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From listmasteranimalgenome.org  Tue Nov 15 12:37:21 2022
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From: "Palti, Yniv" <yniv.paltiusda.gov>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Postdoctoral Opportunity in Bioinformatics: Functional
       Annotation of Salmonid Genomes
Date: Tue, 15 Nov 2022 12:37:21 -0600

USDA-ARS Postdoctoral Fellowship in Bioinformatics: Functional Annotation of
Salmonid Genomes

For more information and to apply please go to
https://www.zintellect.com/...-2022-0394

ARS Office/Lab and Location: A postdoctoral research opportunity is
available with the Genomics Unit at the National Center for Cool and Cold
Water Aquaculture (NCCCWA), located in Leetown, West Virginia in
collaboration with Dr. Christine Elsik from the University of
Missouri-Columbia (MU). The appointment will be physically located in the
Animal Sciences Research Center at the MU campus in Columbia, Missouri.

The Agricultural Research Service (ARS) is the U.S. Department of
Agriculture's chief scientific in-house research agency with a mission to
find solutions to agricultural problems that affect Americans every day from
field to table. ARS will deliver cutting-edge, scientific tools and
innovative solutions for American farmers, producers, industry, and
communities to support the nourishment and well-being of all people; sustain
our nation’s agroecosystems and natural resources; and ensure the economic
competitiveness and excellence of our agriculture. The vision of the agency
is to provide global leadership in agricultural discoveries through
scientific excellence.

The mission of the NCCCWA is to enhance the nation's aquaculture production
of cool and cold-water fish species by developing improved germplasm and
technologies that increase farm efficiency, product quality, and
environmental sustainability. Research encompasses genetics, genomics,
physiology, aquatic animal health, and aquaculture engineering.

Research Project: The selected candidate will conduct research contributing
to our team efforts to develop pan-genome reference to salmonid species.
This will be done by developing a bioinformatic pipeline for genome
annotation and use it to annotate protein coding genes in genome assemblies
from several lineages of different salmonid species, including Atlantic
salmon, rainbow trout and cutthroat trout. In addition, the selected
candidate will use the annotation of the genomes for in-silico functional
comparative genomics between genetic lineages within species and between
species.

Learning Objectives: The participant will gain useful experience in
developing and running bioinformatic pipelines for eukaryotic genome
annotation and comparative genomic analyses. The research will be done under
the mentorship of experienced leaders in the fields of genome annotation in
agricultural animals and genomics of aquatic species.

Mentor(s): The co-mentors for this opportunity are Drs. Yniv Palti
(yniv.palti@usda.gov<mailto:yniv.paltiusda.gov>) and Guangtu Gao from USDA
and Dr. Christine Elsik from the University of Missouri-Columbia (MU).
Please contact Dr. Palti if you have questions about the nature of the
research. The appointment will be physically located in the Animal Sciences
Research Center at the MU campus in Columbia, Missouri. The participant will
collaborate with the Elsik group which has extensive experience in genome
annotation and will have opportunities to interact with others on campus
working in genomics, bioinformatics and research computing.

For examples of recent published genome assemblies from the USDA group see
bioRxiv: 2022.09.28.509896. DOI 10.1101/2022.09.28.509896 and G3
Genes|Genomes|Genetics, 11. DOI 10.1093/g3journal/jkab052. The Elsik group
has recently developed AquaMine (http://aquamine.org/), a data mining system
that integrates genome assemblies and gene annotation data for aquatic
eumetazoan species of importance to US aquaculture and fisheries, with the
goal of enabling researchers to create customized annotation datasets
integrated with their own data.

Anticipated Appointment Start Date: As soon as a qualified candidate is
identified.  Start date is flexible and will depend on a variety of factors.

Appointment Length: The appointment will initially be for one year, but may
be renewed upon recommendation of ARS and is contingent on the availability
of funds.

Level of Participation: The appointment is full-time.

Participant Stipend: The participant will receive a monthly stipend
commensurate with educational level and experience.

Citizenship Requirements: This opportunity is available to U.S. citizens,
Lawful Permanent Residents (LPR), and foreign nationals. Non-U.S. citizen
applicants should refer to the Guidelines for Non-U.S. Citizens
Details (https://orise.orau.gov/...fault.html) page of
the program website for information about the valid immigration statuses
that are acceptable for program participation.

The qualified candidate should have received a doctoral degree in one of the
relevant fields or be currently pursuing the degree and will reach
completion by the start date of the appointment. Degree must have been
received within five years of the appointment start date.

Preferred skills:

  *   Proficiency in scripting languages (e.g., perl, python, bash)
  *   Experience with open-source bioinformatics tools
  *   Experience with genomic data and high throughput sequence analysis
  *   Experience with Linux/Unix and HPC
  *   Strong computational and analytical skills
  *   Strong communication skills in speaking and documented writing ability


Thank you,

Yniv Palti, Ph.D.
Supervisory Research Geneticist
USDA-REE-ARS-NCCCWA
11861 Leetown Road
Kearneysville, WV 25430


 
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