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Tag Archives: metagenomics
Microbiomes of a small conference
The conference season is almost over. There are still a few gems out there worth attending before school starts. I just came back from the Lake Arrowhead Microbial Genomics Conference which took place at a UCLA resort in the mountains. … Continue reading →
Posted in blogging, career, community, conferences, evolution, genomics
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Tagged conference, ecological genomics, Evolution, genomics, metagenomics, microbiome, social media
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Signal Boosting a Comprehensive Review of eDNA and Metabarcoding Studies
Everything is meta these days – metabarcoding, metagenomics, and now meta blog posts that are reviews of reviews. Much like every ecologist at least dabbles in the molecular world, so most of those predisposed to molecular ecology and population genetics … Continue reading →
Posted in bioinformatics, community ecology, DNA barcoding, metagenomics, methods, microbiology, next generation sequencing, population genetics
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Tagged barcode tags, barcoding, bioinformatics, eukaryotes, Illumina, metagenomics, methods, microbial communities, microbial community analysis, microbiome, NGS
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Major new microbial groups expand diversity and alter our understanding of the tree of life
I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading →
Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics
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Tagged assembly, bioinformatics, Evolution, genome, genomics, metagenomics, NGS, phylogenetics
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There are more microbes than meet the eye: exploring the genomic diversity in an aquifer
First: it’s Tuesday, November 8th, 2016 – before you even think about putting your feet up and reading this post, I hope you’ve managed to wrangle yourself one of those highly prized “I voted” stickers. Now, on to more microbial … Continue reading →
Posted in bioinformatics, community ecology, metagenomics, microbiology, next generation sequencing
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Tagged ecology, genomics, metagenomics
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When your programming may be inadequate to the task: new options for metagenome analysis
There’s a lot of data in the form of metagenomes out there, and picking apart those mountains of data to uncover meaningful results is difficult. Recently, we received a suggestion from a reader to discuss a recent program (CLARK-S) developed … Continue reading →
Posted in bioinformatics, community ecology, metagenomics, methods
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Tagged CLARK-S, DESMAN, fine-scale variation, metagenomics, methods, OMICtools
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Understanding diverse microbial communities: An interview with A. Murat Eren (Meren)
It’s clear that microbes play a crucial role in practically every aspect of ecosystems globally. From the deepest, most remote and unexplored regions of the ocean, to the human oral cavity, there are diverse microbial assemblages driving Earth’s biogeochemical cycles. … Continue reading →
Posted in bioinformatics, community ecology, metagenomics, methods
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Tagged anvi'o, genomics, metagenomics, visualization software
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Data, data everywhere and another tool to use: Taxonomer, a web-tool for metagenomics data analysis
Because sequencing. With all the affordable genome and metagenome sequencing available, we’ve reached an unprecedented point at which we can profile microbial communities more accurately than ever before. For this reason, it’s essential to develop efficient methods for data analysis. … Continue reading →
Posted in bioinformatics, community ecology, genomics, metagenomics, methods, microbiology, software
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Tagged metagenomics, sequence analysis, software, web-based tool
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New branches on the tree of life
(Trees from Darwin (1837), Haeckel (1866), and Woese (1990)) We’ve come quite a long way since Darwin sketched out his tree in 1837 connecting, with branch tips representing animals and microbes currently in existence and branches and trunks their ancestors. … Continue reading →
Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, phylogenetics
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Tagged candidate phyla radiation, Evolution, metagenomics, phylogeny, tree of life
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The dangers of not thinking about the relics
No, I’m not talking about Saint Erik’s skull from his beheading in 1160, which (as it turns out) might just be real. A hot topic in microbiology is a different kind of relic. Amazing developments in microbial ecology in recent years … Continue reading →
Posted in bioinformatics, community ecology, metagenomics
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Tagged metagenomics, qPCR, relic DNA
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Making heatmaps with R for microbiome analysis
Arianne Albert is the Biostatistician for the Women’s Health Research Institute at the British Columbia Women’s Hospital and Health Centre. She earned a PhD from the University of British Columbia under the tutelage of Dolph Schluter before branching off into … Continue reading →