[SocBiN] Jobs: Bioinformatics - Evolutionary Genetics, Uppsala University

[Jochen Wolf]

Position in Bioinformatics / Evolutionary Genetics, Uppsala University

A bioinformatics position is available in the research group of Jochen 
Wolf at the Evolutionary Biology Centre in Uppsala, Sweden. The position 
is initially limited to 1-year and after evaluation can be extended.

The research group environment.
We take an integrative approach to the study of evolutionary processes 
applying a large range of methodology ranging from field work to 
population genetic modeling of large genome-scale data sets to 
functional characterization at the single cell level. One of the main 
questions in the group is to understand the micro-evolutionary processes 
and genetic mechanisms underlying species divergence. In addition, we 
engage in comparative approaches to study genome evolution across larger 
timescales. Empirical systems currently include birds (swallows and 
corvids), marine mammals (pinnipeds and killer whales), the European 
hemiclonal water frog system, and experimental evolution in fission 
yeast. Find below a selection of recent publications illustrating recent 
research activities or consult the current lab website 
(http://www.ieg.uu.se/evolutionary-biology/wolf/).

The position.
The successful applicant will be responsible for management of large 
transcriptome and genome sequencing data sets, help with administration 
and compilation of source code, and for the most part, will engage 
actively in ongoing research projects. The applicant is expected to be 
familiar with UNIX environments and has experience in standard 
bioinformatic approaches using high throughput DNA and RNA sequencing 
data from platforms such as Illumina or Pacific Biosciences. Common 
tasks will involve data management, genome assembly and annotation 
(Birds ca. 1.2 Gb, marine mammals: ca. 3Gb), multiple sequence 
alignments, short-read mapping and genotyping. Proficiency in relevant 
programming languages (e.g. awk, bash, Perl, Python, C) is naturally 
assumed. A background in population genomics or comparative genomics is 
a clear asset. Depending on the applicant’s background there will be 
some autonomy in that he or she can develop own research questions or 
participate in teaching activities.

The environment.
The Evolutionary Biology Centre (http://www.ebc.uu.se/) is one of the 
world’s leading research institutions in evolutionary biology. It is 
part of Uppsala University which is considered one of Europe’s leading 
universities in the subject of biology bridging a broad variety of 
disciplines. The scientific environment with numerous seminars, journal 
clubs and social activities offer excellent possibilities for contacts 
and collaborations. Our lab is part of the Department of Evolutionary 
Biology (http://www.ieg.uu.se/evolutionary-biology/?languageId=1/), an 
active environment addressing fundamental evolutionary questions with a 
wide range of different approaches. As a member of the Science for Life 
Laboratory (http://www.scilifelab.se/) we make extensive use of high 
performance computing resources (https://www.uppmax.uu.se/uppnex) and 
extended bioinformatic infrastructure 
(http://www.scilifelab.se/platforms/bioinformatics/). We also actively 
interact with research groups of the nearby BioMedicalCentre 
(http://www.imbim.uu.se/Research). The lab is situated in the student 
town of Uppsala that offers rich opportunities in cultural and outdoor 
activities. Sweden's capital Stockholm is less than an hour's train ride 
away.

By the end of 2016 the research group will transition to the Department 
of Evolutionary Biology at the Ludwig-Maximilians-Universität (LMU) in 
Munich, Germany. Munich University is consistently ranked among the top 
Universities worldwide, in particular the life science branch with its 
newly inaugurated campus offering excellent technical facilities and 
many interaction possibilities including the gene center, several 
Max-Planck-Institutes and the Helmholtz Centre 
(http://www.campusmartinsried.de/en/336-2/#). With the highest 
concentration of supercomputing in Germany the Leibniz Supercomputing 
Centre and its local partners provide access to state-of-the art 
computing facilities (https://www.lrz.de/english/). Munich is Bavaria’s 
capital, a vibrant, yet relaxed city with many traditions still alive 
considered by many to have a high quality of living 
(https://en.wikipedia.org/wiki/Mercer_Quality_of_Living_Survey) and the 
Alps nearby.
How to apply.
Applicants with a proven record with and without a PhD degree are 
encouraged to apply. Applications including a statement of motivation 
including relevant expertise, a CV and the contact details of at least 
two references should be sent as a single .pdf file to 
jochen.wolf at ebc.uu.se subject term ‘bioinformatics position’. The 
position remains open until filled; start date and transition modalities 
from Sweden to Germany are flexible and subject to negotiation.

Recent publications reflecting our research interests.
For a comprehensive account consult the lab’s website 
(http://www.ieg.uu.se/evolutionary-biology/wolf/).


Shafer ABA, Northrup JM, Wikelski M, Wittemyer G, Wolf JBW (2016) 
Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets 
High-Throughput Sequencing. PLoS Biol, 14, e1002350.

Foote AD, Liu Y, Thomas GWC et al. Gibbs RA (2015) Convergent evolution 
of the genomes of marine mammals. Nature Genet, 47, 272–275.

Poelstra JW, Vijay N, Hoeppner MP, Wolf JBW (2015) Transcriptomics of 
colour patterning and coloration shifts in crows. Mol Ecol, 24, 4617–4628.

*Poelstra JW, *Vijay N, *Bossu CM et al. Wolf JBW (2014) The genomic 
landscape underlying phenotypic integrity in the face of gene flow in 
crows. Science, 344, 1410–1414.

Ekblom R, Wolf JBW (2014) A field guide to whole-genome sequencing, 
assembly and annotation. Evol Appl, 7, 1026-1042.

Mugal CF, Wolf JBW, Kaj I (2014) Why time matters: codon evolution and 
the temporal dynamics of dN/dS. Mol Biol Evol, 31, 212–231.

*Vijay N, *Poelstra JW, Künstner A, Wolf JBW (2013) Challenges and 
strategies in transcriptome assembly and differential gene expression 
quantification. A comprehensive in silico assessment of RNA-seq 
experiments. Mol Ecol, 22, 620–634.

Nabholz B, Ellegren H, Wolf JBW (2013) High levels of gene expression 
explain the strong evolutionary constraint of mitochondrial 
protein-coding genes. Mol Biol Evol, 30, 272–284.

Ellegren H, Smeds L et al. Wolf JBW (2012) The genomic landscape of 
species divergence in Ficedula flycatchers. Nature, 491, 756–760.

* shared first authorship

-- 
___________________________
Jochen B. W. Wolf, PhD, Professor
Department of Evolutionary Biology
Evolutionary Biology Centre
Uppsala University
Norbyvägen 18D
SE-752 36 Uppsala
Sweden

phone: ++46 18 471 4120
fax:   ++46 18 471 6310
http://www.ebc.uu.se/Research/IEG/evbiol/research/Wolf/