[R-sig-phylo] bioinformatics/comparative methods post-doc UC-Boulder

2015-06-10 Thread Kyle Dexter
Postdoctoral Position Available in Evolutionary Bioinformatics /
Comparative Transcriptomics

Description:
A 2-year, NSF-funded postdoctoral position in Evolutionary Bioinformatics /
Comparative Transcriptomics is available in the Department of Ecology and
Evolutionary Biology at The University of Colorado, Boulder. The successful
candidate will be expected to generate, assemble, and annotate
transcriptomes from the flowers of a minimum of 48 non-model plant species,
in order to investigate the genomic basis (structural, regulatory) of
flower color evolution (additional research on the impacts of epigenetic
mechanisms of floral color evolution may be possible pending time and
funding). Specifically, this research targets evolution of the Anthocyanin
Biosynthetic Pathway. Candidates should have previous experience with
large-scale genome or transcriptome sequencing, proficiency in necessary
programming languages (e.g., PERL, R), and experience in quantification of
gene expression or co-expression networks. The candidate will be expected
to contribute to supervision of lab personnel and help coordinate basic
activities in the PIs lab including reagent ordering and stocking. The
position will remain open until filled.

Qualifications:
(1) A PhD in bioinformatics, genomics, evolutionary biology, computational
biology, molecular biology, or related discipline
(2) Strong publication record that includes multiple first-authored
publications in the field, and overall high proficiency in scientific
writing
(3) Familiarity with concepts in evolutionary biology
(4) Proficiency in analytical, quantitative, and computational methods with
respect to management of next-generation sequence data, including
programming abilities
(5) Experience in both the generation of and analysis of transcriptome
datasets, preferably on non-model organisms
(6) Experience preparing graphical visualizations of data

Start Date:
Fall or Winter 2015, with some flexibility

To Apply:
Please email your cover letter, curriculum vitae, up to three publications
(first author publications preferred) and names and contact information for
three references to Heather Stone (heather.blair.st...@gmail.com). Please
bundle all items into a single PDF. Specific questions regarding the
research project should be directed to Erin Tripp (erin.tr...@colorado.edu)
prior to applying.

Thanks,
Erin Tripp

--
Assistant Professor, Department of Ecology  Evolutionary Biology
Curator of Botany, Museum of Natural History (COLO Herbarium)
University of Colorado, Boulder
C105 Ramaley Hall, Campus Box 334
Boulder, CO 80309-0350
phone: 303.492.1862 (EBIO)
phone: 303.492.2462 (Herbarium)
fax: 303.492.0823 (or 4195)

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[R-sig-phylo] Pairwise genetic distances for many genes and taxa

2015-06-10 Thread Chris Buddenhagen
Dear r-sig-phylo folks

I am thinking of looking for outlier genes per the recent paper:  Xu X.,
Dunn K.A., Field C. 2015. A Robust ANOVA Approach to Estimating a Phylogeny
from Multiple Genes. Molecular Biology and Evolution.

The starting point for that analysis is a matrix of genes by taxa pairs
(with cells containing genetic distances for each combination).

I have 100s of loci either as separate phylip files or as a single
concatenated phylip file with a separate file specifying locus coordinates.
Any ideas how I could quickly generate the matrix?

Sincerely


Chris Buddenhagen
Florida State University
cbuddenha...@gmail.com

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