The goal of the current proposal is to develop a new flexible framework for metagenomic assembly. This framework will provide novel algorithms for de novo and comparative assembly of metagenomic data, as well as tools for extracting and analyzing genomic variation. In addition, a novel approach will be developed for reconstructing segments of a genome containing a specific 16S rRNA sequence. At the core of this framework are two packages developed in the PIs lab: the open source package AMOS - a flexible and modular assembly package, and Bambus 2 - a genomic scaffolder specifically targeted at metagenomic data. A novel model-based testing framework will be closely integrated with the developments proposed here in order to ensure the correctness of the software being developed. Several levels of test procedures will be run every time the code is changed, on a nightly basis, as well as at regular intervals, allowing errors to be promptly discovered and corrected.

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 te genomes and metagenomes from high-throughput sequencing data.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Dugan, Vivien Grace
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Maryland College Park
Biostatistics & Other Math Sci
Schools of Arts and Sciences
College Park
United States
Zip Code
Almeida, Mathieu; Pop, Mihai; Le Chatelier, Emmanuelle et al. (2016) Capturing the most wanted taxa through cross-sample correlations. ISME J 10:2459-67
Mendelowitz, Lee M; Schwartz, David C; Pop, Mihai (2016) Maligner: a fast ordered restriction map aligner. Bioinformatics 32:1016-22
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
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
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
Almeida, Mathieu; Hébert, Agnès; Abraham, Anne-Laure et al. (2014) Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics 15:1101
Mendelowitz, Lee; Pop, Mihai (2014) Computational methods for optical mapping. Gigascience 3:33
Nguyen, Nam-Phuong; Mirarab, Siavash; Liu, Bo et al. (2014) TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics 30:3548-55
Koren, Sergey; Treangen, Todd J; Hill, Christopher M et al. (2014) Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 15:126

Showing the most recent 10 out of 12 publications