Category Archives: metagenomics

Guest post from Rachid Ounit on CLARK: Fast and Accurate Classification of Metagenomic and Genomic Sequences

Recently I received and email from Rachid Ounit pointing me to a new open access paper he had on a metagenomics analysis tool called CLARK.  I asked him if he would be willing to write a guest post about it … Continue reading

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Do preprints count for anything? Not according to Elife & G3 & some authors ..

Well, just got pointed to this paper: Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms | eLife by Martial Marbouty, Axel Cournac, Jean-François Flot, Hervé Marie-Nelly, Julien Mozziconacci, Romain Koszul.  Seems potentially really interesting. It is similar in … Continue reading

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Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet: Some new papers that may be of interest to people: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus.  Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis … Continue reading

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Story Behind the Paper: Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads (by Rogan Carr and Elhanan Borenstein)

Here is another post in my “Story Behind the Paper” series where I ask authors of open access papers to tell the story behind their paper.  This one comes from Rogan Carr and Elhanan Borenstein.  Note – this was crossposted at … Continue reading

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Discussion of new pathogen discovery papers

Interesting discussion yesterday with authors of new pathogen discovery papers. I will try to write more about this later but am heading out the door so this Storify will have to do for now. //storify.com/phylogenomics/discussion-of-pathogen-discovery-papers/embed?border=false//storify.com/phylogenomics/discussion-of-pathogen-discovery-papers.js?border=false[View the story “Discussion of pathogen … Continue reading

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CAMERA metagenomics resource is shutting down

Just got this email and thought it would be of interest to many out there. Thank you for being a CAMERA user during its operation as a resource forenvironmental genomics. During the past few years, CAMERA has been able tooffer … Continue reading

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Bad microbiology reporting of the month award: C-Net on IBM "Sequencing the City" meeting

Well, I am still really annoyed by this unbearable article on C-Net yesterday: IBM sees big opportunity in sequencing microbes by Daniel Terdiman.  The article is about this “Sequencing the City” meeting organized by IBM that was on Tuesday and Wednesday.  I … Continue reading

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Mini journal club: staged phage attack of a humanizes microbiome of mouse

Doing another mini journal club here.  Just got notified of this paper through some automated Google Scholar searches: Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut Full citation: Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & … Continue reading

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Who are the microbes in your neighborhood? Quite a few are from Melainabacteria – a new phylum sister to Cyanobacteria

I just love this paper … The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | eLife from the labs of Ruth Ley and Jill Banfield (1st author is the co-first authors are Sara … Continue reading

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Great use of metagenomic data: community wide adaptation signatures

OK I have been dreaming about doing something like this for many years.  One of the potentially most useful aspects of shotgun metagenomic data is that you get a sample of many/all members of a microbial community at once.  And … Continue reading

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