From listmaster animalgenome.org Mon Oct 26 14:36:22 2020
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From: Jean-Luc Jannink <jeanluc.workgmail.com>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Post Doctoral Position: Imputation for Database-Wide
GWAS USDA-ARS on Cornell University campus
Date: Mon, 26 Oct 2020 14:36:22 -0500
The position is with the USDA-ARS Plant Soil and Nutrition Research Unit
and our lab is co-located in the Plant Breeding and Genetics Section at
Cornell University. Our lab maintains the largest publicly available data
resource on field and genotyping trials for wheat, barley, and oat: the
Triticeae Toolbox (T3, http://triticeaetoolbox.org). The postdoc will
leverage de novo assembled genomes in these species to create an imputation
engine, which, combined with T3 data, will enable more powerful association
analyses than ever before in these species
The USDA-ARS Plant Soil and Nutrition Research Unit and the Cornell Plant
Breeding & Genetics Section train interdisciplinary scientists in the
elaboration of new breeding methods, the discovery of genetic mechanisms
important for economically important traits, and the creation of genetic
stocks, germplasm, and varieties. We promote a collaborative and
interactive workspace to improve learning, cross connectivity, and mutual
support between basic and applied researchers. We are world leaders in
innovative plant breeding research, teaching, and extension, and we
collaborate globally.
The Jannink lab works with several crop species (wheat, oat, barley,
cassava, and the brown algae sugar kelp) to develop genomic prediction
methods and integrate them optimally into breeding schemes. We work
together to discover, build on, and share new ideas and tools from across
computational disciplines that lead to successful applied breeding
outcomes.
The valuable phenotypic data resource that we have compiled over more than
ten years in T3 contains lines that have been genotyped on a number of
different platforms, preventing a powerful joint analysis. Recent decreases
in the cost of long-read sequencing have facilitated the de novo assembly
of small but diverse panels in our target species. These panels sample a
high percentage of the haplotypes segregating across the genome in
domesticated populations and thus enable whole-genome sequence imputation
for any line that is genotyped at sufficient density. Imputation, in turn,
creates a uniform, high density marker set across lines as needed by many
genotype-to-phenotype mapping analyses. The postdoc will work in this
computational genetics space and collaborate with software developers to
make analyses available to public-sector breeders globally.
We seek a candidate with computational biology expertise and interest in
large-scale genotype-to-phenotype analyses as well as in software
development. Primary tools for the analyses exist. The postdoc will
implement them in robust code deployable in the cloud or local servers,
apply them to data in T3, and publish methodology and discovery articles.
In addition to T3, the campus hosts much relevant software development:
Breedbase ( http://breedbase.org), GOBii ( http://gobiiproject.org),
Breeding Insight ( http://breedinginsight.org), and BrAPI (http://brapi.org).
The postdoc will collaborate whenever fruitful with these efforts to extend
functionality to broader audiences.
Term is two years.
Anticipated Division of Time
- Imputation and GWAS model building and implementation: 35%
- Software development / collaboration: 20%
- Writing: 30%
- Training of lab members and collaborators in computational biology: 15%
Position Requirements
PhD in bioinformatics or computational biology with knowledge of
quantitative or population genetics, or PhD in plant or animal breeding,
quantitative or population genetics with emphasis on computational and
statistical methods. Strong programming skills, ability to collaborate on
software development projects. Proficiency in R. Demonstrated communication
skills, both written and verbal. Management and leadership soft skills a
plus.
How to Apply
For further information, contact Jean-Luc Jannink (jeanluc.janninkusda.gov).
Applications should include a statement of interest relative to the research
proposed here, a CV, and a list of three references. References will only be
contacted if you give permission.
We will review applications holistically, seeking to understand your relevant
skills, your motivation for creating knowledge and problem solving, your
contribution to our group’s diversity and its organizational capacity.
Review of applications will begin immediately and continue until the position
is filled.
--
Jean-Luc Jannink (preferred pronouns: he/him/his)
USDA-ARS, Robert W. Holley Center for Agriculture and Health
Phone: +1 607 255 5266
Fax: +1 607 255 6683
--
Cornell University
Dept. of Plant Breeding and Genetics
258 Emerson Hall
Ithaca, NY 14853
USA
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