University Classification: Assistant Research Scientist / Engineer
Job Code: PRJ1
Pay Level: 5A
Position #:  00012935
Org/Dept/Sub-dept #: 90-9050
Position Reports to: Wade Aldous

Position Specific Summary:

The selected candidate will be responsible for performing bioinformatics analyses of sequencing data to support infectious disease investigations of public health significance conducted by the State Hygienic Lab. The candidate will have the capacity to characterize harmful pathogens, such as SARS-CoV-2, influenza, antibiotic-resistant bacteria, and outbreak strains at the genome level and provide public health data to drive surveillance, disease intervention, and treatment.

The Bioinformatician will provide specialized sequencing and bioinformatics support for several infectious disease sequencing programs. The sequencing data generated will provide real time surveillance for foodborne, healthcare associated infections, and other infectious disease outbreaks. Qualified candidates will have expertise in pathogen genomics and experience building bioinformatics pipelines using workflow managers and containerized algorithms. The candidate will be required to collaborate with molecular biologists and epidemiologists on analyses of next-generation sequencing (NGS) data; develop, implement, and maintain high-quality pipelines for the processing of NGS data; make modifications to existing algorithms and software and writing scripts to implement software on a server or high-performance computing environment; evaluate NGS data analysis methods published in peer-reviewed literature, and extend them to develop and deploy state-of-the-art NGS data analysis solutions; use data analyses to refine and optimize the design of assays (e.g. PCR primers); develop automated analysis reports or live dashboards that include visualizations; and prepares reports, publications, and other communications of analysis results and interpretation.

Position Status: 3 Year Specified Term

Key Areas of Responsibilities and Specific Job Tasks

Classification
Key Areas of Responsibility

Specific Job Duties and Tasks

Experiments, Simulations, Modeling or Theoretical Investigations

· Perform bioinformatic analysis of sequencing data to support infectious disease investigations of public health significance conducted by the State Hygienic Lab

· Characterize and compare sequenced pathogens at the genomic level to provide timely public health data to drive surveillance, disease intervention, and treatment.

· Perform experiments, simulations, or theoretical investigations.

· Collect data and evaluate relevance of data.

· Work independently on basic research tasks with oversight by Faculty or Principal Investigator (PI).

· Contribute to documentation of equipment and procedures.

Data / Research Analysis and Evaluation

· Expertise in pathogen genomics and experience building bioinformatics pipelines using workflow managers and containerized algorithms.

· Collaborate with molecular biologists and epidemiologists on analyses of next-generation sequencing (NGS) data

· Develop, implement, and maintain high-quality pipelines for the processing of NGS data

· Make modifications to existing algorithms and software and writing scripts to implement software on a server or high-performance computing environment

· Evaluate NGS data analysis methods published in peer-reviewed literature to develop and deploy state-of-the-art NGS data analysis solutions

· Develop automated analysis reports or live dashboards with visualizations and prepare reports, publications, and other communications of analysis results and interpretation.

· Analyze data for relevance and data integrity.

· Perform basic data analysis techniques.

· Compare results of scientific investigations to previously published work.

Dissemination of Research Results

· Provide specialized sequencing and bioinformatics support for several infectious disease sequencing programs.

· Interpret sequencing data to provide timely, actionable, real time surveillance for foodborne, healthcare associated infections, and other infectious disease outbreaks.

· Prepare manuscripts for contributing author for publication.

· Present results in departmental seminars and at professional meetings.

Research Proposals / Grants

· Contribute to new or continuing research grant proposals to obtain funding for research activities.

· May serve as co-PI on grants or proposals.

· Contribute to progress reports required by funding agencies.

· Supervise adherence to safety and compliance guidelines when necessary.

Service

· Provide service to the scientific community, University and General Public.

· Review submitted manuscripts and research proposals.

· Consult and collaborate with the research community.

· Participate in public outreach activities as required by funding sources.

· May participate in national and international meetings within the discipline.

Human Resources / Supervision

· Mentor graduate students and fellows on Bioinformatics projects.

· May provide functional and/or administrative supervision for staff.

· Provide direction, assignments, feedback, coaching and counseling to assure outcomes are achieved.

Universal Competencies

Collaboration/Positive Impact

Ability to work with a variety of individuals and groups in a constructive and civil manner and utilize existing resources and learning to achieve or exceed desired outcomes of current and future organizational goals/needs.

Diversity, Equity and Inclusion

Ability to work with a variety of individuals and groups in a constructive and respectful manner while appreciating the unique contribution of an inclusive workforce that brings together the talents of people across multiple identities, including: race, creed, color, religion, national origins, age, sex, pregnancy, disability, veteran or military status, sexual orientation, gender identity, or associational preferences.

Service Excellence/Customer Focus

Ability to meet or exceed customer service needs and expectations and provide excellent service in a direct or indirect manner. Ability to effectively transmit and interpret information through appropriate communication with internal and external customers.

Technical Competencies

Qualitative Research

(Extensive)

· Utilizes experience in collecting, organizing, and making sense of qualitative data.

· Designs and implements research studies.

· Makes recommendations for additional study needs based on information gathered.

· Designs and implements targeted surveys.

· Evaluates assumptions, interpretations and inferences made in research.

· Coaches others in effective questioning techniques.

Quantitative Research

(Extensive)

· Successfully uses quantitative research to prove and disprove theories in multiple applications.

· Uses stochastic, linear and non-linear programming and other analysis techniques.

· Identifies scenarios where quantitative research has failed to deliver needed information.

· Shows others how to derive accurate conclusions based on quantitative trials.

· Articulates and explains all assumptions and variables that factor into research conclusions.

· Communicates recommendations based on research clearly and convincingly.

Research Analysis

(Extensive)

· Analyzes published research reports and their possible implications.

· Interprets new findings and analyzes their validity.

· Implements research analysis standards within the organization.

· Controls the quality of research analysis.

· Advises on advanced research analysis methods.

· Evaluates research analysis best practices within the industry.

Research Documentation

(Working)

· Assists in the preparation of research documentation.

· Applies word processing to produce tables of contents, footnotes and other document components.

· Embeds tables of research data into documents.

· Explains the organization's process for drafting, editing and publishing formal research studies.

· Prepares bibliographies for research documents.

Research Ethics/Compliance

(Working)

· Applies policies and procedures designed to ensure compliance with ethical laws, regulations, and university code.

· Describes several types of issues covered by IRB, WIRB, IACUC, etc. and organizational code for research ethics/compliance.

· Documents the ethical considerations involved in carrying out research activities.

· Follows procedures for reporting violations.

· Participates in resolving issues involving research ethics/compliance.

Research Safety

(Working)

· Ensures that all first-aid equipment is operational and supplies are current and fully stocked.

· Participates in internal and external safety or health inspections.

· Follows established safety guidelines in research procedures to prevent illness or inlury to self or others.

· Seeks and identifies potential or actual safety hazards in storing, handling, transporting, and using various hazardous materials.

· Maintains health and safety records according to organizational and regulatory guidelines.

This description is intended to indicate the kinds of tasks and levels of work difficulty that will be required of positions that will be given this title and shall not be construed as declaring what the specific duties and responsibilities of any particular position shall be. It is not intended to limit or in any way modify the right of any supervisor to assign, direct, and control the work of employees under his or her supervision. The use of a particular expression or illustration describing duties shall not be held to exclude other duties not mentioned that are of similar kind or level of difficulty.

As part of performing the key areas of responsibility and competencies described above, staff members are expected to meet reasonable standards of work quality and quantity, as well as expectations for attendance established by their supervisor. Staff members are also expected to comply with policies governing employee responsibilities and conduct, including those contained in the University Operations Manual.

Proficiency levels are defined as:

Basic Application - Uses basic understanding of the field to perform job duties; may need some guidance on job duties; applies learning to recommend options to address unusual situations.

Working Experience - Successfully completes diverse tasks of the job; applies and enhances knowledge and skill in both usual and unusual issues; needs minimal guidance in addressing unusual situations.

Extensive Experience - Performs without assistance; recognized as a resource to others; able to translate complex nuances to others; able to improve processes; focus on broad issues.

Expert/Leader - Seen as an expert and/or leader; guides, troubleshoots; has strategic focus; applies knowledge and skill across or in leading multiple projects/orgs; demonstrates knowledge of trends in field; leads in developing new processes.

Position Qualifications

Education or Equivalency Required

A PhD degree in bioinformatics, biostatistics, computer science, biology, engineering or related field is required.

Required Qualification

· Knowledge and understanding of either computational and biological issues.

· Proficiency in at least one scripting language, such as R or Python.

· Programming and data analysis experience with Linux.

· Familiarity with public bioinformatics resources and tools.

· Knowledge of best-practice data presentation methods for internal and external audiences.

· Ability to easily integrate into and collaborate with a multidisciplinary team.

· Excellent communication, interpersonal, and relationship management skills.

· Demonstrated experience with, or commitment to diversity in the work, academic, or laboratory environment.

Desirable Qualification

· Previous experience with NGS data analysis.

· Previous public health laboratory experience.

· Considerable knowledge of the theory and application of next generation sequencing, sanger sequencing, and bioinformatics.

· Considerable knowledge of other molecular detection and characterization methods.

· Experience authoring or editing laboratory documents or grants.

· Experience presenting information to a variety of audiences.

· Experience with computers or laboratory information management systems.

See requisition # 21002774 at https://jobs.uiowa.edu

Applicable background checks will be conducted.

The University of Iowa is an equal opportunity/affirmative action employer. All qualified applicants are encouraged to apply and will receive consideration for employment free from discrimination on the basis of race, creed, color, national origin, age, sex, pregnancy, sexual orientation, gender identity, genetic information, religion, associational preference, status as a qualified individual with a disability, or status as a protected veteran.