Tag Archives: archaea

Mendeley groups on environmental PCR, metagenomics, and microbial eukaryotes

As part of my NSF Research Coordination Network grant (RCN EukHiTS), I am currently managing a number of Mendeley groups that amalgamate relevant journal articles on different topics related to environmental PCR, metagenomics, and microbial eukaryotes. These groups are open … Continue reading

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Twisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium

Well, this is one of the bigger screw ups in terms of evolution I have seen at a major journal in a while.  See the following paper in Nature: The catalytic mechanism for aerobic formation of methane by bacteria : Nature. … Continue reading

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Seminar “Gene Regulatory Networks in Archaea” Marc Facciotti, 3/1 11 AM Genome Center 4202

The Genome Center Biological Networks Seminars present: Date: Friday, March 01st , 2013, 11am – 12pm Location: 4202 GBSF ”Gene Regulatory Networks in Archea” Speaker: Marc Facciotti, PhD Assistant Professor, University of California, Davis http://www.bme.ucdavis.edu/facciotti/ For more information regarding the … Continue reading

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Guest post from Kimmen Sjölander about FAT-CAT phylogenomics pipeline

Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru.  Announcing the FAT-CAT phylogenomic annotation webserver. FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and … Continue reading

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Worth a read: Jim Staley on a "Universal Species Concept" and the history of microbial species concepts

Interesting paper came up in my automated google searches for “phylogenomics”: Transitioning Toward a Universal Species Concept for the Classification of all Organisms | InTechOpen.  It is by Jim Staley who has been writing a lot about microbial species concepts in … Continue reading

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RIP Carl Woese: Collecting posts / notes / other information about my main science hero here

My tribute to Carl Woese 12/30/12 Sadly, Carl Woese has passed away.  I am collecting some links and posts about him here in his memory.  He was without a doubt the person who most influenced my career as a scientist. … Continue reading

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Welcome to the Microbial Earth Project

Map of type strains. All interested in microbes and their genomes should check out The Microbial Earth Project.  It “is an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. The … Continue reading

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Get the genomes of up to 12 type strains of bacteria and/or archaea sequenced, for free

Barny Whitman asked me to post this announcement and, well, I am.  I made one edit below (see strikethrough) in honor of Norm Pace. Genomic Sequencing of Prokaryotic Bacterial and Archaeal Type Strains The Community Sequencing Program (CSP) Quarterly Microbial call … Continue reading

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New publication from members of my lab (e.g., @ryneches) & lab of Marc Facciotti on ChIP-seq based mapping of archaeal transcription factors

New publication from members of my lab and the lab of Marc Facciotti on a workflow for ChIP-seq based mapping of archaeal transcription factors. The paper includes a description of new software from Russell Neches in my lab called pique … Continue reading

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New publication from Lizzy Wilbanks, Russell Neches, et al

New publication from members of the lab in Nucleic Acids Research: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. Congrats.  Gonna have to make some new jam …

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