USDA-ARS Bioinformatics Approaches to Emerging Zoonotic Viruses: Nipah Virus and Crimean-Congo Hemorrhagic Fever Virus
*Applications are reviewed on a rolling-basis.
ARS Office/Lab and Location: A research opportunity is currently available with the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), National Bio and Agro-Defense Facility in Manhattan, Kansas with the Zoonotic and emerging disease research unit.
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.
Research Project: The U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS), Zoonotic and Emerging Disease Research Unit (ZEDRU), located at the National Bio and Agro-Defense Facility (NBAF) in Manhattan, Kansas, invites a highly motivated postgraduate participant to engage in advanced bioinformatics research on two of the world’s most dangerous emerging pathogens: Nipah virus (NiV) and Crimean-Congo hemorrhagic fever virus (CCHFV).
Both NiV and CCHFV are high-consequence zoonotic viruses capable of causing severe outbreaks in humans and posing serious risks to livestock health, agricultural security, and public health. NBAF is USDA’s premier high-containment (BSL-4) research facility, uniquely equipped to study these agents in livestock-relevant systems. This appointment provides a unique training opportunity to apply advanced computational approaches to critical real-world questions—contributing to scientific discovery that directly informs outbreak preparedness, countermeasure development, and agricultural resilience.
Learning Objectives: Under the guidance of a mentor, the participant will have the opportunity to:
- Design and conduct bioinformatics research projects focused on Nipah virus and CCHFV under the mentorship of USDA scientists.
- Apply bioinformatics pipelines to analyze genomic, transcriptomic, and proteomic datasets generated from high-containment research programs.
- Develop and apply AI/ML approaches for identifying molecular markers of infectivity, pathogenicity, and transmissibility.
- Integrate multi-omics and ecological data to model virus evolution, host–pathogen interactions, and cross-species transmission risks.
- Collaborate with USDA scientists, academic partners, and interagency collaborators at the forefront of emerging disease research.
- Author and co-author peer-reviewed scientific publications, technical reports, and presentations, gaining experience in high-impact scientific communication.
- Participate in training experiences that prepare the participant for leadership roles in government, academia, or industry at the intersection of computational biology, emerging diseases, and agricultural biosecurity.
This appointment provides access to NBAF’s unparalleled high-containment research environment and the chance to participate in studies that cannot be performed anywhere else in the United States. Participants will join a team tackling some of the most urgent challenges in zoonotic and emerging disease research, applying bioinformatics to inform national preparedness and global health.
Mentor(s): The mentor for this opportunity is Lisa Hensley (lisa.hensley@usda.gov). If you have questions about the nature of the research, please contact the mentor(s).
Anticipated Appointment Start Date: 2025. Start date is flexible and will depend on a variety of factors.
Appointment Length: The appointment will initially be for two years 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. The anticipated annual stipend range is $55,000 - $78,733 for master's level and $66,500 - $103,700 for doctoral level.
Citizenship Requirements: This opportunity is available to U.S. citizens and Lawful Permanent Residents (LPR) only.
ORISE Information: This program, administered by ORAU through its contract with the U.S. Department of Energy (DOE) to manage the Oak Ridge Institute for Science and Education (ORISE), was established through an interagency agreement between DOE and ARS. Participants do not become employees of USDA, ARS, DOE or the program administrator, and there are no employment-related benefits. Proof of health insurance is required for participation in this program. Health insurance can be obtained through ORISE.
Questions: Please visit our Program Website. After reading, if you have additional questions about the application process, please email ORISE.ARS.Plains@orau.org and include the reference code for this opportunity.
Qualifications
The qualified candidate should be currently pursuing or have received a master's or doctoral degree in the one of the relevant fields (e.g. bioinformatics, computational biology, genomics, or a related discipline).
Preferred skills:
- Demonstrated expertise in bioinformatics and computational biology (e.g., genomics, transcriptomics, proteomics).
- Proficiency in scripting/programming (Python, R, Bash, or similar).
- Experience with high-throughput sequencing analysis pipelines (e.g., genome assembly, phylogenetics, variant calling).
- Familiarity with AI/ML approaches for biological data is highly desirable.
- Background in infectious disease virology or zoonotic pathogens.
- Strong record of peer-reviewed publications, scientific writing, and data visualization.
- Ability to design and conduct research projects.
- Experience collaborating across multidisciplinary teams.
- Evidence of prior research experience through peer-reviewed publications, presentations, or dissertation work.
- Interest in applying computational approaches to high-consequence zoonotic viruses such as Nipah virus and CCHFV.
- Strong critical thinking, problem-solving, and collaboration skills.
Stipend
$55,000.00 – $103,700.00 Yearly
Point of Contact
Eligibility Requirements
- Citizenship: LPR or U.S. Citizen
- Degree: Master's Degree or Doctoral Degree.