Job Title: Bioinformatics Engineer
PVN ID: HC-1607-001282
Category: Information Technology

Job Description

General Description

The Center for Translational and Basic Research (CTBR), a scientific research center located on the Upper Eastside of Manhattan is seeking a highly motivated full-time Bioinformatics Engineer with diverse skill sets. Applications involve setting up and maintaining next-generation sequencing data pipelines, provide bioinformatics analysis services to faculty across departments, and participate in various research projects involving large-scale genomic datasets. The position also provides the opportunity to work on cutting-edge bioinformatics and cloud computing software development projects, and use of a private high-performance cluster as part of the research performed in the Bioinformatics Core.







CTBR is  'An AA/EO/ADA Employer' (Affirmative Action/Equal Opportunity Employer/Americans with Disabilities Act).  We encourage minority applicants to apply.

Other Duties

Process, quantify and assess quality of biological samples and prepare the samples for sequencing. Retrieve and

organize results following sequencing experiment completion, and perform data analysis using bioinformatics data

analysis workflows currently available in the lab, in addition to developing new data workflows. As part of the duties for the

position, the candidate will prepare posters and manuscripts for scientific conferences or peer-reviewed journals, in

addition to mentoring more junior members of the lab on the use of sequencing and bioinformatics technologies.


Work closely with the other Bioinformatics Core members in maintaining the genomic data analysis resources, including

keeping the software, databases, genome indexes and operating systems up to date. Help in preparing posters and

presentations for scientific meetings.


  • Applicants with background in molecular biology, genetics or similar field, strong laboratory experience and bioinformatics expertise are encouraged to apply. 
  • Masters or Bachelors with at least 2 years’ experience, in Bioinformatics, Computer Science, Computational Biology or related field.  
  • Strong computer skills on the analysis of genomic data using bioinformatics, in addition to working knowledge of sequencing technologies is required. The applicant must have clearly demonstrated skill for scientific research in the field through scientific publications, conference presentations and similar scholarly achievements. 
  • Programming experience with two scripting languages, either Python, Perl or Ruby, and standard algorithms - data structures.
  • Familiarity with relational database systems and writing SQL queries for data management / storage / retrieval. 
  • Knowledge of next-generation sequencing technologies (primary Illumina, but also IonTorrent, Sanger, 454) data analysis protocols, software and data formats (read quality checks, read mapping and assembly, RNA seq, re-sequencing and SNP discovery).
  • Parsing of next-gen datasets using programming libraries (BioPerl, BioPython)


Preferred Qualifications:

  • Experience with the Galaxy Project platform for Bioinformatics Analysis
  • Cloud Computing, including AWS
  • Cloud API programming through scripting languages
  • Proficient with the UNIX command line
  • Familiar with Ubuntu and Centos Distros

About the Research Foundation

The Research Foundation of The City University of New York (RFCUNY) was established as a not-for-profit educational corporation chartered by the State of New York in 1963. RFCUNY supports CUNY faculty and staff in identifying and obtaining external support (pre-award) from government and private sponsors and is responsible for the administration of all such funded programs (post-award).

RFCUNY stands between CUNY’s principal investigators (PIs) and the sponsors who support them and strives to fulfill its essential responsibilities to both groups. Working closely with individual PIs and Grants Officers on the campuses, RFCUNY oversees employment, accounting, audit, reporting, purchasing, and special responsibilities that include management of a planned giving program; liaison with governmental agencies and foundations; negotiation of agreements; facility construction and renovation; protection and commercialization of intellectual property; and compliance with applicable standards in research involving human subjects, animal care, environmental and radiological safety, and conflicts of interest.

Equal Employment Opportunity Statement

The Research Foundation of the City University of New York is an Equal Opportunity/Affirmative Action/Americans with Disabilities Act/E-Verify Employer. It is the policy of the Research Foundation of CUNY to provide equal employment opportunities free of discrimination based on race, color, age, religion, sex, pregnancy, childbirth, national origin, disability, marital status, veteran status, sexual orientation, gender identity, genetic information, marital status, domestic violence victim status, arrest record, criminal conviction history, or any other protected characteristic under applicable law.

Key Features

Full Time
Annual Salary Range
$90,000.00 - $110,000.00
Closing Date
Sep 25, 2016 (Or Until Filled)
Bargaining Unit