Journal Club at #UCDavis on Co-evolution of Microbiomes and Hosts – ideas wanted

I am going to be running a journal club this quarter at UC Davis for the Population Biology Graduate Group.  The topic is Co-evoution of Microbiomes and Hosts.

Meeting time is 12:10-1:00 PM if you want to participate let me know.

A link to the Draft Outline is here. And I am trying to embed it in this post … 

If anyone has other ideas for interesting papers on co-evolution of microbiomes and hosts, please let me know and I will add them to the list. Stay tuned as each week I will post about the discussion topics and notes from the discussions.

Using Social Media to Promote Your Research (workshop)

I’ll be running a social media workshop next Friday in the Genome Center – anyone on campus is welcome to attend! Details as follows:

Using Social Media
to Promote Your Research

Friday, February 7, 2014
Room 4202, Genome Center

Many view social media as either a fun distraction, a waste of time – or both!  But social media tools can be a tremendous resource for academics seeking to share their research, find new collaborations, and ultimately advance their careers.

Attend this workshop to learn how to:

  • Use social media to share and promote your research
  • Identify appropriate audiences and avoid pitfalls
  • Choose the right platforms to help you achieve your goals

Please pre-register using this online form: (Pre-registration will help to guide the format of the workshop and the type of social media tools covered)

PDF Flyer available here

Fall 2013 Graduate Course in Applied Ecological Genetics: ECL242 / PHR242

Thought this might be of interest


Dynamic graduate level course in ecological genetics offered Fall 2013 at UC Davis.

Applied Ecological Genetics:
Genetics and Genomics for Ecology, Health, and Conservation of Natural Populations

Making genetics friendly and accessible.
This course is an introductory course to the topic for graduate students…and yet packed with great information.

Ecology and Pop Bio grad students sign up for ECL242 CRN 29983
Grad students in all other grad groups sign up for PHR242 CRN 46002 

3 units
10:00-11:50 Wed and Fridays Fall quarter 2013
Instructor: Holly Ernest

For graduate students in any graduate group interested in applications of genetics/genomics for ecology, conservation biology, and natural systems management.  Space as available for post-docs, project scientists, and others.

More info:

Great course for students interested in:
• building skills and knowledge to develop the best questions and approaches for ecological genetic and genomics projects
• gaining knowledge in ecological and conservation genetics/genomics for a career in wildlife and natural resource agencies, nonprofit organizations, and academic institutions.  Genetics and genomics is increasingly a key conservation tool.
• evaluating published genetic analyses for ecological questions and management applications.
• applicable to fields including, but not limited to, conservation ecology, population biology, wildlife health, disease ecology, avian science, plant biology, anthropology, entomology, veterinary medicine, and others.


1. Students will gain understanding of the scope and breadth of genetic/genomic applications for research and applications in ecology, conservation management, and wildlife population health.
2. Students will become familiar with concepts of laboratory and computational techniques commonly used for ecological genetics research.
3. Students will become familiar with key theory underlying genetic data analysis for ecology.
4. Students will gain knowledge and skills in development of well-designed questions, hypotheses and research projects, basic data analysis techniques, and problem-solving in the field of ecological genetics.

• Sampling techniques and strategies
• Molecular markers and lab techniques: including next generation sequencing, whole genome, microsatellites, mitochondrial DNA, etc
• Data analysis
• Study design
• Genetics of endangered species; invasive species
• Introductory material for Ecological genomics – future courses will be offered by Ecology faculty in this area.  ECL242 will help set the foundation for the more advanced genomics courses.
…and much more! … covered in lecture, computer lab, and discussion

Special Guest speakers and sessions tentatively on schedule
• Computer lab sessions: intro to computational aspects of work with genetic data, genotypic data, sequence data;
• Genome research specialists lined up to tell us about: genomics of wild ancestors of crop plants, insects that are key disease vectors, polyploid fish, birds of conservation concern, endangered mammals, genomics and ecotoxicology, etc
• UCD Genome Center talk and tour

Note that this course will likely be one of the core courses for Ecology Grad Group’s proposed new Area of Emphasis (AOE) in Ecological Genetics and Genomics

QIIME workshop at UC Davis (May 2-4, 2013)

UC Davis will be hosting a 2.5 day QIIME workshop following the SMBE Satellite Meeting on Eukaryotic -Omics, running Thursday afternoon May 2nd through Saturday May 4th. Meeting participants and local Bay Area researchers are encouraged to attend.

Due to space constraints, this workshop will be strictly limited to 32 participants.

Click here to complete the application form (form closes March 22, 2013, and this deadline will not be extended)

APRIL WORKSHOP: Phylogenetically correct stats for evolutionary ecologists (RSVP needed)

From CPB Postdoc Luke Mahler:

Dear Davis Ecologists and Evolutionary Biologists,

This Spring Quarter, I’ll be delivering my CPB Postdoctoral Fellowship Workshop, which will be entitled:

“Phylogenetically correct analysis of species data in ecology and evolution”.

This workshop will consist of 3 sessions, to take place over three days:

April 2: 4:10PM-5:30PM (lecture; note this will be the CPB seminar for this week)
April 3: 11:00AM-1:00PM (tutorial 1 – feel free to bring your lunch)
April 4: 1:00PM-3:00PM (tutorial 2)

The format of this workshop will be an introductory lecture followed by two hands-on R tutorials.

In the lecture, which will take place during that week’s CPB seminar slot, my goal is to (1) review why it’s important to account for phylogeny during data analysis, (2) briefly introduce a suite of current methods for doing so, and (3) critically discuss the inherent assumptions and limitations of phylogenetic comparative methods, outlining best practices for conducting basic analyses.

In tutorials, I will lead participants in a series of computer exercises (all in R) designed to provide hands-on experience implementing the most commonly used phylogenetic statistical analyses. In the first tutorial, participants will learn how to prepare and import phylogenetic trees and species data set for analysis, how to visually explore these data, and how to measure phylogenetic signal and select an appropriate model of trait evolution. In the second tutorial, we’ll conduct a number of phylogenetic statistical analyses with a focus on linear models and principal component analysis. We’ll discuss parameter estimation and interpretation under these models, and will cover techniques for assessing sensitivity of results to phylogenetic uncertainty.

The target audience for this workshop are scientists at any stage who are familiar with phylogenetic trees but don’t necessarily have specialized knowledge about how to work with trees when analyzing ecological or other comparative data. No prior experience using R is necessary, although attendees will need to bring their own laptops, and will need to install R in advance of the workshop (it’s free). Attendees do not need to bring data files – we’ll analyze example data sets which I will provide. Faculty, postdocs, and students are all welcome to attend.

If you are interested in attending this workshop, PLEASE CONTACT ME BY EMAILING We haven’t decided yet where to hold the workshop – this decision will be based on anticipated attendance. We’ll do our best to secure a room that can accommodate everyone who interested in attending, but can’t guarantee there will be room for you if you don’t let me know in advance.

Thanks, and I hope you can make it.

Luke Mahler

Center for Population Biology Postdoctoral Fellow
2320 Storer Hall
University of California, Davis
One Shields Avenue
Davis, CA 95616, USA

Bionformatics Workshops at UC Davis Genome Center

From the UC Davis Genome Center

Our RNASeq Bioinformatics Analysis Workshop has reached its capacity. However, we still have a few seats open for two other workshops. We will be offering our 5th annual week-long Next Generation Sequencing Data Analysis Course on Sept. 10 – 14, 2012. More information will come later at our training website

The workshops this year will focus on hands-on and problem solving skills in addition to lectures on basic concepts and terminologies.
The topics are:
1. (FULL) RNASeq Bioinformatics Analysis, May 21-22, 2012 (No prior programming experience necessary)
2. (2 Seats) Data Analysis and Visualization using R, May 23-24, 2012 (Basic programming experience required)
3. (6 Seats) Cloud Computing for Bioinformatics, May 29-30, 2012 (Basic programming experience and system administration knowledge required)

More information can be found at

New Course=> PHA 250 Functional Genomics: from Bench to Bedside


PHA250: Functional Genomics: from Bench to Bedside
CRN: 84839
Spring 2012
Tuesdays/Thursdays 9:00-10:30am
Location: Tupper 2133

Instructor of Record (IOR): David Segal

COURSE GOALS AND ORGANIZATION: The purpose of the course is to familiarize
students with topics in Functional Genomics, with an emphasis on clinical
relevance and applications (e.g., genetic variation and disease, cancer
therapeutics, and biomarker discovery). Specific topics that will be covered
include detection of altered gene sequences, and measurements of the changes
in chromatin and RNA that occur in human diseases. Technologies that will be
covered include DNA and RNA microarrays and next generation sequencing
methods. Other topics will include data visualization and interpretation.
The overall goal of the class is to provide an overview of the cutting edge
technologies currently being developed in basic science laboratories, and
illustrate how these technologies can be used to improve public health.
Students will actively participate in group presentations. There will be
four guest lecturers who will add breadth to the program.

PREREQUISITE: Permission of Instructor
UNITS: 3 U (letter grade)


EVE198 / EVE161 Microbial Phylogenomics Course Spring 2012


EVE 198 – Spring Quarter 2012 – CRN 74485 – 3 units P/NP grading

Microbial Phylogenomics:  The Evolutionary Diversification of Microbes and their Genomes

Professor Jonathan Eisen



TR 1:40-3:00pm

Room 1344 Storer Hall

 Prerequisites for this EVE 198 / Jonathan Eisen course are BIS 2ABC (or its equivalent, for transfer students). (This course is moving through the course approval process, and will eventually be EVE 161!)