Postdoc position in Computational Biology / Infectious Disease w/ Ashlee Earl at the Broad
My friend, the brilliant Ashlee Earl is recruiting a post doc ... posting this for her.POSTDOC – COMPUTATIONAL BIOLOGIST (INFECTIOUS DISEASE)Requisition Number: 1571 http://www.broadinstitute.org/careers/job-openings/job-openings-0The goal of the Bacterial Genomics Group at Broad is to develop and implement genomic and metagenomic methods to answer pressing questions related to bacteria and their role in human health. Specifically, we seek to understand the evolution and spread of bacterial pathogens (and antibiotic resistance) including the interactions that these pathogens have with their host and host-associated micro...
Source: The Tree of Life - January 9, 2015 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Haloferax volcanii, model archaea, and me
When I was a graduate student I was looking around for an extremophile - especially an evolutionarily novel one. And I settled on this species Haloferax volcanii - a model halophilic archaeon largely because Ford Doolittle and colleagues had started to turn it into a genetic model organism (and because Patrick Keeling, from Ford's lab convinced me it was a good thing to do). So I started work on this species - doing DNA repair studies in the lab. See my PhD thesis for some of the work I did which I never published outside of the thesis for multiple reasons. But I continued to be interested in this s...
Source: The Tree of Life - January 2, 2015 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Really shameful overselling the microbiome from the American Society for Microbiology regarding lupus
Well, this press release is from October:Study Suggests Altering Gut Bacteria Might Mitigate Lupus But I just discovered it and it definitely deserves an award. An Overselling the Microbiome Award. The PR, sadly and amazingly from the American Society for Microbiology which should know better, discusses a paper from the ASM Published journal Applied and Environmental Microbiology. The PR does an OK job discussing what was in the paper - a study of the microbiome in mice including those that are a model for lupus. The researchers characterized the microbiome is mice with and without the lup...
Source: The Tree of Life - January 1, 2015 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Quick post: Viruses - don't forget about the viruses
OK OK. Everyone, everywhere keeps telling me "Viruses - don't forget about the viruses" whenever I talk about microbial communities or discuss work we are doing in my lab. Yes, I say "I know, I know" but then I panic and think "We can't even deal with the diversity of bacteria and archaea out there. We generally ignore the microbial eukaryotes. How the hell are we going to include viruses too?" But, in the end, if we are going to study microBIOMEs (as in, ecosystems that include viruses), then, well, we need to include all the players.(I note - as I am writing this, my son asked me what I am d...
Source: The Tree of Life - December 27, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Paper of possible interest: Exploring interactions of plant microbiomes
Just got alerted to this new (open access) paper that seems like it should be of interest to those working on plant microbiomes Scientia Agricola - Exploring interactions of plant microbiomes. It has some useful summaries of work that has been done on plant microbiomes.
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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Source: The Tree of Life - December 26, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
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 concept and in many aspects to a paper we published in PeerJ earlier in the year (see Beitel et al., 2014 Beitel CW, Froenicke L, Lang JM, Korf IF, Michelmore RW, Eisen JA, Darling AE. (2014) Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing...
Source: The Tree of Life - December 24, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Buzzfeed includes microbiomes in "77 facts" but alas, gets the facts (and the math) wrong
Well, I admit it - I clicked on this Buzzfeed link someone posted on Facebook - 77 Facts That Sound Like Huge Lies But Are Actually Completely True. There are some pretty funny and interesting things on the list. However, I note - I did not click on the link per se for entertainment. I clicked on it to see if there was anything about microbes on the list. And happily, there was. Alas, what there was, was, well, a bit wrong:Let's start with #67. "There is 10 times more bacteria in your body than actual body cells". Well, alas, this is a nice bit of information. But it is...
Source: The Tree of Life - December 23, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Crosspost - papers for sale
Crossposting from ICIS Blog (even though this is short - always good to reveal where things are posted first).Well, this is much more elaborate than I could ever have imagined: For Sale: “Your Name Here” in a Prestigious Science Journal – Scientific American. Seems that there are services out there to help people write, in essence, bogus scientific papers filled with pithy somewhat reasonable sounding phrases about certain topics. Seems we could all use some more comprehensive full text analyses of papers to try and flag such activities.
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evo...
Source: The Tree of Life - December 21, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Great idea from Nicole King - Lists of Women Speakers - more examples wanted
Just been pointed to this compilation from Nicole King (a brilliant professor at Berkeley): Lists of Women Speakers | The King Lab.She has put together a collection of a few links:As a resource for those who are interested in increasing the number of female speakers at their scientific conferences, seminar series, etc., I offer here a compendium of female speakers from diverse fields. I've started with lists that I could find easily, but if you know of additional lists, please feel free to send along the links. I would also be happy to maintain similar lists for underrepresented minorities if any such list...
Source: The Tree of Life - December 18, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types
A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition): The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets.Basically, Angela prepared meals for these three dietsFood was purchased and prepared in a standard American home kitchen by the same individual using typical kitchen cleaning practices inclu...
Source: The Tree of Life - December 10, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Some history of hype regarding the human genome project and genomics
Just taking some notes here - relates to a discussion going on online. Would love pointers to other references relating to hype and the human genome project (including references that think it was not overhyped). I note - see some of my previous posts about this issue including: Human genome project oversold? sure but lets not undersell basic science and various Overselling Genomics awards. Here are some things I have found:White House press conference on announcing completetion of the human genomeGenome science will have a real impact on all our lives -- and even more, on the lives of our children. I...
Source: The Tree of Life - December 6, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Some notes on "Citations for Sale" about King Abdulaziz University offerring me $$ to become an adjunct faculty
This article stemmed from a blog post by Lior Pachter. I was interviewed by the Daily Cal reporter about this because I had sent Lior some of the communications I had had with people from KAU where they tried to get me to do this.I am posting here some of the email discussions / threads that I shared with Lior and Megan.Thread #1.Here is one thread of emails in which KAU tried to get me to become an Adjunct Professor. I have pulled out the text of the emails and removed the senders ID just in case this would get him in trouble.Received this email 3/6/14Dear Prof Jonathan, How are you? I hope every thing is...
Source: The Tree of Life - December 5, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
A night with Matt Groening and the importance of faeces, feces and faces
So - I participated in a fundraiser for Emily Levine's "The Edge of Chaos" film a week ago. And one of the key guests was Matt Groening. Not only did I get to hang out with him and discuss fecal transplants with him (really) but I had a front row seat to Matt discussing the history of how he came up with the general outline of the Simpson's characters.And in addition to this being just awesome to witness, one part of it struck me. See the video below and in particular the part that struck me was the beginning: Groeningbasically said that only a few simple changes in faces can be recognized by people very easily...
Source: The Tree of Life - November 24, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Whole issues of Genome Biology/Genome Medicine on "Genomics of Infectious Disease"
Wow this has really got some nice papers: BioMed Central | Article collections | Genomics of infectious diseases special issue. I note - this goes well as a follow up to the series I co-coordinated in PLOS a few years back: Genomics of Emerging Infectious Disease - PLOS CollectionsFrom their site:Infectious diseases are major contributors to global morbidity and mortality, and have a devastating impact on public health. The World Health Organization estimates that 1 in 3 deaths worldwide are due to an infectious disease, with a disproportionate number occurring in developing regions. While the completi...
Source: The Tree of Life - November 23, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Strangest microbial headline of month: Bacteria on Russian ‘sex satellite’ survive reentry
There is really not much to say other than to point everyone to this article: Bacteria on Russian ‘sex satellite’ survive reentry | Science | The GuardianIt defininely wins the strangest microbial headline of the month. The article restates some of the silly claims about how what they are finding supports panspermia .. but ignore the article and just enjoy the headline.
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
-------- (Source: The Tree of Life)
Source: The Tree of Life - November 22, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
