Bioinformatician C

Pennsylvania, United States
05 May 2020
End of advertisement period
05 Jul 2020
Academic Discipline
Life sciences, Veterinary Science
Contract Type
Full Time

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.

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.

Job Profile Title

Bioinformatician C  

Job Description Summary

We are seeking an experienced bioinformatician to work closely on genome-scale research projects with the labs of Dr. Christopher Lengner and Dr. Andres Blanco in the Department of Biomedical Sciences. Dr. Lengner and Dr. Blanco’s groups aim to identify and understand gene expression and epigenomic programs that govern cell fate decisions in mammalian tissues and cancers. We commonly employ RNA-seq (single cell and bulk), ChIP-seq, ATAC-seq, and CRISPR/Cas9 pooled format genetic screens, and we are looking for a bioinformatician who will be excited to help us process and analyze these datasets, train and oversee students generating such datasets, and develop/maintain analysis pipelines and data storage platforms. We expect the candidate to be self-motivated and enthusiastic about interfacing with experimentalists within the Lengner and Blanco labs, as well as with collaborating labs within Penn as well as outside Penn. Command of a programming language (eg. Python, PERL, etc.) and statistical packages available in R is required, as is familiarity with genomic databases such as NCBI, ENCODE, and UCSC genome browser.  

Job Description

Analysis of next-generation sequencing data such as RNA-seq (single cell and bulk), ChIP-seq, ATAC-seq and pooled format CRISPR/Cas9 screening data. Integration of these datasets into unified analyses. Analysis and visualization of datasets. Development of computational pipelines integrating evolving barcode datasets with the aforementioned datasets.  Training of graduate students and postdoctoral fellows in computational analyses.  Maintenance of computational pipelines and oversight of data storage.  Preparing figures and figure legends for grants and manuscripts. Formal and informal meetings with PIs and other group members. Detailed duties include:

  • Design, develop, implement and maintain high-quality pipelines for the processing of large quantities of next-generation sequencing (NGS) data.
  • Develop and apply general statistical methods, machine learning (ML), visual analytical (VA) and other advanced applications for the analysis of (large scale) biomedical data.
  • Implement and manage biomedical data with databases, query interfaces and web applications. Retrieve biomedical NGS data from public resources and organize the data for easy analysis and sharing.
  • Prepare results in tabular, written summary, & graphical summary form suitable for publication and peer review.
  • Provide bioinformatics support to faculty and their staff. Requires designing and performing complex computational analysis, exploration of parameter settings, comparison of results across different methods, and the summary and visualization of data and results for presentation to faculty and their staff.
  • Independently designs, implements, tests, deploys, documents, and maintains analytical applications, analysis pipelines, and results reporting methodologies. This duty includes computer programming necessary to make modifications to existing algorithms and software or to write scripts to implement software in a server or high-performance computing environment.
  • Conducts training on the use of bioinformatics methods and software. This duty will involve leading small group training sessions to educate users about the methods and software used. A typical training session will include an overview of the method being used, its strengths and weaknesses, a summary of the parameter settings and their usefulness, and an overview of the output and results generated.
  • Maintains knowledge of cutting-edge methods and best practices for computational and statistical analysis of complex data.
  • Oversees lower bioinformaticians (students/postdocs) or leads the study designs, strategic development and method evaluation of major projects.


Masters’s degree and 5-7 years of experience in bioinformatics/computational biology or equivalent combination of education and experience is required. Masters-level training in bioinformatics, computer science, or related disciplines is required. This position requires strong programming skills, prior analysis of biological datasets, and ability to learn new types of next-generation sequencing-based analyses. Proficiency in a programming language (eg. Perl, Python, etc.) and R statistical packages is required. Intermediate understanding of statistical principles is required. This position requires training students and interacting with collaborating labs, and as such organizational skills and interpersonal skills are highly valued.

This position is contingent upon funding. A cover letter is required along with a resume.

Job Location - City, State

Philadelphia, Pennsylvania  

Department / School

School of Veterinary Medicine  

Pay Range

$72,837.00 - $138,391.00  

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.