Energy Department Expanding Microbial Genome Efforts

Jeffrey L. Fox

doi:10.1128/microbe.2.169.2

Faculty Opinions recommendation of Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.5045977.5007055 ◽

2010 ◽

Author(s):

Kim Lewis ◽

Lawrence Mulcahy

Keyword(s):

Microbial Genome

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Bacillus minimum genome factory: effective utilization of microbial genome information

Biotechnology and Applied Biochemistry ◽

10.1042/ba20060111 ◽

2007 ◽

Vol 46 (3) ◽

pp. 169 ◽

Cited By ~ 65

Author(s):

Katsuya Ozaki ◽

Katsutoshi Ara ◽

Kouji Nakamura ◽

Kunio Yamane ◽

Junichi Sekiguchi ◽

...

Keyword(s):

Microbial Genome ◽

Effective Utilization ◽

Genome Information

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Development of Microbial Genome-Probing Microarrays using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

Environmental Science & Technology ◽

10.1021/es802245e ◽

2008 ◽

Vol 42 (22) ◽

pp. 8614-8614

Author(s):

Ho-Won Chang ◽

Youboong Sung ◽

Kyoung-Ho Kim ◽

Young-Do Nam ◽

Seong Woon Roh ◽

...

Keyword(s):

Multiple Displacement Amplification ◽

Single Cells ◽

Microbial Genome

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The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Standards in Genomic Sciences ◽

10.1186/s40793-015-0077-y ◽

2015 ◽

Vol 10 (1) ◽

Cited By ~ 152

Author(s):

Marcel Huntemann ◽

Natalia N. Ivanova ◽

Konstantinos Mavromatis ◽

H. James Tripp ◽

David Paez-Espino ◽

...

Keyword(s):

Operating Procedure ◽

Genome Annotation ◽

Standard Operating Procedure ◽

Microbial Genome ◽

Annotation Pipeline ◽

Standard Operating

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The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

Bioinformatics ◽

10.1093/bioinformatics/bty941 ◽

2018 ◽

Vol 35 (13) ◽

pp. 2332-2334 ◽

Cited By ~ 16

Author(s):

Federico Baldini ◽

Almut Heinken ◽

Laurent Heirendt ◽

Stefania Magnusdottir ◽

Ronan M T Fleming ◽

...

Keyword(s):

Microbial Communities ◽

Microbial Interactions ◽

Microbial Genome ◽

Metagenomic Data ◽

Metabolic Interactions ◽

Constraint Based Modeling ◽

Genome Scale

Abstract Motivation The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes. Results To address this gap, we created a comprehensive toolbox to model (i) microbe–microbe and host–microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox. Availability and implementation The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

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