Computational Biologist/Software Engineer (Pathobiology)

University of Pennsylvania Philadelphia, PA Full-time Information Services / Technology (IT)

Posted on April 23, 2024

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Computational Biologist/Software Engineer (Pathobiology)

University Overview

The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that provide opportunities for undergraduate, graduate and continuing education, all influenced by Penn's distinctive interdisciplinary approach to scholarship and learning. As an employer Penn has been ranked nationally on many occasions with the most recent award from Forbes who named Penn one of America's Best Large Employers in 2023.

Penn offers a unique working environment within the city of Philadelphia. The University is situated on a beautiful urban campus, with easy access to a range of educational, cultural, and recreational activities. With its historical significance and landmarks, lively cultural offerings, and wide variety of atmospheres, Philadelphia is the perfect place to call home for work and play.

The University offers a competitive benefits package that includes excellent healthcare and tuition benefits for employees and their families, generous retirement benefits, a wide variety of professional development opportunities, supportive work and family benefits, a wealth of health and wellness programs and resources, and much more.

Posted Job Title
Computational Biologist/Software Engineer (Pathobiology)

Job Profile Title
Bioinformatician B

Job Description Summary
This position is for a full-time, computational scientist in the Moncla lab at the University of Pennsylvania School of Veterinary Medicine. Our lab uses viral genome sequences to understand viral emergence, evolution, and transmission, with a particular focus on how novel RNA viruses evolve to infect new species. We are interested in problems that impact public health, and are invested in developing and maintaining tools that enable academic and public health labs to make actionable decisions for understanding viral emergence and evolution. We are particularly interested in respiratory viruses that pose current and emerging challenges for human and animal health. One of our lab's focus areas is highly pathogenic avian influenza viruses, and using viral genomes to track evolution and reconstruct viral transmission histories. We maintain the avian influenza phylogenies hosted on Nextstrain.org/flu/avian, and are looking for a full-time person to broadly contribute to these efforts. Specifically, the ideal hire would (1) build, test, and deploy a database for housing viral sequence data, (2) develop new viral phylodynamics resources, (3) improve, automate, and develop pipelines for viral phylodynamics and analysis of genomic sequence data, (4) write documentation, (5) write reports, (6) serve as an in-house computational expert to assist lab members with computational tasks, git questions, and coding development. We are committed to open science practices, and aim to make our work publicly-available and reproducible, and all work for this position would be hosted on public repositories to make it available for other academic labs, public health labs, and public health agencies.

The ideal candidate would have substantial training in both biology and computer science, and be able to operate mostly independently in tasks 1 and 6. This position is in-person, though there is flexibility surrounding part-time work-from-home. The ideal candidate would be fluent in advanced python, git, and databasing, and would have a PhD or a Masters degree with + years of experience. The ideal hire would also work well in teams and be open to assisting other team members in computational tasks and learning best practices for coding. Interested applicants should submit a CV, cover letter, at least one code sample, potentially including link(s) to relevant Github repositories. Applicants asked to interview will be expected to understand the goals of the lab, pass a technical interview, and interview with the lab.

Job Description

Job Responsibilities

Database building, testing, maintenance: Our lab curates and store tens of thousands of viral genome sequences, and uses these sequences to infer transmission and evolution patterns. The candidate would be tasked with developing, building, testing, and maintaining a database that our lab could use for these needs. The ideal candidate would be able to lead this development with input from other lab members, but would be solely responsible for building it.
Viral phylodynamics resource development, improvement, and automation: Our lab uses bioinformatics pipelines for next-generation sequence data analysis, mapping, variant calling, and for phylodynamic analysis. The candidate would work with the PI and other lab members to develop new pipelines, and to restructure and optimize existing pipelines to work more efficiently and automatically.
Developing documentation for new and existing software pipelines. The candidate would develop extensive user documentation to allow new and existing software to be used by academic and public health labs with cursory computational expertise.
The candidate will training/help lab members on coding best practices, git issues/questions, and assist with various computational tasks, like curating and cleaning large data files and writing documentation.
The candidate would contribute to scientific reports on avian influenza evolution and transmission patterns and contribute to progress reports for funding agencies.
Perform additional duties as assigned.

This position is contingent upon grant funding.

Qualifications

Bioinformatician B: Master of Science in Computational Biology, Biology or related field or bioinformatics and 3 to 5 years of experience or equivalent combination of education and experience is required.
Bioinformatician C: Master of Science in Computational Biology, Biology or related field or bioinformatics and 5 to 7 years of experience or equivalent combination of education and experience is required.
PhD in Computational Biology, Biology or related field or bioinformatics preferred.
Advanced Python, Git and experience with databasing required.
Experience with AWS and high-performing computing desired.

The qualified applicant will have significant training in biology and biological concepts, and advanced training/expertise in aspects of computer science/data engineering that are related to the described tasks.

Job Location - City, State
Philadelphia, Pennsylvania

Department / School
School of Veterinary Medicine

Pay Range
$61,046.00 - $110,000.00 Annual Rate
Salary offers are made based on the candidate's qualifications, experience, skills, and education as they directly relate to the requirements of the position, as well as internal and market factors and grade profile.

Affirmative Action Statement
Penn adheres to a policy that prohibits discrimination on the basis of race, color, sex, sexual orientation, gender identity, religion, creed, national or ethnic origin, citizenship status, age, disability, veteran status, or any other legally protected class.

Special Requirements
Background check required after a conditional job offer is made. Consideration of the background check will be tailored to the requirements of the job.

University Benefits

Health, Life, and Flexible Spending Accounts: Penn offers comprehensive medical, prescription, behavioral health, dental, vision, and life insurance benefits to protect you and your family's health and welfare. You can also use flexible spending accounts to pay for eligible health care and dependent care expenses with pre-tax dollars.
Tuition: Take advantage of Penn's exceptional tuition benefits. You, your spouse, and your dependent children can get tuition assistance here at Penn. Your dependent children are also eligible for tuition assistance at other institutions.
Retirement: Penn offers generous retirement plans to help you save for your future. Penn's Basic, Matching, and Supplemental retirement plans allow you to save for retirement on a pre-tax or Roth basis. Choose from a wide variety of investment options through TIAA and Vanguard.
Time Away from Work: Penn provides you with a substantial amount of time away from work during the course of the year. This allows you to relax, take vacations, attend to personal affairs, recover from illness or injury, spend time with family—whatever your personal needs may be.
Long-Term Care Insurance: In partnership with Genworth Financial, Penn offers faculty and staff (and your eligible family members) long-term care insurance to help you cover some of the costs of long-term care services received at home, in the community or in a nursing facility. If you apply when you're newly hired, you won't have to provide proof of good health or be subject to underwriting requirements. Eligible family members must always provide proof of good health and are subject to underwriting.
Wellness and Work-life Resources: Penn is committed to supporting our faculty and staff as they balance the competing demands of work and personal life. That's why we offer a wide variety of programs and resources to help you care for your health, your family, and your work-life balance.
Professional and Personal Development: Penn provides an array of resources to help you advance yourself personally and professionally.
University Resources: As a member of the Penn community, you have access to a wide range of University resources as well as cultural and recreational activities. Take advantage of the University's libraries and athletic facilities, or visit our arboretum and art galleries. There's always something going on at Penn, whether it's a new exhibit at the Penn Museum, the latest music or theater presentation at the Annenberg Center, or the Penn Relays at Franklin Field to name just a few examples. As a member of the Penn community, you're right in the middle of the excitement—and you and your family can enjoy many of these activities for free.
Discounts and Special Services: From arts and entertainment to transportation and mortgages, you'll find great deals for University faculty and staff. Not only do Penn arts and cultural centers and museums offer free and discounted admission and memberships to faculty and staff. You can also enjoy substantial savings on other goods and services such as new cars from Ford and General Motors, cellular phone service plans, movie tickets, and admission to theme parks.
Flexible Work Hours: Flexible work options offer creative approaches for completing work while promoting balance between work and personal commitments. These approaches involve use of non-traditional work hours, locations, and/or job structures.
Penn Home Ownership Services: Penn offers a forgivable loan for eligible employees interested in buying a home or currently residing in West Philadelphia, which can be used for closing costs or home improvements.
Adoption Assistance: Penn will reimburse eligible employees on qualified expenses in connection with the legal adoption of an eligible child, such as travel or court fees, for up to two adoptions in your household.

To learn more, please visit: https://www.hr.upenn.edu/PennHR/benefits-pay

To apply, visit https://wd1.myworkdaysite.com/en-US/recruiting/upenn/careers-at-penn/job/Hill-Pavilion/Computational-Biologist-Software-Engineer--Pathobiology-_JR00089217-1

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