Tag: Misc.

Absence of women from Middle East policy debates

For those who think about the underrepresentation of women in science meetings – this may be of interest: The mysterious absence of women from Middle East policy debates – The Washington Post.  65 percent of the events in Washington DC relating to the Middle East had no female speakers.  Disheartening and something that needs to be dealt with.

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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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Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu

I could spend a lot of time on this website: Bioart and Bacteria – The Artwork of Anna Dumitriu.  I found out about it from a Tweet from Dumutriu:

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And it is right up my alley (being interested in the interface between art and science, especially in relation to microbes).  Lots of interesting sections here including:

Sequence
Super-organism
Don’t Try This At Home
[micro]biologies: the bacterial sublime

Modernising Medical Microbiology

And many more.  I do not know much about the artist but really glad she pointed me to this.  

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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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A long (and I think good) listen: Tim Ferriss podcast on "the microbiome"

So – I have been travelling a lot lately.  On one of my trips – to Las Vegas and neighboring areas – I was interviewed by Tim Ferriss for his blog.  Jessica Richman of uBiome was also interviewed – she was in SF, Ferriss was somewhere else, and I was on the phone in Vegas.  As soon as it was over I got caught up in the work I was doing there (field work for a new NSF Funded Project on “microbial dark matter”.  Anyway – the interview was entertaining and I think interesting.  And then it came out while I was on the road again for another trip.  So I am just getting around to posting about it now.  Anway – here are some links for the podcast.

Ferriss’ blog post about it: Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome…

Direct links

I note – I have never done such a long interview for a show before (it was about two hours) but Ferriss was remarkably adept at making it relaxing and fun (for me at least).  Even the part about Jim Watson …

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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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Open Faculty Position, Asst. Professor Microbiologist Plant-Soil Systems

Bayer Crop Science in West Sacramento hiring a Bioinformaticist …

Just got this email

Dear Dr. Eisen

I am a Sr Bioinformatics Scientist working within the Biologics Division at Bayer CropScience. We are looking to fill a Bioinformatics Scientist position here in our West Sacramento facility. We are interested in hiring someone with either a MSc and relevant years of experience or someone with a PhD and 1-3 years of postdoctoral experience. I would greatly appreciate it if you could circulate the attached job position or forward the attached job ad to the appropriate candidate(s).

Many thanks.

Best,
Dilara Ally
Senior Bioinformatics Scientist

Biologics

BioinformaticsScientistII_2014.pdf

UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note – I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the “show”.

 I will try to write more about this later but just one note – I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now – I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

//storify.com/phylogenomics/uc-1/embed//storify.com/phylogenomics/uc-1.js[View the story “Symposium at #UCDavis on new partnership w/ Mars: #UCDavisMARS #GlobalFood” 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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EvoDevo meeting, Clark Kerr, Aug 5-9, 2015

Just got this email from friend and colleague Nipam Patel at Berkeley:
I wanted to bring this meeting to your attention.

Registration is now available for the Evo Devo meeting that will be held at Clark Kerr (Berkeley Campus) from Aug. 5-9th, 2015.

http://www.evodevopanam.org

http://www.evodevopanam.org/meetings–events.html

Registration and abstract deadline is April 1st. People can register now, and abstract submission will probably be available in about a week or so. There will be plenty of slots for students, postdocs, and faculty to speak (chosen from submitted abstracts) and there should be a great poster session as well.

Please pass this information on to anyone else you think might be interested.

Cheers,

Nipam

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-0

The 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 microbiota. We devise and carry out large-scale studies that employ genomic, metagenomic and transcriptomic data sets to understand human pathologies caused by e.g., Mycobacterium tuberculosis, carbapenem resistant Enterobacteriaceae, enterococci and uropathogenic Escherichia coli. We do this in close collaboration with clinical and academic researchers from across the Broad community and around the globe.

We are seeking a creative and highly motivated postdoctoral researcher in Computational Biology.  The ideal candidate should be broadly conversant with bioinformatics techniques for genomic data analysis including metagenomic analysis. They should also be familiar with microbial ecology principles, statistics and have made significant contributions to their area of study.

Responsibilities include:

  • Developing data analysis strategies, writing algorithms and deploying computational tools for the exploration of large genomic, metagenomic and metatranscriptomic data sets
  • Collaborating closely with experimental and computational researchers to interpret analytical results for publication
  • Communicating scientific findings in writing and orally

A Ph.D. in Computer Science, Bioinformatics, Biostatistics, Physics, Biological Sciences or a related field

  • Must be proficient in working in the Unix environment.  Solid coding proficiency in some combination of Python, Perl, Scala, Java, C/C++ and R. Experience with cluster computing and parallelization preferred.
  • Comfort and experience with programming for biological data analysis
  • Demonstrated ability to analyze and interpret metagenomic data
  • Excellent ability to communicate scientific material
  • Excellent collaborative skills and unrelenting enthusiasm for genomic science

EOE/Minorities/Females/Protected Veterans/Disabilities

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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.

——–

Rob Knight at #UCDavis 1/5

The 2015 Hurley Distinguished lecture will be held on Monday, January 5th. Dr. Rob Knight will be presenting a talk on “Dynamics of the Human Microbiome.” This event will be held in Genome Auditorium, 1005 GBSF, from 12:10-1pm.

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 species.  And when I was working at TIGR, an NSF Program Officer approached me asking me to help get the genome sequencing done for this species.  So, well, I did: The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon.  And I became interested in other haloarchaea and eventually started working with Marc Facciotti, in the lab next to mine, in sequencing from across the diversity of the haloarchaea: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response.

Anyway – enough about me.  The whole point here is to point people to a new paper:  BMC Biology | Abstract | Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii , and its use for gene discovery.  Further evidence for the use of Haloferax volcanii as a model species.  Tools continue to become available for genetic and experimental studies in this species.  So – if you are looking for an unusual and interesting organisms to work on – consider working on this species …

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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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