Eisen Lab Blog

What to do with old Knome exome data …

A little discussion from Twitter More coming but thought I would post this

//storify.com/phylogenomics/old-knome-exome-data-what-to-do-with-it/embed?border=false//storify.com/phylogenomics/old-knome-exome-data-what-to-do-with-it.js?border=false[View the story “Old Knome Exome Data – what to do with it?” 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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Kudos to Dana Devries, Alex Martin, et al. for new cat butt microbe genome report 

Kudos to the students Dana Devries and Alex Martin and to their mentors Holly Ganz and David Coil for their new genome report.  The paper is part of our “cat butt” project.

See De Vries DR, Martin AL, Ganz HH, Eisen JA, Coil DA. 2016. Draft genome sequence of Enterococcus faecalis strain UCD-PD3. Genome Announc 4(6):e01386-16. doi:10.1128/genomeA.01386-16.

Link: Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3

Today at #ucdavis: Solomon Katz: The nutritional significance of the biocultural evolution of cuisine practices: implications for the future of the food system

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UC Davis
Department of Food Science & Technology Special Seminar
Tuesday, December 6, 2016
2:10 PM
Sensory Theater
Robert Mondavi Institute

Solomon Katz
Emeritus Professor of Anthropology
University of Pennsylvania

“The nutritional significance of the biocultural evolution of cuisine practices: implications for the future of the food system”

ABSTRACT: Over the last two decades there is substantial evidence that a coevolution occurred between the Neolithic rise of agriculture and the social routinization of cuisine practices. This coevolutionary process involving our cultures, genomes and microbiomes allowed a relatively small number of highly productive crops to replace the much broader pre-Neolithic diet with a series of exo-digestive food processing technologies that provided the necessary transformations to maintain the nutritional balance of our agricultural diets. This seminar tracks these evolutionary processes and their implications for the contemporary human diet as humanity adapts to rapidly changing demands on our food system over the remainder of this century and beyond.

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TODAY at #UCDavis Nels Elde on “How pathogenic microbes shape host cells and genomes”

Today at 4:10 pm in 1003 Giedt Hall Nels Elde (University of Utah) will be delivering this week’s Ecology and Evolution Seminar Series.

From his website, “The Elde lab uses host-pathogen interactions to study the evolutionary process and evolutionary approaches to understand the selective forces shaping cellular pathways.”

Today, Nels will be speaking on How pathogenic microbes shape host cells and genomes.

#UCDavis CPB Seminar: Vince Buffalo Using the footprint of linked selection to estimate quantitative genetic parameters

CPB Seminar Reminder for Tuesday, November 29, 2016, 4:10pm in 1022 Life Sciences

Speaker: Vince Buffalo
Graduate Student, Population Biology Graduate Group, Coop Lab, UC Davis
Title: “Using the footprint of linked selection to estimate quantitative genetic parameters”
Host: Graham Coop

10/31 at #UCDavis – Priscilla Cooper on DNA repair pathway crosstalk in maintenance of genome stability

Cooper 10_31.pdf

Wed Nov 2 at #UCDavis – John Roth on “Mutation, selection, and the tyranny of the obvious”

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. John Roth

"Mutation, selection, and the tyranny of the obvious"

Wednesday, November 2, 2016

4:10 pm

1022 Life Sciences

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Roth 11-2-16.doc

A gloomy day at the #UCDavis Genome Center Halloween Symposium – a model for a #manel #yammm

It is a gloomy day, at least for me, at #UCDavis today.

Yes it is raining and cloudy.  But that is not the gloomy part. I like rain and clouds and we don’t get enough of either around here. The issue for me is the Symposium happening today in my building.  Run by the UC Davis Genome Center, which I am a part of.  What is the problem?

Well here is the flier


That is nine presenters.  Eight of which are men. 

  • S. Dinesh-Kumar
  • Brett Phinney
  • Anthony Herren
  • Jessica Franco
  • Jack Cuniff
  • John Yates
  • John Muchena
  • Ilias Tagkopoulos
  • Nuno Bandeira
That comes to 11% female speakers.  Not a good ratio.  But you know this is just one sample right?  It could be a random anomaly, or something else.

So – lets look at last years Halloween symposium.

That is five speakers, all men.


  • Mingcheng Luo UC Davis
  • Chris Streck 10X
  • Marco Blanchette Dovetail
  • Matthew Seetin PacBio
  • Matthew Settles, UC Davis
Four speakers. All male.
2014

  • Bruce Draper UC Davis, Molecular and Cellular Biology
  • Bruce Conklin, Gladstone Institute of Cardiovascular Disease, UCSF
  • David Segal, UC Davis, Genome Center
  • Dana Carroll, University of Utah, Department of Biochemistry
So over the last three years we have 94% male presenters. It is a better if you go back further. 2013 was 50-50.  2012 was  ~ 70-% male.  2011 was  55:45 or so.  But over the last three years something has devolved.  And no, I will not be attending.  And yes, I have made comments about this, but maybe too few.  
It is so frustrating to keep seeing this happening over and over in academia and science.  And to see it so close to home, well, it is really extraordinarily disappointing. 
I sent the organizers which I think has some great examples of how to run a diverse meeting.
Below are some articles worth looking at on the topic. 

I certainly feel partially responsible for this, because it is in my building and run by my Center.   Now I had nothing to do with this even, but still …  I will do my best to make sure this does not happen ever again at the UC Davis Genome Center.  But I will not be attending this year’s meeting.  
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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.

——–

Today at #UCDavis: Virginia Walbot “Building a Maize Anther using Cell-Cell Signaling.”

Plant Biology​ ​
Graduate Group​ ​
Seminar Series

Oct 21 – 12: 10 LSA 1022

Virginia Walbot (Stanford University)

“Building a Maize Anther using Cell-Cell Signaling.”

Bayer-Grad Scholar-MicrobialGenomics/Machine Learning Opening Available

Got forwarded this:

We have a Grad Scholar opening available at Bayer in our West Sacramento, CA location. Job description attached.

Link: https://career.bayer.us/en/job/Graduate-Scholar-Microbial-Genomics-Machine-Learning–0000175538.html

Grad SchBLX_Bionformatics_09062016_Description – revised.docx