Category: Opportunities Outside IOB

University of Oklahoma¢s Laboratories for Molecular Anthropology
and Microbiome Research is seeking an Assistant Research Professor |
Adjust Lecturer. Position requires PhD Degree in Biology and 5 years
of experience in bioinformatics with experience working in the area of
ancient biomolecules, NGS, and metagenomics, with academic publications
and teaching experience. Experience with programming and shell scripting
languages C++, Perl, R and Python are required. Salary is 75k plus fringe.

Start date: August 2014

Inquiries and applications (CV and three references) directed to Dr. Cecil
M. Lewis (cmlewis AT ou.edu) with “Assistant Research Professor |
Adjunct Lecturer” in the subject line.

A postdoc position is available in the newly formed Herbarium Genomics
group at the Max Planck Institute for Developmental Biology.
Scientific focus is the generation and analysis of DNA sequences from
both present-day and historic samples (herbaria and archaeological
remains) to address evolutionary questions in three main research
avenues:

–        Identification and timing of key events in plant domestication

–        Colonization of new ecological niches by invasive or introduced species

–        Plant-pathogen epidemics in recent history

Initial appointments are normally for 2 years. The position is
available immediately.

Candidates will have demonstrated experience in next generation
sequencing analyses and strong computational skills, including
proficiency in at least one major programming or scripting language
and use of a Linux/Unix environment. A good understanding of molecular
and evolutionary biology, statistics and proficiency in R is a plus.

Our research is highly interdisciplinary and greatly benefits from an
interactive environment with computational biologists, molecular
biologists and evolutionary geneticists for daily discussions on
campus. The working language is English. We work closely with local
experts in plant genomics and ancient DNA, Detlef Weigel at the MPI
and Johannes Krause at the University of Tuebingen, as well as a
series of collaborators with expertise in plant pathology, taxonomy
and archaeology. Additional information on the group, the institute,
and Tuebingen can be found on our website
(http://www.weigelworld.org/research/projects/herbariumgenomics).

Please send applications with CV, statement of interest, name of 2
references and the subject line <herbarium genomics postdoc> to:
hernan [DOT] burbano [AT] tuebingen [DOT] mpg [DOT] de

Incomplete applications will not be considered.

A postdoc position is available in the newly formed Herbarium Genomics
group at the Max Planck Institute for Developmental Biology.
Scientific focus is the generation and analysis of DNA sequences from
both present-day and historic samples (herbaria and archaeological
remains) to address evolutionary questions in three main research
avenues:

–        Identification and timing of key events in plant domestication

–        Colonization of new ecological niches by invasive or introduced species

–        Plant-pathogen epidemics in recent history

Initial appointments are normally for 2 years. The position is
available immediately.

Candidates will have demonstrated experience in next generation
sequencing analyses and strong computational skills, including
proficiency in at least one major programming or scripting language
and use of a Linux/Unix environment. A good understanding of molecular
and evolutionary biology, statistics and proficiency in R is a plus.

Our research is highly interdisciplinary and greatly benefits from an
interactive environment with computational biologists, molecular
biologists and evolutionary geneticists for daily discussions on
campus. The working language is English. We work closely with local
experts in plant genomics and ancient DNA, Detlef Weigel at the MPI
and Johannes Krause at the University of Tuebingen, as well as a
series of collaborators with expertise in plant pathology, taxonomy
and archaeology. Additional information on the group, the institute,
and Tuebingen can be found on our website
(http://www.weigelworld.org/research/projects/herbariumgenomics).

Please send applications with CV, statement of interest, name of 2
references and the subject line <herbarium genomics postdoc> to:
hernan [DOT] burbano [AT] tuebingen [DOT] mpg [DOT] de

Incomplete applications will not be considered.

We are looking for a highly motivated young scientist specialized in
bio-informatics (NGS data management, programming and modeling) and with
good knowledge in genomics to apply for a post-doctoral position at the
UNESP (Universidade Estadual Paulista) laboratory of Molecular Evolution
in São José do Rio Preto (Brazil), through a post-doctoral program
sponsored by a Brazilian Funding Agency. Portuguese is not mandatory;
the working language will be English.

The post-doctoral position will aim to analyze the data obtained from
the re-sequencing of different Coffea canephora genotypes representative
of the natural genetic diversity of this species in Africa. It will
take advantage of the forthcoming publication of the model genome of
C. canephora and a long experience of the collaborative network involved
in this project. The application must include a project, already defined
but which will be implemented by the candidate with great support from the
participating teams and should be completed according to the candidate’s
research experiences.

The position is for one year renewable once.

Candidates must send their CV and a cover letter to Claudia
Marcia Carareto (carareto@ibilce.unesp.br), Valérie
Poncet (valerie.poncet@ird.fr) and Alexandre de Kochko
(alexandre.dekochko@ird.fr) ASAP.

Coffee is the world’s second largest agricultural commodity and
agricultural employment. Brazil is the first coffee producer worldwide;
it is also an important consumer. Coffea canephora (Robusta) provides 33%
of the global coffee production and 22% of the Brazilian coffee production
(2013). Climate change (warming and changes in rainfall patterns) may
have strong negative impacts on coffee production. The world’s foremost
climate science group, the Intergovernmental Panel on Climate Change
(IPCC 2014)1, has indeed included the negative effects of warming on
coffee as part of a landmark report on the global impacts of climate
change. Adaptive strategies to mitigate these effects may largely depend
on our knowledge of how crops respond to climate variability and on the
availability of genetic resources within wild populations. But in spite of
this threat, climate effects on coffee tree yields and genetic diversity
for adaptive traits have so far been poorly analyzed or only partially
on specific cultivated varieties. Moreover, even though C. canephora not
being the most preferred coffee on the market, it constitutes the highest
genetic diversity in the Coffea genus and therefore exploring its genetic
background in relation to physiological adaptability offers the highest
opportunity for improving and sustaining coffee productivity worldwide.

In the proposed research we will address the issue of Coffea canephora
resilience by:

Assessing the genetic diversity and structural genomic differences in
C. canephora by analyzing data issued from the resequencing of a set
of wild genotypes representative of the species genetic structure. In
addition, partial resequencing (GBS) of a large set of both cultivated and
wild genotypes is also conducted; cultivated Brazilian genotypes (Conilon)
are part of this effort. The postdoctoral fellow will take a particular
attention to the possible variations of alleles and/or paralogs linked
to the species adaptive capability provoked by possible insertions of
mobile elements. A particular attention will be paid to genes potentially
involved in drought tolerance. Evolutionary scenarios will also be drawn
to explain phylogenetic relationships within C. canephora and define
the present mechanisms involved in its genetic differentiation.

The project will take advantage of the first C. canephora genome to be
publicized soon.

A postdoc position is available in the Chemical Ecology unit,
Sustainable Agro-Ecosystems and Bioresources department of the
Research and Innovation Centre (CRI).

The position is related to the project “Scopazzi” funded by the
Autonomous Province of Trento (Accordo di Programma) and the
Association of Fruit and Vegetable Producers in Trentino (APOT) and
aimed at providing new insights into the biology and ecology of the
insects vectors of apple proliferation for the development of
sustainable control strategies.

The successful candidate will work on genomics and evolution of two
insects (hemipterans C. melanoneura and C. picta) which are the main
vectors of the “apple proliferation”, phytoplasma causing illness in
the apple trees. Successful candidate will apply bioinformatics tools
to get new insights in the evolution, biology and ecology of these
insect vectors.

Please read the position details to understand if you are eligible for
the position. In order to apply send your cv and fill the application
form. Application and profile are also available at the bottom of the
page.

Deadline for application: June 22, 2014.

More info and the full call at:
http://www.fmach.it/Servizi-Generali/Lavora-con-noi/Annunci-lavoro-e-borse-di-studio/Post-Doc-in-Evolutionary-Genomics-of-insect-vectors-of-apple-disease-151_CRI_IVAD-deadline-June-22-2014

A two-year post-doc position in population genomics is currently
available at Stockholm University, Sweden, in the research group of
Dr. Tanja Slotte.

Background
Plant mating systems, such as shifts from outcrossing to selfing, have
profound effects on levels and structuring of genetic variation, and are
expected to have a marked effect on the impact of natural selection. We
are interested in quantifying the demographic and selective effects of
mating system shifts using population genomic data. For a recent example
of our work on this topic in Capsella rubella, see Slotte et al. 2013
Nature Genetics 45:831-5.

Project
The post-doc will contribute to population genomic analyses of several
parallel mating system shifts in the Brassicaceae. This will include
investigating population structure, demographic shifts and assessing the
impact of natural selection in populations and species that differ in
their outcrossing rates. Whole-genome and whole-transcriptome sequence
data sets are already available, and more are currently being generated
in the lab. The project offers plenty of opportunities for post-docs to
pursue their own ideas using available genomic data.

Scientific Environment
The Slotte lab (http://tanjaslottelab.wordpress.com) is part
of the Dept. of Ecology, Environment and Plant Science, Stockholm
University. We are located at Science for Life Laboratories in Stockholm
(http://www.scilifelab.se), which holds considerable expertise in
high-throughput sequencing technology and bioinformatics. The working
atmosphere is international with English as the working language, and
the position offers excellent opportunities for scientific exchange with
both genomicists, evolutionary biologists and ecologists at SciLifeLab
and Stockholm University. The city of Stockholm is known for its beauty,
its buildings and architecture and its abundant clean and open water.

Qualifications
We are looking for a post-doc with a strong background and interest in
population genetics, and with the prerequisite bioinformatic skills
to carry out analyses of population genomic data sets. Experience in
next-generation sequencing analyses and strong computational skills are
therefore a benefit, and candidates should have knowledge in at least
one major programming or scripting language and be able to work in a
Linux/Unix environment. A good understanding of statistics and proficiency
in R is a plus. Candidates should have a PhD either in a field related to
population genetics/evolutionary genetics or bioinformatics/computational
biology.

Application Information
The application deadline is the 20th of June, 2014. The position is
available immediately, or as agreed upon with the successful candidate.

Applications should include: 1) a letter of interest / background (2 pages
max), 2) complete CV, 3) the names and e-mail addresses of three referees.

Applications should be sent by e-mail to Tanja.Slotte@scilifelab.se with
the subject line <population genomics position>.

Please feel free to contact me by email for more information about
the position or questions about the project before submitting your
application.

A 2-year postdoctoral research position is available in the group of
Jochen Wolf at the Evolutionary Biology Centre in Uppsala, Sweden, as
part of a project funded by funded by the European (ERC) and Swedish
Research councils (VR).

Background.
We are a young, growing research group that applies an integrative
approach to study evolutionary processes in natural populations. Major
research themes include the evolutionary processes and genetic
mechanisms underlying species divergence (e.g. Wolf et al. 2010a,
Ellegren et al. 2012, Poelstra et al. in press) and genome evolution
(e.g. Mugal et al. 2014).

The position is part of a long-term research program on the genomics of
speciation in an avian model system. The European crow hybrid zone
between all-black carrion crows and grey-coated hooded crows is a
textbook example of incipient speciation involving colour-mediated
social selection (Meise 1928, Wolf et al. 2010b). We generated an
annotated hooded crow genome draft generated data for integrated
analyses of comparative genome re-sequencing data, transcriptome
expression profiling and functional assays on plumage colouration. We
find that only a small well-defined part of the genome diverged between
the two sub-species which is associated with gene expression divergence
in pigmentation genes causing differences in eumelanin production in
growing feather follicles (Poelstra et al. in press).

The project.
Tissue based RNA-seq data integrates across many cell types and has poor
resolution in understanding cell-type specific divergence in gene
expression. In the crow system, we are specifically interested in
expression patters in melanocytes, the cell types that are responsible
for melanin production and eventually colour deposition into the
feathers. The successful candidate will use  in situ proximity (mRNA)
ligation assays developed by colleagues in Uppsala (Larsson et al. 2010)
to 1) obtain positional information of gene expression and 2) quantificy
relative mRNA abundance in single melanocyte cells. He/she will
establish this method on cross-sections of growing feather material to
specifically pinpoint the action of candidate genes from the
melanogenesis pathway (for more information on the method see
http://www.igp.uu.se/research/molecular_tools/ola_soderberg/).

Qualification.
The successful applicant has demonstrated skills in molecular and
histological techniques, e.g. cyro-sectioning of difficult material; RNA
in situ hybridisation, ideally fluorescent multiplexed;
immunohistochemistry, confocal microscopy. Experience with quantitative
approaches and in situ Proximity-Ligation-Assays are a clear advantage.
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 has been ranked first
place among all European Universities in the subject of biology (CHE
European ranking) and successfully bridges a broad variety of
disciplines. The scientific environment with numerous seminars, journal
clubs and social activities offer excellent possibilities for contacts
and collaborations. A graduate school in ‘The Genomics of Phenotypic
Diversity in Natural Populations’ directed by Jochen Wolf
(http://www.ebc.uu.se/education/postgrad/gradschool/) provides a
framework for courses, high-profile seminars and other activities for
PhD students. Our lab is part of the Department of Evolutionary Biology
(http://www.ebc.uu.se/Research/IEG/evbiol/), 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 have excellent access to advanced
laboratory infrastructure and high performance computing resources. 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.

How to apply.
Applications  should include a CV, a statement of motivation and the
contact details of at least two references. Use the following online
portal to apply:
http://www2.personalavd.uu.se/jobb/appform.php?lang=en&case=UFV-PA%202014/1595
The positions remains open until filled. Starting date is flexible. For
more information contact jochen.wolf@ebc.uu.se or see
http://www.ebc.uu.se/Research/IEG/evbiol/research/Wolf/.

A postdoctoral position is available immediately at the Computational
Genomics and Bioinformatics Group in the Department of Computer Engineering
in Bilkent University, Ankara, Turkey. The position is joint with the Somel
Lab of the Department of Biological Sciences in Middle East Technical
University.

As the Computational Genomics and Bioinformatics Group, we develop
combinatorial algorithms to analyze genomic sequence data to discover,
genotype, and phase genomic variants with a special focus on structural
variation and segmental duplication. We are also interested in de novo
genome assembly and transcriptome analysis. We apply our algorithms on
sequence data generated from the genomes of various organisms including
humans, to catalog normal variation, and study genome evolution.

The successful candidate will be responsible for leading a project that
involves de novo assembly and further analysis of the genome of pearl
mullet (Chalcalburnus tarichi). The pearl mullet is the only fish (and the
only vertebrate) that lives in Lake Van in eastern Turkey, and it shows
remarkable adaptation to the saline and extremely alkaline (pH 9.8) lake
water. The genetic and physiological mechanisms underlying this unique
trait, as well as the pearl mullet’s population structure, remain unknown.

The project will include the following steps:
•    De novo assembly and the annotation of the pearl mullet genome using
both Illumina and Pacific Biosciences data.
•    Comparative genomics analysis to understand the evolution of the
Cyprinidae family and adaptive evolution of the pearl mullet.
•    Transcriptome analysis for genome annotation; identification of gene
expression networks underlying adaptation to alkaline water.
•    Population genomics analysis of samples from different sections of the
lake to understand the pearl mullet’s migration and breeding patterns and
population history.
More details can be found in our lab web page at:
http://donut.cs.bilkent.edu.tr

Requirements:
•    Ph.D. degree in bioinformatics, genomics, computer science, or related
fields. Ph.D. candidates who expect to graduate soon are welcome to apply.
•    Experience in genome assembly and annotation is strongly preferred.
•    Experience in evolutionary genetics, population genomics, or
transcriptome analysis is a plus.
•    Strong programming skills in at least one high level programming
language; such as C, C++, Java, or Python.

A competitive salary and subsidized on-campus accommodation will be
provided. The successful candidate will also be encouraged to apply for the
TÜBİTAK 2232 (for Turkish candidates) and the Co-Funded Brain Circulation
Scheme fellowship programs (all candidates; gross monthly salary €4,167;
deadline September 19, 2014; URL: http://www.cocirc.tubitak.gov.tr/node/9).
The initial appointment will be for one year, with renewal available for
two more years.

Applicants should email a cover letter, CV, brief research statement and
list of 3 references to Dr. Can Alkan (calkan@cs.bilkent.edu.tr), or Dr.
Mehmet Somel (somel.mehmet@gmail.com). Please combine all files into a
single PDF and use the subject line “Postdoc Application (Pearl Mullet):
(name)”.

A position is available for a highly motivated postdoctoral researcher in
the group of Laurent Duret at The Laboratoire de Biométrie et Biologie
Evolutive, CNRS, Université Lyon 1.

The researcher will be involved in the comparative analysis of programmed
genome rearrangements in the ciliate Paramecium. In paramecia, as in
other ciliates, genome rearrangements occur during the development of
the somatic macronucleus (MAC) from the germline micronucleus (MIC), in
each sexual generation. Rearrangements include the precise elimination
of ~45.000 single-copy Internal Eliminated Sequences (IESs), which
are believed to be degenerate remnants of ancient transposable element
insertions. We are sequencing MIC genomes of different strains and species
of the Paramecium genus to reconstruct the evolutionary history of IESs
and to test the hypothesis that polymorphisms in these elements result
in sexual incompatibility.

Candidates must hold a Ph.D. in computational biology, evolutionary
genetics/genomics, molecular evolution or a related field. Experience
in comparative genome-wide analyses, next-gen sequencing data, and
bioinformatic programming are preferred. Programming skills in either
perl, python, or other languages suitable for bioinformatic analyses
are required.

This is a two-year position. The position is open immediately and the
start date is negotiable (but not later than January 1st 2015).

To formally apply, please send the following in PDF format to Laurent
Duret (Laurent.Duret@univ-lyon1.fr):

1. A curriculum vitae, including names of 3 referees.  2. A brief
statement describing current and future research goals

https://lbbe.univ-lyon1.fr/-Duret-Laurent-.html?lang=en

A postdoctoral position in Bioinformatics/Computational Biology is available in Tony Capra’s research group at Vanderbilt University in Nashville, TN. Our general focus is comparative and evolutionary genomics. We have active projects investigating gene regulatory changes in recent human evolution, modeling variation in protein structures, and developing methods for phylogenetics. For more information about the group and our work, visit http://www.capralab.org/.

A record of successful publications and a PhD in bioinformatics, computer science, statistics, or a similar discipline is required. Strong programming and analytical skills are essential for this position. Experience in evolution, genetics, and bioinformatics is preferred, but not strictly necessary. Interested applicants should send a CV and a cover letter in PDF format outlining qualifications and research interests to Tony Capra <tony.REPLACE_WITH_LASTNAME@vanderbilt.edu> with the phrase “postdoc application” in the subject line.