Who are the contaminants in your sequencing project? (crosspost from #microBEnet)
This was originally posted on microBEnet: Who are the contaminants in your sequencing project? Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination occurring in some other material added to the PCR reaction. Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs. But if that does not happen, it is possible to try to detect contamination after it has happened. Below I post some papers related to post-sequencing detection of con...
Source: The Tree of Life - August 1, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Bat tour at Yolo Basin Wetlands
Did our second evening bat tour at the local Yolo Basin Wetlands last night. It was very nice. They start off with a lecture and bat introduction at the Visitor Center and then a convoy heading out to the wetlands and drove way way into the back (the side near Sacramento) to just next to the causeway. Then we waited until sunset and out came the bats. Thousands and thousands of them. It was cool. Here are some videos and pics. And also some responses to my Tweets about it.10 grams worth of mosquito eating mammalian cuteness pic.twitter.com/Bo90MJc82W— Jonathan Eisen (@phylogenomi...
Source: The Tree of Life - July 26, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
How do journals like this even exist? Lovely spam! Wonderful spam!
Just got this email. I consider this almost unquestionable proof that this is a spam open access journal (e.g., I don't do any work in this field ..)Dear Dr. Jonathan A. Eisen,Greetings from the Journal of Immunology and Immunotherapeutics!!!At the outset, it’s your eminence & reputation in the quality of research field for which you have been invited to become Editorial Board member for our Journal. We are aware of your reputation for quality of research and trustworthiness in the field of “Immunology and Immunotherapeutics” and that is why you are being requested to be an Editorial Board Member of o...
Source: The Tree of Life - July 24, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM
Just got this invitation. I have edited it to remove some of the identifying factors since I think the specific details do not matter.Dear Dr. Eisen: I am writing to invite you to present a lecture in the endowed XXXX Lecture Series at XXXX Univsersity. The XXXX Lecture is a platform to allow leaders in the areas of XXXX to communicate research advances to a general audience. Recent speakers include XXXX and XXXX and XXXX. For your talk, we were hoping you could discuss advances in understanding human microbiomes and their significance to health. I think this is an enormously important ar...
Source: The Tree of Life - July 21, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Is this a new form of #OpenAccess Spam - spammy blog comments pointing to Bentham
Well, this is very very weird and not sure what to make of it. In the last week the filter that Google runs for Blogger Comments has picked up a slew of highly spammy comments coming from one account. And all of the comments include a link to Bentham Science publishers - one of the annoying Spammy new publishers. See some of them below (note I have removed the links to Bentham but trust me, this went to a Bentham site). Anyone else getting Spam comments pointing to Bentham? Jesica Mack has left a new comment on your post "Science SPAMMER of the month: OMICS publishing gro...": For me it has been a s...
Source: The Tree of Life - July 12, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Paper of interest: Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease
For those interested in microbiomes it is definitely worth looking at this paper: BMC Genomics | Abstract | Whole genome and exome sequencing of monozygotic twins discordant for Crohn's diseaseSimple summary - they have sets of identical twins where one twin has Crohn's and the other does not. They looked for somatic mutations that could like the ones with Crohn's and did not find any. Sure - a negative result. Could be anything. But the next obvious thing to do (which they report they are already doing) is to look at the microbioata in these people. Alas, they probably do not have data f...
Source: The Tree of Life - July 10, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Fun times with whooping cough in #DavisCA
Just got this email. I have removed the specific sender / facility since that does not seem needed for my purposes here. I have replaced the name of the site with "Our Facility". Anyway - thought some people would be interested in the things that can happen when too many people in your community do not vaccinate their kids. From: Office Administration Subject: Possible Exposure to Whooping Cough - PertussisDate: June 25, 2014 at 12:55:59 PM PDTTo: Office Administration Dear Parent or Guardian,Our Facility was informed this morning that a student who has been attending a class since...
Source: The Tree of Life - June 25, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Hawk moths in my yard in #DavisCA
(Originally posted on my DavisCalifornia blog but I am consolidating blogs now so moved it here).Just a few pics I got tonight ... finally learning how to use my flash.Photos taken with a Nikon D90 camera, Speedlight SB-910 flash and a Nikkor AF-S 105 mm Micro lens.
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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 - June 15, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Hawk moths in my yard in #DavisCA
Just a few pics I got tonight ... finally learning how to use my flash. Photos taken with a Nikon D90 camera, Speedlight SB-910 flash and a Nikkor AF-S 105 mm Micro lens.
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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 - June 15, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Please make it stop - overselling the microbiome award for rugby, exercise, microbiome stories
Well, I think today's lesson is, many people, including many scientists and science reporters, just do not get that there is a difference between correlation and causation. I know - this is like beating a dead horse since many write about this issue. But it just needs to be called out every time until it stops. And today's fun comes from stories and the original research articles about how exercise supposedly alters the gut microbiome. I was pointed to this just a few minutes ago on Twitter:Seems like more appropriate title would b "rugby players have different diets" http://t.co/nzNsnHCYtA @phylogenomics...
Source: The Tree of Life - June 10, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Discussion of new pathogen discovery papers
Discussion of pathogen discovery papers" on Storify]
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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 - June 6, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
ASUCD (Associated Students, #UCDavis) Excellence in Education Awards
Very proud of this. I was a finalist in the "Excellence in Education" awards given out by the UC Davis Undergraduate group ASUCD Associated Students, University of California, Davis. And David Coil, Project Scientist in my lba was another finalist. The award for my college (College of Biological Sciences) went to Jay Rosenheim, who is a great teacher, so no shame in losing to him.Just got back from @ASUCDofficial Excellence in Education awards - check out @davidacoil - one of the finalists pic.twitter.com/AMOztcwApx— Jonathan Eisen (@phylogenomics) June 3, 2014 Oh and here is another finalist for the @ASUCDoffici...
Source: The Tree of Life - June 4, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
Love this - The Aggie Transcript #UCDavis Undergraduate Life Sciences Journal
I just love things like this: The Aggie Transcript | An undergraduate life sciences journal at UC Davis. From their site:The Aggie Transcript is is a forum for undergraduate UC Davis students to share news, original writing, and art related to the life sciences.Here are some recent posts:Mapping neurons through online gaming by Jenny CadeEvolution of Tooth Ename by Marisa SanchezNew Target For Alzheimer’s Treatment by David IvanovIs your spit making you fat? by Daniel FriedmanViral Evolution by Ashlee ChangThe hunter-gatherer gut microbiome by Jenny CadeWhat a great idea.
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Source: The Tree of Life - May 31, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
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 a number of important community resources, including an exceptionallywell curated environmental genomic database, the ability for researchers todeposit molecular sequence datasets with associated environmentalparameters (metadata), open access to computational resources to enablemetagenomic comparisons, educational resources, and helpdesk services.These efforts have been funded through the Gordon and ...
Source: The Tree of Life - May 28, 2014 Category: Medical Scientists Authors: Jonathan Eisen Source Type: blogs
