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From listmasteranimalgenome.org  Thu Nov  9 15:12:18 2023
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From: "Thallman, Mark - REE-ARS" <mark.thallmanusda.gov>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: USDA Postdoc Position in Improving Computational Efficiency of
Date: Thu, 09 Nov 2023 15:12:19 -0600

A postdoctoral position aiming to make it feasible to compute restricted
maximum likelihood (REML) estimates of variance components in mixed models
with many more traits, effects, and levels of effects than is currently
feasible is available immediately at the U.S. Meat Animal Research Center.
These improvements will be accomplished by combining theoretical
developments that reimagine many aspects of the computational approaches
currently used in variance component estimation (VCE).

Position Description:

The primary objective of the position is to investigate and report on
computational aspects of REML variance component estimation. There are
multiple potential manuscripts for which theory development, software
implementation, and numerical confirmation are substantially developed and
writing could commence immediately with a bit of collaborative expansion
from the candidate and PI. Additional potential manuscripts which require
more development to reach the writing stage could be undertaken as part of
this position. There are many other opportunities for theory development,
implementation in software, numerical confirmation, and publication in
areas that have only been explored superficially. It is expected that the
successful candidate will write several manuscripts on VCE from the
previous categories. After that, the position could go in several different
ways. Writing could continue on the queue of manuscripts to obtain as many
publications as possible. Depending on interests and aptitudes, focus could
shift to making substantial contributions to theoretical developments
and/or programming. For candidates with strong interest and training in
animal breeding and/or livestock genomics, there is ample opportunity to
perform advanced and challenging analyses on existing data from the
Germplasm Evaluation Project (GPE; see below) and publish novel papers.

Potential Impact:

It is expected that the successful candidate will contribute directly or
indirectly to the development of an R package for analysis of mixed models
and REML estimation of variance components. It is anticipated that this R
package (and/or other software that implements the published computational
approaches) will make it feasible to routinely estimate variance components
in genetic evaluations of tens of millions of animals including many
genotyped animals. This will not only improve the genetic evaluations, but
also make it feasible to estimate genomic, epigenetic, and other effects
for which sufficient power does not exist in research populations. It is
also anticipated that this R package and/or the published computational
approaches will make it feasible to analyze many more traits
simultaneously; this would allow correlations with high dimensional -omics
pipelines (e.g., transcripts, metabolism, etc.) to improve the accuracy of
genomic evaluations of economically important traits of livestock. Although
the objectives for this project are motivated by problems in genetics, many
other disciplines use mixed models and software with improved estimation of
variance components would benefit those disciplines as well.

Required Qualifications:

* Must be sufficiently familiar with REML and the mixed model equations to
  write manuscripts describing the theory and implementation of improved
  approaches to computing REML estimates
* Excellent communication (including written) skills and ability to work
  collaboratively
* Must be awarded a Ph.D. by May, 2024
* Must be a U.S. citizen or permanent resident

Preferred Qualifications:

* Ph.D. in animal breeding, genetics, statistics, computer science,
  mathematics, or similar field of study
* Interest and aptitude in development and application of statistical
  theory
* Experience in R programming and principles of software development
* Interest in livestock breeding, genetic evaluation, and/or genomics

Compensation and Benefits:

This federal government position is funded for 2 years starting at the GS-
11-1 level (salary for 2023 is $69,107). For calendar year 2024, it is will
probably be higher but the exact amount won't be known until January.
Federal employees typically receive an automatic increase in January of
each year determined by the administration in office. Additionally there is
a roughly 3.3% step increase to GS-11-2 after 12 months of employment
conditional on satisfactory performance. The benefits package includes
excellent health and life insurance, 13 days per year of annual leave, 11
federal holidays, 13 days per year of sick leave and considerable
flexibility for telework and work schedule. The successful candidate will
accrue years of service for the Federal Employees Retirement System and is
eligible for participation in the Thrift Savings Plan (TSP) and the
government will match employee contributions to the TSP account up to 5% of
salary.

About the U.S. Meat Animal Research Center:

The U.S. Meat Animal Research Center (USMARC) has among the largest, if not
the largest research populations of beef cattle, swine, and sheep in the
world. It is located on 55 contiguous square miles near Clay Center, NE.
USMARC conducts research to improve the productivity and end-product
quality and safety of beef cattle, swine and sheep. USMARC is a very
collaborative environment. Postdocs interact with leading scientists and
other postdocs in animal breeding, genomics, metagenomics, animal health,
meat quality, meat safety, reproductive physiology, nutrition, precision
livestock management, and waste management.

The U.S. Meat Animal Research Center is a facility of the U.S. Department
of Agriculture's (USDA) Agricultural Research Service, which provides the
funding for this postdoctoral position.

About the Germplasm Evaluation Project:

The principle investigator for this project is a co-leader of the USMARC
Germplasm Evaluation (GPE) Project which has operated continuously since
1970. The GPE population is based on sampling industry sires that are
highly representative of 18 breeds of beef cattle. It typically produces
about 3,000 calves per year comprised of the 18 breeds and many crosses
among them that are measured for dozens of economically important traits.
More than 40,000 past and current members of the population have
phenotypes, pedigree, and tissue samples in the freezer. The combination of
genotypes and genomic sequence provide sufficient information to impute
genomic sequence to about 30,000 past and current GPE animals. Many
potential analyses and manuscripts are waiting in the queue. The issues to
be addressed by this position were largely motivated by challenges
encountered in analyzing data from the GPE project.

To Apply:

Please submit a statement of interest, c.v., academic transcripts, and
contact information for 2 references to Mark.Thallmanusda.gov. The
position is open until filled.

For More Information:

Please contact Mark Thallman (Mark.Thallmanusda.gov; 402-762-4261) with
any questions. I will be on vacation without access to official email and
telephone from November 16-30. Please direct questions during this period
to Larry Kuehn (Larry.Kuehnusda.gov; 402-762-4352); otherwise I will
respond when I return.


USDA/ARS is an equal opportunity provider and employer.
Regards,
Mark
R. Mark Thallman, Ph.D.
Research Geneticist
U.S. Meat Animal Research Center
P.O. Box 166
Clay Center, NE  68933-0166
Tel:   402-762-4261
Email: Mark.Thallmanusda.gov


 
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