Algorithms and Software for the Assembly of Metagenomic Data

宏基因组数据组装的算法和软件

• 批准号: 10530592
• 负责人: Mihai Pop
• 金额: $ 65.26万
• 依托单位: UNIV OF MARYLAND, COLLEGE PARK
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-03-21 至 2024-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10530592
• 关键词: Address; Algorithms; Biological; Certification; Chromosomes; Collection; Communities; Complement; Complex Mixtures; Computer software; DNA Modification Process; Data; Devices; Disease; Effectiveness; Elements; Emerging Technologies; Future; Genes; Genome; Genomic Segment; Genomics; Graph; Health; Hi-C; High-Throughput Nucleotide Sequencing; Human; Individual; Label; Laboratories; Lead; Link; Manuals; Measures; Metagenomics; Methods; Microbe; Molecular Conformation; Operon; Organism; Pattern; Play; Regulatory Element; Research; Role; Sampling; Software Tools; Source; Speed; Structure; Taxonomy; Technology; Validation; Variant; Visual; computerized tools; contig; deep sequencing; experience; improved; metagenome; microbial community; microbial genome; nanopore; novel strategies; programs; rRNA Genes; reconstruction; reference genome; scale up; success; targeted sequencing; tool; user friendly software; whole genome

Abstract 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).

摘要

项目成果

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

• DOI: 10.1371/journal.pcbi.1008928
• 发表时间: 2021-05
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Medvedev P;Pop M
• 通讯作者: Pop M

Automated ensemble assembly and validation of microbial genomes.

• DOI: 10.1186/1471-2105-15-126
• 发表时间: 2014-05-03
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Koren S;Treangen TJ;Hill CM;Pop M;Phillippy AM
• 通讯作者: Phillippy AM

Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population.

杂交打破了蓝藻种群长期共同进化的物种障碍。

• DOI: 10.1101/2023.06.06.543983
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Birzu,Gabriel;Muralidharan,HariharaSubrahmaniam;Goudeau,Danielle;Malmstrom,RexR;Fisher,DanielS;Bhaya,Devaki
• 通讯作者: Bhaya,Devaki

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

• DOI: 10.1186/s12864-016-2777-0
• 发表时间: 2016-06-08
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Pop M;Paulson JN;Chakraborty S;Astrovskaya I;Lindsay BR;Li S;Bravo HC;Harro C;Parkhill J;Walker AW;Walker RI;Sack DA;Stine OC
• 通讯作者: Stine OC

The impact of transitive annotation on the training of taxonomic classifiers.

• DOI: 10.3389/fmicb.2023.1240957
• 发表时间: 2023
• 期刊: Frontiers in microbiology
• 影响因子: 5.2