Eisen Lab Blog

#UCDavis Prof. Dawn Sumner video interview on being involved in Mars Curiosity Rover landing

I am getting really excited about the upcoming Curiosity landing on Mars. So cool that Dawn Sumner – Geology Prof. from UC Davis is going to be involved …
 

Also check out:

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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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Holy s$&# – I am going back to #SciFoo

Well, I cannot wait until Friday.  I am going back to SciFoo.  Best.  Meeting.  Ever.  Went in 2006 & 2007.  Changed my life.  Here are some posts – back when I was a very newbie blogger:

2006

2007
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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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Nice new memory efficient metagenome assembly method from C. Titus Brown –

Interesting new #OpenAccess PNAS paper from C. Titus Brown: Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.  Of course, if you follow Titus on Twitter or his blog you would know about this already because not only has he posted about it but he posted a preprint of the paper on arXiv in December.

Check out the press release from Michigan State.  Some good lines there like “Analyzing DNA data using traditional computing methods is like trying to eat a large pizza in a single bite.”

A key point in the paper: “The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory.” This is important because right now most assemblers for genome data use a ton of memory.

Anyway the software behind the paper is available on GitHub here.  Assemble away.

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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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Uggh – Robert Krulwich blogs about butterflies as hybrids resurrecting BS from Williamson

Oh for the love of …

Was browsing Twitter when I saw this:

So I had to check it out.  First I clicked on the link to my blog since I didi not know what post this was referencing.  Uh oh.  It was a post entitled “Just grand -Donald Williamson published more crap on larval “evolution” – this time in one of the #OMICS journals“

Then with dread I clicked on the link to NPR and found a blog post from none other than Robert Krulwich: Are Butterflies Two Different Animals in One? The Death And Resurrection Theory : Krulwich Wonders… : NPR.  In it Krulwich references some book by Bernd Heinrich which itself discusses the theory (if you can call it that) that butterfly and moth metamorphosis represents the death of one organism and the “resurrection” of another.  And furthermore that this is due to a past hybridization event between two species where somehow the genomes merged and the organisms maintained distinct lives linked by the metamorphosis stage.

The problem with this?  Well, a lot of it comes from the ridiculous papers of Donald Williamson, which have been shown quite clearly to be bogus.  Yes, as Krulwich notes, this theory of two species in one “startles” but so does the theory that humans closest relatives are dolphins because they are smarter than chimps.  As does the theory that bacteria are in fact little planets of their own orbiting around animals attracted to them by microgravity.  A theory being startling is a good thing only if the theory is not complete unadulterated crap. http://storify.com/phylogenomics/robert-krulwich-at-nprscience-botches-discussion-o.js?template=slideshow[View the story “Robert Krulwich at NPRScience botches discussion of bogus hybridization story” on Storify]

——–
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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Infectious Disease Genomics and Global Health: Abstract Deadline Extended

Having problems reading this? See a web version.
Infectious Disease Genomics and Global Health
1-3 October 2012

Abstract Deadline Extended: 18 August> Final abstracts and registrations are invited for the fifth Wellcome Trust/Cold Spring Harbor conference on Infectious Disease Genomics and Global Health.

The scientific organising committee encourage abstract submissions as the majority of the conference programme will be drawn from submitted abstracts. Genomic technologies promote cross-fertilisation amongst previously disparate fields, and we therefore welcome abstracts covering any area relevant to the genomics of infectious disease. Please note the abstract deadline has been extended until 18 August. For further details, abstract submission instructions and to register, please visit the conference website.

Scientific organisers
Matt Berriman (Wellcome Trust Sanger Institute, UK)
Jane Carlton (New York University, USA)
Julian Parkhill (Wellcome Trust Sanger Institute, UK)
George Weinstock (Washington University School of Medicine, USA)

Keynote speaker
Peter Hotez (Baylor College of Medicine, USA)
Scientia pro bono humani generis: OMICs in the pursuit of global health and poverty reduction

Epidemiology and public health
Janet Cox-Singh (University of St Andrews, UK)
Plasmodium knowlesi functional genomics – an opportunity to scrutinise malaria pathophysiology
Abdoulaye Djimde (University of Science, Techniques and Technology of Bamako, Mali)
Investigating a potential outbreak of cutaneous Leishmaniasis in Mali

Population genomics
Jonathan Juliano (University of North Carolina, USA)
Understanding within host diversity of Plasmodium falciparum using ultra deep sequencing
Christophe Fraser (Imperial College London, UK)
Predicting multi-drug resistance in the pneumococcus: a co-existential crisis

Parasites and vectors
Chris Plowe (University of Maryland School of Medicine, USA)
Genome-wide studies of clinical resistance of Plasmodium falciparum to artemisinins
Joanne Webster (Imperial College London, UK)
Schistosomiasis in a changing world

Bacteria
Sharon Peacock (University of Cambridge, UK)
Using bacterial genomics to improve global health: opportunities and obstacles
Sebastien Gagneux (Swiss Tropical & Public Health Institute, Switzerland)
Evolutionary forces in Mycobacterium tuberculosis: impact on global control efforts

Neglected tropical diseases
Serap Aksoy (Yale School of Public Health, USA)
Host dependence on symbiome functions: tsetse flies and trypanosome transmission
Sam Kariuki (KEMRI, Kenya)
Endemic tropical disease outbreaks in Africa: application of genomics to our understanding epidemiology and options for targeted control

Viruses
Ian Lipkin (Columbia University, USA)
Microbe hunting in the 21st century
Elodie Ghedin (University of Pittsburgh, USA)
Comparative genomics of virus emergence and transmission

For your diary
Registration deadline: 3 September

Please note: owing to building work at Hinxton, this year’s conference will take place at the Møller Centre, Churchill College – part of the historic University of Cambridge.

Our full events poster is also available for download and updates can be followed on Twitter. Please feel free to forward this information to your colleagues, who can sign up for our regular updates here.
For further information please contact coursesandconfs To unsubscribe from future Scientific Conference updates, email us at coursesandconfs
with the subject line ‘Unsubscribe’.
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The Wellcome Trust is a charity registered in England and Wales, no. 210183. Its sole trustee is The Wellcome Trust Limited, a company registered in England and Wales, no. 2711000 (whose registered office is at 215 Euston Road, London NW1 2BE, UK)

Yes Virginia, even the cervix has a #microbiome ……….. or does it?

Just read over the following paper: PLoS ONE: The Cervical Microbiome over 7 Years and a Comparison of Methodologies for Its Characterization

It is interesting and has lots of tidbits worth looking at in more detail including

  • An analysis of methods for classifying sequence reads as to which organism they likely come from
  • comparison of amplification and sequencing methods
  • long time period covered in the sampling
  • and much more
But what struck me more than anything is that, well, they referred to the microbial community that they were sampling as the “cervical microbiome.”  And though what they discuss here is fascinating in many ways, I am beginning to wonder if every site on the human body (or sites on other organisms) should have its own microbiome.    Or, another way of looking at this is – where do we draw the line between niches?  Is there a eyebrow microbiome?  A left elbow microbiome?  A testicle microbiome?  Certainly, I view the microbes that live in and on people as part of an ecosystem.  But I think just as biomes in the world around us should be defined by – well – something bigger than just GPS coordinates – so too microbiomes should probably be a bit bigger than just the microbes found in a particular body site.  Starting to wonder if we are going to see a proliferation of microbiomes just as we have seen a proliferation of OMIC words.  Ooh — this could give me something new to give an award for.  
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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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My Tree of Life doodle on our food container from dinner at Seasons in #DavisCa

P537
——–
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.

——–

William Shatner, Mars, Curiosity, Rover … fun fun fun

William Shatner narrates video detailing how Curiosity will land on Mars next week http://cdn-akm.vmixcore.com/vmixcore/js?auto_play=0&cc_default_off=1&player_name=uvp&width=512&height=332&player_id=1aa0b90d7d31305a75d7fa03bc403f5a&t=V0xL7FpdMBTgI9wbokivyCDQbYr3dNMyMc Hat tip to Dawn Sumner, UC Davis Geology professor working on Curiosity mission, for pointing me to this. Don’t like that? Well, here is a narration by Wil Wheaton http://cdn-akm.vmixcore.com/vmixcore/js?auto_play=0&cc_default_off=1&player_name=uvp&width=512&height=332&player_id=1aa0b90d7d31305a75d7fa03bc403f5a&t=V0J_fCVbhIlC6m5frWM2NxUQEaE4C8GCK_

——–
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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Posts from #microBEnet that may be of interest

Quick post here – posting links to recent blog posts on the microBEnet blog that may be of interest here.  The microBEnet blog is part of the microBEnet project that I run on microbiology of the built environment.

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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.

——–

Lab meeting August 1st, 2012

James Angus Chandler will be presenting this week for our lab meeting from 1:30 to 3:30pm in room 5206 in the Genome Center.