Through this proposal, we will develop new computational tools for reconstructing nearly- complete microbial genomes from complex mixtures, as well as their strain structure. We will build upon our initial successes in developing metagenomic assembly algorithms capable of characterizing strain variants (7, 8), as well as upon our experience in using co-abundance across samples to link/bin together genes originating from the same organism (9). In addition, we will develop algorithms able to use information generated by emerging technologies, such as chromosome conformation information generated by Hi-C (10-12), or information about DNA modifications as generated by new nanopore sequencing devices(13, 14).

Public Health Relevance

Metagenomics studies are starting to elucidate the roles microbes play in human health and disease. This proposal will enhance future metagenomic studies by providing full featured, efficient, and robust algorithms and tools for reconstructing the genomes and metagenomes from high-throughput sequencing data.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Brown, Liliana L
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University of Maryland College Park
Biostatistics & Other Math Sci
Earth Sciences/Resources
College Park
United States
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Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter et al. (2017) Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods 14:1063-1071
Ghurye, Jay; Pop, Mihai; Koren, Sergey et al. (2017) Scaffolding of long read assemblies using long range contact information. BMC Genomics 18:527
Olson, Nathan D; Treangen, Todd J; Hill, Christopher M et al. (2017) Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Brief Bioinform :
Almeida, Mathieu; Pop, Mihai; Le Chatelier, Emmanuelle et al. (2016) Capturing the most wanted taxa through cross-sample correlations. ISME J 10:2459-67
Pop, Mihai; Paulson, Joseph N; Chakraborty, Subhra et al. (2016) Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 17:440
Rashid, Mahamud-Ur; Almeida, Mathieu; Azman, Andrew S et al. (2016) Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1. FEMS Microbiol Lett 363:
Morris, Alison; Paulson, Joseph N; Talukder, Hisham et al. (2016) Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome 4:38
Mendelowitz, Lee M; Schwartz, David C; Pop, Mihai (2016) Maligner: a fast ordered restriction map aligner. Bioinformatics 32:1016-22
Simpson, Jared T; Pop, Mihai (2015) The Theory and Practice of Genome Sequence Assembly. Annu Rev Genomics Hum Genet 16:153-72
Pop, Mihai; Salzberg, Steven L (2015) Use and mis-use of supplementary material in science publications. BMC Bioinformatics 16:237

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