Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Quick post – Nature Publishing Group buys into #OpenAccess publisher Frontiers

In case you have not hear – Nature Publishing Group continues to play around with open publishing and other open science initiatives (when they switch some of their big journals to fully OpenAccess I will stop referring to it as playing around …).  The latest is that Nature has bought into the Frontiers publishing group which publishes a series of Open Access journals.  For more on this see:

Hat tip to many people who have sent this info to me.  Not 100% sure what to make of it, but it is interesting …
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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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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 seminar series, upcoming talks and how to subscribe in our mailing list, please visit http://www.bionets.ucdavis.edu/

Halophiles 2013 Conference

Forwarding this:

Dear colleague,

You are cordially invited to participate and submit an abstract to the 10th international congress on halophilic microorganisms – Halophiles 2013, which will be held on the campus of the University of Connecticut, Storrs from June 23rd – 27th 2013.

This conference will bring together an exciting cohort of scientists from many fields of halophile research including but not limited to biodiversity, evolution, ecology, astrobiology, biogeochemistry, biochemistry, physiology, protein structure/function, genetics, genomics, metagenomics, and biotechnology.

Please visit our website for more details. www.regonline.com/halophiles2013

Key Dates:
Deadline for Abstract Submission – April 30th
Deadline for canceling with full refund – May 24th
Deadline for canceling 50% refund – June 7th

Please, kindly forward this invitation to your colleagues.

Sincerely,
Thane Papke, Organizing Chairpeson

The Xtranormal Case for OpenPub (from Jarrett Byrnes of OpenPub and NCEAS)

From Jarrett Byrnes as part of the OpenPub working group at NCEAS

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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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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 for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea — and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately). 

FAT-CAT is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.
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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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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 the last few years.  In addition to trying to bridge the gap between bacteria/archaea and eukaryotes in terms of species concepts.  Not sure how I feel about everything in the paper but it has a really nice history of how species have been defined for bacteria. He breaks down this history into four periods

  • Discovery of microorganisms,
  • Advent of pure cultures and phenotypic features,
  • Introduction of molecular analyses and
  • Gene sequencing and genomics.
And goes through a bit of detail on each one.  He also discusses what he sees as a need for a universal species concept and even makes some suggestions about how it might be implemented.  Definitely worth a read.  
Some related posts of mine and or links of potential interest:
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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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#DavisCA lockdown update

The following is a joint communication from the Davis Police Department and Davis Joint Unified School District.
On February 21, 2013, at approximately 10:25 am, the Davis Police Department received a call from administrators at Davis Senior High School reporting a male subject possibly armed with a handgun north of the library parking lot. As a precaution, four schools were placed on lockdown: Davis Senior High School; North Davis Elementary School, St. James Elementary School, and King High School. There is no information to indicate that the subject was ever on any of the campuses in the immediate area. The lockdown lasted approximately 35 minutes.
Officers responded and detained a male subject matching the description provided by the reporting party.  Through the course of the investigation, it was determined that the subject had been in possession of a BB gun, which he discarded prior to police contacting him.
The BB gun was located in the vicinity of where the male subject was detained.
A second subject, who was with the male, was detained as well. Both individuals were released from the scene. Due to the fact that the subject was never on any of the campuses and also never threatened or brandished the BB gun, no criminal charges are being pursued at this time. The Davis Police Department will continue to investigate this incident for any legal recourse.  The male subject is described as being in his late teens and not enrolled at any of the schools.
Anyone with information about this incident is urged to contact the Davis Police Department at 530-747-5400.
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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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#DavisCA lockdown lifted

Just got this email:

The DHS lockdown has been lifted.  I want to thank the students, staff and the Davis Police Department for their immediate and professional response during this time.   Again, all of our students are safe.
Winfred Roberson
Superintendent

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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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#DavisCA schools on lockdown 2/21/13

Just got this email and thought I would post

Your students are safe.  The district received reports that someone was armed in the vicinity of Oak Avenue and B Streets.  The police were summoned and the suspects have been detained.  We want to assure parents/guardians all safety protocols are in place and all precautions were taken.  DHS, North Davis, King High and DSIS schools were on lockdown and have been released.  DHS remains on lockdown pending further investigation.   Additional information will be forthcoming as it becomes available.
Winfred Roberson
Superintendent

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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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NCEAS 3-week intensive workshop in ecological analysis and synthesis

Forwarding this email

Hello NCEAS friends,

The National Center for Ecological Analysis and Synthesis (NCEAS) is
pleased to invite applications from early-career researchers for a 3-week
intensive workshop in ecological analysis and synthesis, to take place at
NCEAS in Santa Barbara CA June 19-July 10, 2013.

All travel and living expenses of participants will be covered during the
workshop, thanks to generous support from the Packard Foundation.

Applications are due March 1. For more information and application
instructions, go to:
http://www.nceas.ucsb.edu/news/nceas-summer-institute-2013

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