11/3 at #UCDavis: Dr. Sarah Mathew “The Evolution of Large Scale Cooperation in Humans: Insights from Turkana Warfare”

Evolutionary Anthropology Colloquium Series
Mondays at 4:10 pm in 273 SS&H

November 3rd:
The Evolution of Large Scale Cooperation in Humans: Insights from Turkana Warfare

Dr. Sarah Mathew
School for Human Evolution & Social Change
Arizona State University

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La Biology and Mathematics in the Bay Area (BaMBA) at #UCDavis 11/22

Got this in the old email tubes (note – I spoke at BaBMA a few years back – great meeting).

Dear Colleagues,

The Biology and Mathematics in the Bay Area (BaMBA) Day is an annual meeting aimed at creating a fairly informal atmosphere to explore the role of mathematics in biology. Going beyond traditional applied mathematics, the topics include sophisticated computational methods, biophysical methods, discrete mathematics and topological methods. Our goal is to encourage dialogue between researchers and students from different disciplines in an atmosphere that promotes the open exchange of ideas and viewpoints to discuss the role of mathematics in modern molecular biology. Please join us for a day full of enticing discussions!

BaMBA 9 will be held 9am-6pm on Saturday, November 22nd, in 1002 Geidt Hall on the UC Davis campus. The talks by keynote speakers will be followed by a poster session.

Keynote speakers:

Ileana Streinu, Smith College

Sean Mooney, Buck Institute

Michael Levitt, Stanford

Sharon Aviran, UC Davis

Stephen Kowalczykowski, UC Davis

Participation in BaMBA is free and open to everyone, but registration is required. Attendance is limited to 150, and the registration deadline is Monday November 17th, 2014. Undergraduates, graduates, and post-docs involved in mathematical and computational investigations of biological systems are invited to submit an abstract for a poster presentation. For more information, please visit the BaMBA website at http://bambameeting.org/ .


The BaMBA 9 Organizing Committee:

Javier Arsuaga (Mathematics and Molecular & Cellular Biology, UC Davis)

Sami Khuri (Computer Science, SJSU)

Michael Levitt (Computational Structural Biology, Stanford)

Mariel Vazquez (Mathematics and Microbiology & Molecular Genetics, UC Davis)


National Science Foundation

UC Davis departments of Mathematics, Microbiology & Molecular Genetics, Molecular and Cellular Biology

UC Davis Colleges of Biological Sciences

UC Davis College of Letters and Science, Division of Mathematical & Physical Sciences

Previous meetings:

BaMBA 8, UC Berkeley


BaMBA 6, Stanford

BaMBA 5, UC Santa Cruz

BaMBA 4, UC Davis

BaMBA 3, San Jose State University

BaMBA 2, Mathematical Sciences Research Institute, Berkeley

BaMBA 1, San Francisco State University

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#UCDavis teaching position for Experimental Ecology and Evolution in the Field Winter & Spring




(Jan. 2, 2015 through Jun. 12, 2015)


Experimental Ecology and Evolution in the Field

EVE/ENT 180A (Winter) and EVE/ENT 180B (Spring)

Responsibilities: A 100% position teaching EVE/ENT 180A and EVE/ENT 180B Experimental Ecology and Evolution – (4 units each). Lecture/laboratory – 3 hours, fieldwork – 3 hours. Experimental design in field ecology. Examination of primary literature, experimental design, independent and collaborative research, analysis of data, development of original research paper based on field experiments.

Requirements:Ph.D. and demonstrated effective teaching in the subject course or equivalent course.

Salary: Commensurate upon qualifications.

Please submit letter of application, including summary of qualifications, CV, two letters of recommendation and any applicable teaching evaluation summaries via the link below which contains additional information about the position.

To apply online please visit: https://recruit.ucdavis.edu/apply/JPF00428


This position may be covered by a collective bargaining unit.

The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for diversity.

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Faculty position in Population Genomics and Computational Biology at CSU Monterey Bay


Assistant Professor, Population Genetics and Computational Biology

The Biology program within the Division of Science and Environmental Policy at California State University, Monterey Bay seeks a population geneticist with strong computational biology skills to fill a tenure track assistant professor position. The applicant should be a dedicated teacher capable of successfully involving undergraduates in research. The successful candidate will work with other faculty to develop undergraduate curricula, professional outreach programs, and extramural research or programmatic funding. Additional information on the Division and the Biology program can be found at sep.csumb.edu, the university and its vision at about.csumb.edu/vision-statement, and our exceptional undergraduate research program at uroc.csumb.edu.

The successful candidate will:

(1) teach upper division evolutionary biology & population genetics,

(2) develop and teach upper division bioinformatics & systems biology or a new upper division course in genomics or other computationally intensive branch of biology,

(3) develop and maintain a research program that provides opportunities for undergraduates,

(4) occasionally teach genetics or help with lower division instruction, and

(5) contribute to the development of this new university.

  • Ph.D. in biology or related field at time of hire.
  • Demonstrated excellence in teaching.
  • Expertise in Population Genetics.
  • Expertise in Computational Biology.
  • Research interests that leverage CSU Monterey Bay’s unique location at the interface between land and sea on the Central California coast.
  • Expertise in a computationally intensive field of study such as transcriptomics that can be applied to projects suitable for the undergraduate research environment.
  • A strong background in evolutionary or conservation biology.
  • Experience mentoring student research and/or internships.
  • Desire and ability to teach and mentor students from diverse cultural, ethnic, educational, and economic backgrounds.
  • A record of writing successful proposals for extramural funding.
  • Experience with course and curriculum development.

All prospective applicants must apply on-line at https://mocha.csumb.edu/uhr/jobs/login_applicant.jsp

1) Letter of Interest

2) CV

3) Teaching Statement (2 page max)

4) Research Statement (2 page max)

5) Contact information for 3 professional references


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Advice needed from a future reviewer…

I found myself writing this email to some collaborators, but halfway through realized that it’d be nice to get EVERYBODY’s input. Probably, one of you is going to review my next paper, so how awesome would it be for you to just tell me what you think now, and make both of our lives easier later.

To test whether taxa vary significantly across groups of samples, we first need to filter the OTU table to get rid of OTUs that are not present in most of the samples and/or that do not vary across samples. This must happen for statistical reasons.

As far as I know, there are two ways to do this. One, is to remove OTUs that occur in fewer than 25% of the samples (25% is suggested by the QIIME folks). The other is to calculate the variance of the OTUs across samples and remove the OTUs that have a variance less than 0.00001 (0.00001 is an arbitrary number thrown out there by the phyloseq developer.)

A third option would be to apply both criteria.

My inclination would be to go with the third option, but mostly because I want to limit as much as possible the number of hypothesis tests that we do in order to avoid draconian p-value corrections.

I’m not a big fan of arbitrary thresholds, but they are so frequently required that I’ve made my peace with them. However, if someone can suggest a non-arbitrary threshold, that’d be great.

But mostly, I want to make sure that everyone agrees now on the method that we use so that I only have to do this once. Thoughts?

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Talk at #UCDavis: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

Talk: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century


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At #UCDavis: the UC #OpenAccess Policy & what it means for you (10/22, 1:30-3 pm)

The UC Open Access Policy and what it means for you (10/22 from 1:30-3pm)

A Discussion with Catherine Mitchell and Dr. Robert Powell on the UC OA policy
Date & Time: Wednesday, October 22, 2014 from 1:30-3:00pm
Location: Shields Library, Nelle Branch Room, 2nd floor (at the far end of the main reading room)

The UC Open Access Policy (http://osc.universityofcalifornia.edu/open-access-policy/ or http://uc-oa.info) was passed by the UC Academic Senate on July 24, 2013, and is going into effect for all UC campuses, including UC Davis, on November 1, 2014. The policy grants UC faculty the right to make their articles freely available to the public by depositing a pre-publication copy in an open access repository. What does this policy mean for faculty at UC Davis?

Come to this talk by Catherine Mitchell of the California Digital Library (CDL), who will describe the tools and services that CDL is developing to support the policy, and Dr. Robert Powell of Chemical Engineering, who will give background on the policy and its passage through the UC Senate. Afterwards a Q&A panel will be held with the speakers, UC Davis librarians and open access researchers to answer questions and discuss the implications of the policy and open access.

This talk is being held during Open Access Week 2014, an annual international event to raise awareness about open access issues.

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UC #OpenAccess policy comments wanted from Academic Senate members by 1/7/15

The University invites comments on the proposed draft Presidential Policy on Open Access, which is based on the Academic Senate Open Access Policy for all Academic Senate members adopted on July 24, 2013.

The proposed new policy extends open access rights and responsibilities to all non-Senate members of the UC community who are authors of scholarly articles, including faculty, other academic personnel, students, administrators, and staff. The policy allows non-Senate authors of scholarly articles to maintain legal control over their research articles while making their work freely available to the public. In addition, the proposed policy outlines procedures for implementing the policy for all UC authors, both Senate and non-Senate. Although the policy assumes all authors will make their scholarly articles available to the public, there is a procedure, which authors must undertake proactively, to opt out of the open access process.

The proposal is located on the UCOP Academic Personnel and Programs website, “Policies under review,” under the “Systemwide Review” tab at http://www.ucop.edu/academic-personnel-programs/academic-personnel-policy/policies-under-review/index.html. If you prefer these documents as attachments, please let me know.

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Today at #UCDavis: Phillip Romero from UCSF: Data-Driven Exploration of Sequence and Function

Dr. Phillip Romero, UCSF
4:10 p.m. Chemistry in Rm 179
Seminar Title: “Data-Driven Protein Engineering: Learning the Sequence-Function Mapping from Experimental Data”

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Seminar at #UCDavis 10/30 – Scott Edmunds on “Open Publishing for the Big-Data Era”

Seminar of possible interest

Thursday, Oct 30th
12:10 PM to 01:30 PM
SS&H 1246

Scott Edmunds
from Gigascience / BGI

"Open Publishing for the Big-Data Era"

For more information see:

Additional information below:

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