gastroenterology, 2021

   Bib

   @article{pisarevsky2021fr578,
     title = {Fr578 ORAL TANNINS REDUCE PROINFLAMMATORY CYTOKINES ASSOCIATED WITH DIARRHEA AND PNEUMONIA IN HOSPITALIZED COVID-19 PATIENTS.},
     author = {Pisarevsky, Ana A and Mingorance, Fabiana Lopez and Vega, Patrica and Stefanolo, Juan P and Repetti, Julieta A and Ludue{\~n}a, Guillermina and Pepa, Pablo D and Olmos, Juan I and Fermepin, Marcelo Rodr{\'\i}guez and Molino, Silvia and others},
     year = {2021},
     journal = {Gastroenterology},
     publisher = {Elsevier},
     volume = {160},
     number = {6},
     pages = {S--371}
   }

10. Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater

    Nicolae Sapoval, Esther Lou, Loren Hopkins, and 4 more authors

    medRxiv, 2021

    Bib

    @article{sapoval2021enhanced,
      title = {Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater},
      author = {Sapoval, Nicolae and Lou, Esther and Hopkins, Loren and Ensor, Katherine B and Schneider, Rebecca and Treangen, Todd J and Stadler, Lauren B},
      year = {2021},
      journal = {medRxiv},
      publisher = {Cold Spring Harbor Laboratory Press},
      pages = {2021--09}
    }

11. Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community

    Nicolae Sapoval, P Jacob Bueno Mesquita, Yunxi Liu, and 8 more authors

    medRxiv, 2021

    Bib

    @article{sapoval2021intrahost,
      title = {Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community},
      author = {Sapoval, Nicolae and de Mesquita, P Jacob Bueno and Liu, Yunxi and Wang, Roger and Liu, Tian Rui and Garza, Josie and Williams, Torrey and Cadiz, Carmelli and Tan, Gene S and Van Bakel, Harm and others},
      year = {2021},
      journal = {medRxiv},
      publisher = {Cold Spring Harbor Laboratory Press},
      pages = {2021--10}
    }

12. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission

    Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, and 8 more authors

    Genome research, 2021

    Bib

    @article{sapoval2021sars,
      title = {SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission},
      author = {Sapoval, Nicolae and Mahmoud, Medhat and Jochum, Michael D and Liu, Yunxi and Elworth, RA Leo and Wang, Qi and Albin, Dreycey and Ogilvie, Huw A and Lee, Michael D and Villapol, Sonia and others},
      year = {2021},
      journal = {Genome research},
      publisher = {Cold Spring Harbor Lab},
      volume = {31},
      number = {4},
      pages = {635--644}
    }

13. Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in young C57BL/6 mice

    Sirena Soriano, Kristen Curry, Qi Wang, and 3 more authors

    bioRxiv, 2021

    Bib

    @article{soriano2021fecal,
      title = {Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in young C57BL/6 mice},
      author = {Soriano, Sirena and Curry, Kristen and Wang, Qi and Chow, Elsbeth and Treangen, Todd and Villapol, Sonia},
      year = {2021},
      journal = {bioRxiv},
      publisher = {Cold Spring Harbor Laboratory},
      pages = {2021--11}
    }

14. A deep learning model for predicting next-generation sequencing depth from DNA sequence

    Jinny X Zhang, Boyan Yordanov, Alexander Gaunt, and 8 more authors

    Nature communications, 2021

    Bib

    

    @article{zhang2021deep,
      title = {A deep learning model for predicting next-generation sequencing depth from DNA sequence},
      author = {Zhang, Jinny X and Yordanov, Boyan and Gaunt, Alexander and Wang, Michael X and Dai, Peng and Chen, Yuan-Jyue and Zhang, Kerou and Fang, John Z and Dalchau, Neil and Li, Jiaming and others},
      journal = {Nature communications},
      volume = {12},
      number = {1},
      pages = {4387},
      year = {2021},
      publisher = {Nature Publishing Group UK London}
    }

15. PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

    Qi Wang, Bryce Kille, Tian Rui Liu, and 2 more authors

    Nature communications, 2021

    Bib

    @article{wang2021plasmidhawk,
      title = {PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment},
      author = {Wang, Qi and Kille, Bryce and Liu, Tian Rui and Elworth, RA Leo and Treangen, Todd J},
      year = {2021},
      journal = {Nature communications},
      publisher = {Nature Publishing Group UK London},
      volume = {12},
      number = {1},
      pages = {1167}
    }

2020

1. KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities

   Advait Balaji, Nicolae Sapoval, Charlie Seto, and 5 more authors

   bioRxiv, 2020

   Bib

   @article{balaji2020komb,
     title = {KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities},
     author = {Balaji, Advait and Sapoval, Nicolae and Seto, Charlie and Elworth, RA Leo and Nute, Michael G and Savidge, Tor and Segarra, Santiago and Treangen, Todd J},
     year = {2020},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {2020--05}
   }

2. Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications

   Jessica Chopyk, Daniel J Nasko, Sarah Allard, and 5 more authors

   Water Research, 2020

   Bib

   @article{chopyk2020comparative,
     title = {Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications},
     author = {Chopyk, Jessica and Nasko, Daniel J and Allard, Sarah and Bui, Anthony and Treangen, Todd and Pop, Mihai and Mongodin, Emmanuel F and Sapkota, Amy R},
     year = {2020},
     journal = {Water Research},
     publisher = {Pergamon},
     volume = {169},
     pages = {115250}
   }

3. Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact

   Willian A Silveira, Hossein Fazelinia, Sara Brin Rosenthal, and 8 more authors

   Cell, 2020

   Bib

   @article{da2020comprehensive,
     title = {Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact},
     author = {da Silveira, Willian A and Fazelinia, Hossein and Rosenthal, Sara Brin and Laiakis, Evagelia C and Kim, Man S and Meydan, Cem and Kidane, Yared and Rathi, Komal S and Smith, Scott M and Stear, Benjamin and others},
     year = {2020},
     journal = {Cell},
     publisher = {Elsevier},
     volume = {183},
     number = {5},
     pages = {1185--1201}
   }

4. To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics

   RA Leo Elworth, Qi Wang, Pavan K Kota, and 7 more authors

   Nucleic acids research, 2020

   Bib

   @article{elworth2020petabytes,
     title = {To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics},
     author = {Elworth, RA Leo and Wang, Qi and Kota, Pavan K and Barberan, CJ and Coleman, Benjamin and Balaji, Advait and Gupta, Gaurav and Baraniuk, Richard G and Shrivastava, Anshumali and Treangen, Todd J},
     year = {2020},
     journal = {Nucleic acids research},
     publisher = {Oxford University Press},
     volume = {48},
     number = {10},
     pages = {5217--5234}
   }

5. Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides

   RA Leo Elworth, Christian Diaz, Jing Yang, and 3 more authors

   PLoS Pathogens, 2020

   Bib

   @article{elworth2020synthetic,
     title = {Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides},
     author = {Elworth, RA Leo and Diaz, Christian and Yang, Jing and de Figueiredo, Paul and Ternus, Krista and Treangen, Todd},
     year = {2020},
     journal = {PLoS Pathogens},
     publisher = {Public Library of Science San Francisco, CA USA},
     volume = {16},
     number = {8},
     pages = {e1008649}
   }

6. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine

   Medhat Mahmoud, Alejandro Rafael Gener, Michael M Khayat, and 8 more authors

   F1000Research, 2020

   Bib

   @article{mahmoud2020methods,
     title = {Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine},
     author = {Mahmoud, Medhat and Gener, Alejandro Rafael and Khayat, Michael M and English, Adam C and Balaji, Advait and Zhou, Anbo and Hehn, Andreas and Fungtammasan, Arkarachai and Chrisman, Brianna Sierra and Chin, Chen-Shan and others},
     year = {2020},
     journal = {F1000Research},
     publisher = {F1000 Research Limited},
     volume = {9},
     number = {1141},
     pages = {1141}
   }

2019

1. SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest

   Dreycey Albin, Dan Nasko, RA Leo Elworth, and 8 more authors

   In 2019 IEEE international conference on bioinformatics and biomedicine (BIBM), 2019

   Bib

   @inproceedings{albin2019seqscreen,
     title = {SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest},
     author = {Albin, Dreycey and Nasko, Dan and Elworth, RA Leo and Lu, Jacob and Balaji, Advait and Diaz, Christian and Shah, Nidhi and Selengut, Jeremy and Hulme-Lowe, Chris and Muthu, Pravin and others},
     year = {2019},
     booktitle = {2019 IEEE international conference on bioinformatics and biomedicine (BIBM)},
     pages = {1729--1736},
     organization = {IEEE}
   }

2. Diversified race sampling on data streams applied to metagenomic sequence analysis. bioRxiv

   Benito Geordie Benjamin Coleman, Li Chou, RA Leo Elworth, and 2 more authors

   2019

   Bib

   @article{benjamin2019diversified,
     title = {Diversified race sampling on data streams applied to metagenomic sequence analysis. bioRxiv},
     author = {Benjamin Coleman, Benito Geordie and Chou, Li and Elworth, RA Leo and Treangen, Todd J and Shrivastava, Anshumali},
     year = {2019}
   }

3. Diversified RACE sampling on data streams applied to metagenomic sequence analysis

   Benjamin Coleman, Benito Geordie, Li Chou, and 3 more authors

   bioRxiv, 2019

   Bib

   @article{coleman2019diversified,
     title = {Diversified RACE sampling on data streams applied to metagenomic sequence analysis},
     author = {Coleman, Benjamin and Geordie, Benito and Chou, Li and Elworth, RA Leo and Treangen, Todd J and Shrivastava, Anshumali},
     year = {2019},
     journal = {bioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {852889}
   }

4. MetaCarvel: linking assembly graph motifs to biological variants

   Jay Ghurye, Todd Treangen, Marcus Fedarko, and 2 more authors

   Genome biology, 2019

   Bib

   @article{ghurye2019metacarvel,
     title = {MetaCarvel: linking assembly graph motifs to biological variants},
     author = {Ghurye, Jay and Treangen, Todd and Fedarko, Marcus and Hervey, W Judson and Pop, Mihai},
     year = {2019},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {20},
     pages = {1--14}
   }

5. RAMBO: Repeated And Merged BloOm filter for ultra-fast Multiple Set Membership Testing (MSMT) on large-scale data

   Gaurav Gupta, Minghao Yan, Benjamin Coleman, and 4 more authors

   arXiv preprint arXiv:1910.02611, 2019

   Bib

   @article{gupta2019rambo,
     title = {RAMBO: Repeated And Merged BloOm filter for ultra-fast Multiple Set Membership Testing (MSMT) on large-scale data},
     author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Elworth, RA and Medini, Tharun and Treangen, Todd and Shrivastava, Anshumali},
     year = {2019},
     journal = {arXiv preprint arXiv:1910.02611}
   }

6. Sub-linear sequence search via a Repeated And Merged Bloom Filter (RAMBO): indexing 170 TB data in 14 hours

   Gaurav Gupta, Minghao Yan, Benjamin Coleman, and 3 more authors

   arXiv preprint arXiv:1910.04358, 2019

   Bib

   @article{gupta2019sub,
     title = {Sub-linear sequence search via a Repeated And Merged Bloom Filter (RAMBO): indexing 170 TB data in 14 hours},
     author = {Gupta, Gaurav and Yan, Minghao and Coleman, Benjamin and Elworth, RA Leo and Treangen, Todd and Shrivastava, Anshumali},
     year = {2019},
     journal = {arXiv preprint arXiv:1910.04358}
   }

7. Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new Cα, Cβ, and Cγ-linked thioether-containing peptides

   Graham A Hudson, Brandon J Burkhart, Adam J DiCaprio, and 4 more authors

   Journal of the American Chemical Society, 2019

   Bib

   

   @article{hudson2019bioinformatic,
     title = {Bioinformatic mapping of radical S-adenosylmethionine-dependent ribosomally synthesized and post-translationally modified peptides identifies new C{$\alpha$}, C{$\beta$}, and C{$\gamma$}-linked thioether-containing peptides},
     author = {Hudson, Graham A and Burkhart, Brandon J and DiCaprio, Adam J and Schwalen, Christopher J and Kille, Bryce and Pogorelov, Taras V and Mitchell, Douglas A},
     journal = {Journal of the American Chemical Society},
     volume = {141},
     number = {20},
     pages = {8228--8238},
     year = {2019},
     publisher = {ACS Publications}
   }

8. Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

   Nathan D Olson, Todd J Treangen, Christopher M Hill, and 4 more authors

   Briefings in bioinformatics, 2019

   Bib

   @article{olson2019metagenomic,
     title = {Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes},
     author = {Olson, Nathan D and Treangen, Todd J and Hill, Christopher M and Cepeda-Espinoza, Victoria and Ghurye, Jay and Koren, Sergey and Pop, Mihai},
     year = {2019},
     journal = {Briefings in bioinformatics},
     publisher = {Oxford University Press},
     volume = {20},
     number = {4},
     pages = {1140--1150}
   }

9. Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster

   Qi Wang, RA Elworth, Tian Rui Liu, and 1 more author

   In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019

   Bib

   @inproceedings{wang2019faster,
     title = {Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster},
     author = {Wang, Qi and Elworth, RA and Liu, Tian Rui and Treangen, Todd J},
     year = {2019},
     booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
     organization = {Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik}
   }

2018

1. Hierarchically visualizing metagenome assembly graphs with metagenomescope

   Marcus Fedarko, Jay Ghurye, Todd Treangen, and 1 more author

   2018

   Bib

   @article{fedarko2018hierarchically,
     title = {Hierarchically visualizing metagenome assembly graphs with metagenomescope},
     author = {Fedarko, Marcus and Ghurye, Jay and Treangen, Todd and Pop, Mihai},
     year = {2018}
   }

2. Bioinformatic expansion and discovery of thiopeptide antibiotics

   Christopher J Schwalen, Graham A Hudson, Bryce Kille, and 1 more author

   Journal of the American Chemical Society, 2018

   Bib

   

   @article{schwalen2018bioinformatic,
     title = {Bioinformatic expansion and discovery of thiopeptide antibiotics},
     author = {Schwalen, Christopher J and Hudson, Graham A and Kille, Bryce and Mitchell, Douglas A},
     journal = {Journal of the American Chemical Society},
     volume = {140},
     number = {30},
     pages = {9494--9501},
     year = {2018},
     publisher = {ACS Publications}
   }

3. Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018

   Jacquelyn S Meisel, Daniel J Nasko, Brian Brubach, and 8 more authors

   Microbiome, 2018

   Bib

   @article{meisel2018current,
     title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018},
     author = {Meisel, Jacquelyn S and Nasko, Daniel J and Brubach, Brian and Cepeda-Espinoza, Victoria and Chopyk, Jessica and Corrada-Bravo, H{\'e}ctor and Fedarko, Marcus and Ghurye, Jay and Javkar, Kiran and Olson, Nathan D and others},
     year = {2018},
     journal = {Microbiome},
     publisher = {BioMed Central},
     volume = {6},
     pages = {1--10}
   }

4. RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

   Daniel J Nasko, Sergey Koren, Adam M Phillippy, and 1 more author

   Genome biology, 2018

   Bib

   @article{nasko2018refseq,
     title = {RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification},
     author = {Nasko, Daniel J and Koren, Sergey and Phillippy, Adam M and Treangen, Todd J},
     year = {2018},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {19},
     pages = {1--10}
   }

5. Traumatic brain injury in mice induces acute bacterial dysbiosis within the fecal microbiome

   Todd J Treangen, Justin Wagner, Mark P Burns, and 1 more author

   Frontiers in immunology, 2018

   Bib

   @article{treangen2018traumatic,
     title = {Traumatic brain injury in mice induces acute bacterial dysbiosis within the fecal microbiome},
     author = {Treangen, Todd J and Wagner, Justin and Burns, Mark P and Villapol, Sonia},
     year = {2018},
     journal = {Frontiers in immunology},
     publisher = {Frontiers Media SA},
     volume = {9},
     pages = {2757}
   }

6. You can’t always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details

   Todd J Treangen, and Mihai Pop

   EMBO reports, 2018

   Bib

   @article{treangen2018you,
     title = {You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details},
     author = {Treangen, Todd J and Pop, Mihai},
     year = {2018},
     journal = {EMBO reports},
     volume = {19},
     number = {12},
     pages = {e47036}
   }

2017

1. MetaCompass: reference-guided assembly of metagenomes

   Victoria Cepeda, Bo Liu, Mathieu Almeida, and 4 more authors

   BioRxiv, 2017

   Bib

   @article{cepeda2017metacompass,
     title = {MetaCompass: reference-guided assembly of metagenomes},
     author = {Cepeda, Victoria and Liu, Bo and Almeida, Mathieu and Hill, Christopher M and Koren, Sergey and Treangen, Todd J and Pop, Mihai},
     year = {2017},
     journal = {BioRxiv},
     publisher = {Cold Spring Harbor Laboratory},
     pages = {212506}
   }

2. Gaurav Gupta

   Gaurav Gupta

   2017

   Bib

   @article{gupta2017gaurav,
     title = {Gaurav Gupta},
     author = {Gupta, Gaurav},
     year = {2017}
   }

3. Draft Genome Sequences from a Novel Clade of Bacillus cereusáSensu Lato Strains, Isolated from the International Space Station

   Venkateswaran Kasthuri, Checinska Sielaff Aleksandra, Ratnayake Shashikala, and 8 more authors

   Microbiology Resource Announcements, 2017

   Bib

   @article{kasthuri2017draft,
     title = {Draft Genome Sequences from a Novel Clade of Bacillus cereus{\'a}Sensu Lato Strains, Isolated from the International Space Station},
     author = {Kasthuri, Venkateswaran and Aleksandra, Checinska Sielaff and Shashikala, Ratnayake and Pope, Robert K and Blank, Thomas E and Stepanov, Victor G and Fox, George E and van Tongeren Sandra, P and Torres, Clinton and Allen, Jonathan and others},
     year = {2017},
     journal = {Microbiology Resource Announcements},
     publisher = {American Society for Microbiology},
     number = {32}
   }

4. Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.

   Nathanael D Olson, Chris M Hill, Vistoria Cepeda-Espinoza, and 4 more authors

   2017

   Bib

   @article{olson2017metagenomic,
     title = {Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.},
     author = {Olson, Nathanael D and Hill, Chris M and Cepeda-Espinoza, Vistoria and Ghurye, Jay and Koren, Sergey and Treangen, Todd J and Pop, Mihai},
     year = {2017},
     publisher = {Nathanael D. Olson, Chris M. Hill, Vistoria Cepeda-Espinoza, Jay Ghurye~…}
   }

5. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station

   Robert K Pope, Thomas E Blank, Victor G Stepanov, and 8 more authors

   2017

   Bib

   @article{pope2017draft,
     title = {Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station},
     author = {Pope, Robert K and Blank, Thomas E and Stepanov, Victor G and Fox, George E and van Tongeren, Sandra P and Torres, Clinton and Allen, Jonathan and Jaing, Crystal and Pierson, Duane and Perry, Jay and others},
     year = {2017}
   }

6. Draft genome sequences from a novel clade of Bacillus cereus sensu lato strains, isolated from the International Space Station

   Kasthuri Venkateswaran, Aleksandra Checinska Sielaff, Shashikala Ratnayake, and 8 more authors

   Genome announcements, 2017

   Bib

   @article{venkateswaran2017draft,
     title = {Draft genome sequences from a novel clade of Bacillus cereus sensu lato strains, isolated from the International Space Station},
     author = {Venkateswaran, Kasthuri and Checinska Sielaff, Aleksandra and Ratnayake, Shashikala and Pope, Robert K and Blank, Thomas E and Stepanov, Victor G and Fox, George E and van Tongeren, Sandra P and Torres, Clinton and Allen, Jonathan and others},
     year = {2017},
     journal = {Genome announcements},
     publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
     volume = {5},
     number = {32},
     pages = {10--1128}
   }

2016

1. Limitations of current approaches for reference-free, graph-based variant detection

   Amelia Bateman, Todd J Treangen, and Mihai Pop

   In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2016

   Bib

   @inproceedings{bateman2016limitations,
     title = {Limitations of current approaches for reference-free, graph-based variant detection},
     author = {Bateman, Amelia and Treangen, Todd J and Pop, Mihai},
     year = {2016},
     booktitle = {Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
     pages = {499--500}
   }

2. Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers

   Michelle Davison, Todd J Treangen, Sergey Koren, and 2 more authors

   PloS one, 2016

   Bib

   @article{davison2016diversity,
     title = {Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers},
     author = {Davison, Michelle and Treangen, Todd J and Koren, Sergey and Pop, Mihai and Bhaya, Devaki},
     year = {2016},
     journal = {PloS one},
     publisher = {Public Library of Science San Francisco, CA USA},
     volume = {11},
     number = {9},
     pages = {e0160574}
   }

3. Mash: fast genome and metagenome distance estimation using MinHash

   Brian D Ondov, Todd J Treangen, Páll Melsted, and 4 more authors

   Genome biology, 2016

   Bib

   @article{ondov2016mash,
     title = {Mash: fast genome and metagenome distance estimation using MinHash},
     author = {Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
     year = {2016},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {17},
     pages = {1--14}
   }

4. Identification and genomic analysis of a novel Group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru

   Todd J Treangen, George Schoeler, Adam M Phillippy, and 2 more authors

   PLoS neglected tropical diseases, 2016

   Bib

   @article{treangen2016identification,
     title = {Identification and genomic analysis of a novel Group C orthobunyavirus isolated from a mosquito captured near Iquitos, Peru},
     author = {Treangen, Todd J and Schoeler, George and Phillippy, Adam M and Bergman, Nicholas H and Turell, Michael J},
     year = {2016},
     journal = {PLoS neglected tropical diseases},
     publisher = {Public Library of Science San Francisco, CA USA},
     volume = {10},
     number = {4},
     pages = {e0004440}
   }

2014

1. Automated ensemble assembly and validation of microbial genomes

   Sergey Koren, Todd J Treangen, Christopher M Hill, and 2 more authors

   BMC bioinformatics, 2014

   Bib

   @article{koren2014automated,
     title = {Automated ensemble assembly and validation of microbial genomes},
     author = {Koren, Sergey and Treangen, Todd J and Hill, Christopher M and Pop, Mihai and Phillippy, Adam M},
     year = {2014},
     journal = {BMC bioinformatics},
     publisher = {BioMed Central},
     volume = {15},
     pages = {1--9}
   }

2. Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923

   Todd J Treangen, Rosslyn A Maybank, Sana Enke, and 8 more authors

   Genome announcements, 2014

   Bib

   @article{treangen2014complete,
     title = {Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923},
     author = {Treangen, Todd J and Maybank, Rosslyn A and Enke, Sana and Friss, Mary Beth and Diviak, Lynn F and Karaolis, David KR and Koren, Sergey and Ondov, Brian and Phillippy, Adam M and Bergman, Nicholas H and others},
     year = {2014},
     journal = {Genome announcements},
     publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
     volume = {2},
     number = {6},
     pages = {10--1128}
   }

3. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

   Todd J Treangen, Brian D Ondov, Sergey Koren, and 1 more author

   Genome biology, 2014

   Bib

   @article{treangen2014harvest,
     title = {The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes},
     author = {Treangen, Todd J and Ondov, Brian D and Koren, Sergey and Phillippy, Adam M},
     year = {2014},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {15},
     pages = {1--15}
   }

4. A new rhesus macaque assembly and annotation for next-generation sequencing analyses

   Aleksey V Zimin, Adam S Cornish, Mnirnal D Maudhoo, and 8 more authors

   Biology direct, 2014

   Bib

   @article{zimin2014new,
     title = {A new rhesus macaque assembly and annotation for next-generation sequencing analyses},
     author = {Zimin, Aleksey V and Cornish, Adam S and Maudhoo, Mnirnal D and Gibbs, Robert M and Zhang, Xiongfei and Pandey, Sanjit and Meehan, Daniel T and Wipfler, Kristin and Bosinger, Steven E and Johnson, Zachary P and others},
     year = {2014},
     journal = {Biology direct},
     publisher = {BioMed Central},
     volume = {9},
     pages = {1--15}
   }

2013

1. Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis

   Robin Harrington, Brian D Ondov, Diana Radune, and 8 more authors

   Genome announcements, 2013

   Bib

   @article{harrington2013genome,
     title = {Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis},
     author = {Harrington, Robin and Ondov, Brian D and Radune, Diana and Friss, Mary Beth and Klubnik, Joy and Diviak, Lynn and Hnath, Jonathan and Cendrowski, Stephen R and Blank, Thomas E and Karaolis, David and others},
     year = {2013},
     journal = {Genome announcements},
     publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},
     volume = {1},
     number = {1},
     pages = {10--1128}
   }

2. De novo likelihood-based measures for comparing metagenomic assemblies

   Christopher M Hill, Irina Astrovskaya, Howard Huang, and 4 more authors

   In 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

   Bib

   @inproceedings{hill2013novo,
     title = {De novo likelihood-based measures for comparing metagenomic assemblies},
     author = {Hill, Christopher M and Astrovskaya, Irina and Huang, Howard and Koren, Sergey and Memon, Atif and Treangen, Todd J and Pop, Mihai},
     year = {2013},
     booktitle = {2013 IEEE International Conference on Bioinformatics and Biomedicine},
     pages = {94--98},
     organization = {IEEE}
   }

3. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

   Todd J Treangen, Sergey Koren, Daniel D Sommer, and 6 more authors

   Genome Biology, 2013

   Bib

   @article{treangen2013metamos,
     title = {MetAMOS: a modular and open source metagenomic assembly and analysis pipeline},
     author = {Treangen, Todd J and Koren, Sergey and Sommer, Daniel D and Liu, Bo and Astrovskaya, Irina and Ondov, Brian and Darling, Aaron E and Phillippy, Adam M and Pop, Mihai},
     year = {2013},
     journal = {Genome Biology},
     publisher = {BioMed Central Ltd},
     volume = {14},
     number = {1},
     pages = {R2}
   }

2012

1. Structure, function and diversity of the healthy human microbiome

   Huttenhower Curtis, Martin J Blaser, Gevers Dirk, and 8 more authors

   Nature (London), 2012

   Bib

   @article{curtis2012structure,
     title = {Structure, function and diversity of the healthy human microbiome},
     author = {Curtis, Huttenhower and Blaser, Martin J and Dirk, Gevers and Kota, Karthik C and Rob, Knight and Liu, Bo and Wang, Lu and Sahar, Abubucker and White, James R and Badger, Jonathan H and others},
     year = {2012},
     journal = {Nature (London)},
     volume = {486},
     number = {7402},
     pages = {207--214}
   }

2. Deep sequencing of the oral microbiome reveals signatures of periodontal disease

   Bo Liu, Lina L Faller, Niels Klitgord, and 8 more authors

   PloS one, 2012

   Bib

   @article{liu2012deep,
     title = {Deep sequencing of the oral microbiome reveals signatures of periodontal disease},
     author = {Liu, Bo and Faller, Lina L and Klitgord, Niels and Mazumdar, Varun and Ghodsi, Mohammad and Sommer, Daniel D and Gibbons, Theodore R and Treangen, Todd J and Chang, Yi-Chien and Li, Shan and others},
     year = {2012},
     journal = {PloS one},
     publisher = {Public Library of Science San Francisco, USA},
     volume = {7},
     number = {6},
     pages = {e37919}
   }

3. Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone

   Adam Phillippy, and Todd Treangen

   Genome Biology, 2012

   Bib

   @article{phillippy2012irreconcilable,
     title = {Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone},
     author = {Phillippy, Adam and Treangen, Todd},
     year = {2012},
     journal = {Genome Biology},
     publisher = {BMC},
     volume = {13},
     number = {181}
   }

4. GAGE: A critical evaluation of genome assemblies and assembly algorithms

   Steven L Salzberg, Adam M Phillippy, Aleksey Zimin, and 8 more authors

   Genome research, 2012

   Bib

   @article{salzberg2012gage,
     title = {GAGE: A critical evaluation of genome assemblies and assembly algorithms},
     author = {Salzberg, Steven L and Phillippy, Adam M and Zimin, Aleksey and Puiu, Daniela and Magoc, Tanja and Koren, Sergey and Treangen, Todd J and Schatz, Michael C and Delcher, Arthur L and Roberts, Michael and others},
     year = {2012},
     journal = {Genome research},
     publisher = {Cold Spring Harbor Lab},
     volume = {22},
     number = {3},
     pages = {557--567}
   }

2011

1. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

   Jacob Enk, Alison Devault, Regis Debruyne, and 7 more authors

   Genome biology, 2011

   Bib

   @article{enk2011complete,
     title = {Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths},
     author = {Enk, Jacob and Devault, Alison and Debruyne, Regis and King, Christine E and Treangen, Todd and O'Rourke, Dennis and Salzberg, Steven L and Fisher, Daniel and MacPhee, Ross and Poinar, Hendrik},
     year = {2011},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {12},
     pages = {1--8}
   }

2. Bambus 2: scaffolding metagenomes

   Sergey Koren, Todd J Treangen, and Mihai Pop

   Bioinformatics, 2011

   Bib

   @article{koren2011bambus,
     title = {Bambus 2: scaffolding metagenomes},
     author = {Koren, Sergey and Treangen, Todd J and Pop, Mihai},
     year = {2011},
     journal = {Bioinformatics},
     publisher = {Oxford University Press},
     volume = {27},
     number = {21},
     pages = {2964--2971}
   }

3. ScaffViz: visualizing metagenome assemblies

   Sergey Koren, Todd Treangen, and Mihai Pop

   Genome Biology, 2011

   Bib

   @article{koren2011scaffviz,
     title = {ScaffViz: visualizing metagenome assemblies},
     author = {Koren, Sergey and Treangen, Todd and Pop, Mihai},
     year = {2011},
     journal = {Genome Biology},
     publisher = {Springer},
     volume = {12},
     pages = {1--27}
   }

4. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

   Bo Liu, Theodore Gibbons, Mohammad Ghodsi, and 2 more authors

   BMC Genomics, 2011

   Bib

   @article{liu2011accurate,
     title = {Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences},
     author = {Liu, Bo and Gibbons, Theodore and Ghodsi, Mohammad and Treangen, Todd and Pop, Mihai},
     year = {2011},
     journal = {BMC Genomics},
     publisher = {BioMed Central Ltd},
     volume = {12},
     number = {Suppl 2},
     pages = {S4}
   }

5. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

   Todd J Treangen, and Eduardo PC Rocha

   PLoS genetics, 2011

   Bib

   @article{treangen2011horizontal,
     title = {Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes},
     author = {Treangen, Todd J and Rocha, Eduardo PC},
     year = {2011},
     journal = {PLoS genetics},
     publisher = {Public Library of Science San Francisco, USA},
     volume = {7},
     number = {1},
     pages = {e1001284}
   }

6. Next generation sequence assembly with AMOS

   Todd J Treangen, Dan D Sommer, Florent E Angly, and 2 more authors

   Current Protocols in Bioinformatics, 2011

   Bib

   @article{treangen2011next,
     title = {Next generation sequence assembly with AMOS},
     author = {Treangen, Todd J and Sommer, Dan D and Angly, Florent E and Koren, Sergey and Pop, Mihai},
     year = {2011},
     journal = {Current Protocols in Bioinformatics},
     volume = {33},
     number = {1},
     pages = {11--8}
   }

7. Repetitive DNA and next-generation sequencing: computational challenges and solutions

   Todd J Treangen, and Steven L Salzberg

   Nature Reviews Genetics, 2011

   Bib

   @article{treangen2011repetitive,
     title = {Repetitive DNA and next-generation sequencing: computational challenges and solutions},
     author = {Treangen, Todd J and Salzberg, Steven L},
     year = {2011},
     journal = {Nature Reviews Genetics},
     publisher = {Nature Publishing Group}
   }

2010

1. Repeatoire: Detecting intragenomic repeat families within the context of intergenomic comparisons

   Todd J Treangen, and Eduardo PC Rocha

   ISBRA 2010, 2010

   Bib

   @article{treangen2010repeatoire,
     title = {Repeatoire: Detecting intragenomic repeat families within the context of intergenomic comparisons},
     author = {Treangen, Todd J and Rocha, Eduardo PC},
     year = {2010},
     journal = {ISBRA 2010},
     pages = {34}
   }

2009

1. Genesis, effects and fates of repeats in prokaryotic genomes

   Todd J Treangen, Anne-Laure Abraham, Marie Touchon, and 1 more author

   FEMS microbiology reviews, 2009

   Bib

   @article{treangen2009genesis,
     title = {Genesis, effects and fates of repeats in prokaryotic genomes},
     author = {Treangen, Todd J and Abraham, Anne-Laure and Touchon, Marie and Rocha, Eduardo PC},
     year = {2009},
     journal = {FEMS microbiology reviews},
     publisher = {Blackwell Publishing Ltd Oxford, UK},
     volume = {33},
     number = {3},
     pages = {539--571}
   }

2. A novel heuristic for local multiple alignment of interspersed DNA repeats

   Todd J Treangen, Aaron E Darling, Guillaume Achaz, and 3 more authors

   IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2009

   Bib

   @article{treangen2009novel,
     title = {A novel heuristic for local multiple alignment of interspersed DNA repeats},
     author = {Treangen, Todd J and Darling, Aaron E and Achaz, Guillaume and Ragan, Mark A and Messeguer, Xavier and Rocha, Eduardo PC},
     year = {2009},
     journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)},
     booktitle = {2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008)},
     publisher = {IEEE Computer Society Press},
     volume = {6},
     number = {2},
     pages = {180--189},
     organization = {Springer}
   }

2008

1. The impact of the neisserial DNA uptake sequences on genome evolution and stability

   Todd J Treangen, Ole Herman Ambur, Tone Tonjum, and 1 more author

   Genome biology, 2008

   Bib

   @article{treangen2008impact,
     title = {The impact of the neisserial DNA uptake sequences on genome evolution and stability},
     author = {Treangen, Todd J and Ambur, Ole Herman and Tonjum, Tone and Rocha, Eduardo PC},
     year = {2008},
     journal = {Genome biology},
     publisher = {BioMed Central},
     volume = {9},
     pages = {1--17}
   }

2007

1. Analyzing patterns of microbial evolution using the mauve genome alignment system

   Aaron E Darling, Todd J Treangen, Xavier Messeguer, and 1 more author

   Comparative genomics, 2007

   Bib

   @article{darling2007analyzing,
     title = {Analyzing patterns of microbial evolution using the mauve genome alignment system},
     author = {Darling, Aaron E and Treangen, Todd J and Messeguer, Xavier and Perna, Nicole T},
     year = {2007},
     journal = {Comparative genomics},
     publisher = {Humana Press},
     pages = {135--152}
   }

2006

1. Procrastination leads to efficient filtration for local multiple alignment

   Aaron E Darling, Todd J Treangen, Louxin Zhang, and 3 more authors

   In International Workshop on Algorithms in Bioinformatics, 2006

   Bib

   @inproceedings{darling2006procrastination,
     title = {Procrastination leads to efficient filtration for local multiple alignment},
     author = {Darling, Aaron E and Treangen, Todd J and Zhang, Louxin and Kuiken, Carla and Messeguer, Xavier and Perna, Nicole T},
     year = {2006},
     booktitle = {International Workshop on Algorithms in Bioinformatics},
     pages = {126--137},
     organization = {Springer Berlin Heidelberg Berlin, Heidelberg}
   }

2. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

   Todd Treangen, and Xavier Messeguer

   BMC bioinformatics, 2006

   Bib

   @article{treangen2006m,
     title = {M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species},
     author = {Treangen, Todd and Messeguer, Xavier},
     year = {2006},
     journal = {BMC bioinformatics},
     publisher = {BioMed Central Ltd},
     volume = {7},
     number = {1},
     pages = {433}
   }