Sequencing and beyond: integrating molecular'omics' for microbial community profiling
EA Franzosa, T Hsu, A Sirota-Madi… - Nature Reviews …, 2015 - nature.com
High-throughput DNA sequencing has proven invaluable for investigating diverse
environmental and host-associated microbial communities. In this Review, we discuss …
environmental and host-associated microbial communities. In this Review, we discuss …
Synthetic ecology of microbes: mathematical models and applications
AR Zomorrodi, D Segrè - Journal of molecular biology, 2016 - Elsevier
As the indispensable role of natural microbial communities in many aspects of life on Earth
is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions …
is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions …
Unraveling the functional dark matter through global metagenomics
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions
and activities,. Exploration of this vast sequence space has been limited to a comparative …
and activities,. Exploration of this vast sequence space has been limited to a comparative …
Deep sequencing of the oral microbiome reveals signatures of periodontal disease
The oral microbiome, the complex ecosystem of microbes inhabiting the human mouth,
harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within …
harbors several thousands of bacterial types. The proliferation of pathogenic bacteria within …
The methylomes of six bacteria
Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens,
Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81 …
Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81 …
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …
The 2012 nucleic acids research database issue and the online molecular biology database collection
MY Galperin, XM Fernández-Suarez - Nucleic acids research, 2012 - academic.oup.com
Abstract The 19th annual Database Issue of Nucleic Acids Research features descriptions of
92 new online databases covering various areas of molecular biology and 100 papers …
92 new online databases covering various areas of molecular biology and 100 papers …
The other face of restriction: modification-dependent enzymes
WAM Loenen, EA Raleigh - Nucleic acids research, 2014 - academic.oup.com
The 1952 observation of host-induced non-hereditary variation in bacteriophages by
Salvador Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that …
Salvador Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that …
EcoGene 3.0
J Zhou, KE Rudd - Nucleic acids research, 2012 - academic.oup.com
Abstract EcoGene (http://ecogene. org) is a database and website devoted to continuously
improving the structural and functional annotation of Escherichia coli K-12, one of the most …
improving the structural and functional annotation of Escherichia coli K-12, one of the most …
Progress and opportunities in microbial community metabolomics
Highlights•Microbiome-associated metabolite pools aid discovery of novel functions.•Guilt-
by-association approaches identify microbial derivatives of standard metabolites.•Machine …
by-association approaches identify microbial derivatives of standard metabolites.•Machine …