Skin microbiota biogeography

Over at Nothing In Biology Makes Sense! I wrote about a recent paper that analyzed the biogeography of skin microbiota. If you’re interested in your body as a conglomerate of unique ecosystems and want to know more – go check out “What’s lurking on your glabella“.

Oh et al. (2014) showed that individual microbial species showed different patterns across body sites and individuals.


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Dec 4 at #UCDavis: Leonardo Art Science Evening Rendezvous (L.A.S.E.R.)

Got this by email:

Please join us for the UC Davis Leonardo Art Science Evening Rendezvous where four speakers will present on their interdisciplinary work in the sciences and in the arts.

L.A.S.E.R.-UC DAVIS Continue reading

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Registration Open for Data Rights & Data Wrongs workshop, 12/10 at #UCDavis

Data Rights & Data Wrongs

A workshop organized by
Innovating Communication in Scholarship (ICIS)

University of California, Davis

Date & Time: December 10, 2014 from 9:00 am – 5:00 pm

Location: MPR, Student Community Center, UC Davis


Full Agenda:

Keynote talks:
Dr. Christine Borgman, Professor & Presidential Chair, iSchool, UCLA
John Wilbanks, Chief Commons Officer, Sage Bionetworks

Scholars are increasingly subject to pressures from funding bodies, disciplinary norms, professional and personal ethics, and institutional directives to share their research data and make it available for reuse. There is, however, a great deal of heterogeneity across the research enterprise with respect to what is meant by ‘data’ and ‘data sharing,’ why data sharing is deemed important, and what data management strategies are considered most effective. Moreover, data are often difficult and costly to produce and share. Therefore, many scholars view these as a significant product of their intellectual labor for which they should receive some sort of credit towards tenure and promotion, authorial recognition through citation, or financial compensation. While balancing all of these considerations is desirable to promote increased access to data, it is difficult to guarantee that the concerns of all research stakeholders will be met given (1) the diverse forms that data can take, as well as the mobility and malleability of data given widespread access to new information technologies, (2) the complex and variable legal status of data as not-quite/not-always property, and (3) the ethical considerations and legal restrictions implicated in the sharing and reuse of data related to sensitive topics such as personal health information, national security, and vulnerable populations. This workshop will address theoretical concerns and pragmatic solutions that can be harnessed to help researchers comply with requirements or desires to share their data in ways they deem appropriate for their goals.

11_07 Data Rights flyer.pdf

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Wanted: Program Directors in the Division of Mathematical Sciences (DMS)

Got this by email:
Dear Colleagues,

The Division of Mathematical Sciences (DMS), within the Directorate for Mathematical and Physical Sciences, National Science Foundation (NSF), announces a nationwide search for mathematical sciences professionals to fill Program Director positions. Formal consideration of interested applications will begin on November 18, 2014 and will continue until selections are made.

NSF Program Directors bear the primary responsibility for carrying out the Agency’s overall mission. To discharge this responsibility requires not only knowledge in the appropriate disciplines, but also a commitment to high standards, a considerable breadth of interest and receptivity to new ideas, a strong sense of fairness, good judgment, and a high degree of personal integrity.

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At #UCDavis today: Semi-Conductor Sequencing on the Ion Torrent Platform – 12:30 Vet Med 3B room 1105

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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. Continue reading

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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.

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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, the university and its vision at, and our exceptional undergraduate research program at

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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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