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Job Req ID:  86896

Sr. Programmer Analyst

The Department of Genetic Medicine is seeking a Senior Programmer Analyst who will function as a member of the software application development team at the Center for Inherited Disease Research, a high-throughput production genomics facility under contract to the NIH and providing fee-based services to Hopkins physicians and scientists. Responsibilities include collecting and analyzing user requirements, designing and building data and function flows, and participating in programming work involving extremely large and ever-increasing quantities of genomic data. Central to the position is development of automated storage, retrieval, and analysis pipelines that incorporate state-of-the-art bioinformatic techniques and statistical methodologies applicable to Genome-Wide Association Studies and high-throughput sequencing projects; the implementation of complex Laboratory Information Management Systems (LIMS); and participation in the formulation of procedures and protocols as they relate to functional areas.


Specific Duties & Responsibilities:

  • Leads and participates in major life cycle software development, including user requirements collection, analysis, functions design and program coding, and system implementation and maintenance.
  • Regularly develops complex software using both established and novel design choices.
  • Performs application and system programming work at high level.
  • Develops and deploys technology to support complex bioinformatics software solutions, including client/server, distributed, and dynamically generated Web applications, using Java, Python, C#, C++, Scala, and/or other programming languages as well as necessary technologies, such as RMI and Sun (Oracle) Grid Engine, and the Django Web Framework.
  • Designs and implements database schemas and/or object-relational mapping, for example, using technologies such as Hibernate, JDBC, or NoSQL technologies.
  • Creates detailed technical documentation.
  • Co-authors posters and peer-reviewed publications; represents the CIDR software development team at conferences and other professional gatherings.
  • Participates in application, database, and software development, troubleshooting, and maintenance.
  • Examines and evaluates emerging technologies related to genotyping, studies of inherited disease, computer science, and the discipline of bioinformatics.
  • Performs other duties and special projects as assigned.


Minimum Qualifications (Mandatory):

  • Bachelor’s Degree in Computer Science, Computer Information Systems, Biology/Biochemistry, Mathematics, or Physics.
  • Three years of related work experience with computer systems and applications.
  • Additional education may substitute for required experience and additional related experience may substitute for required education, to the extent permitted by the JHU equivalency formula.*


* JHU Equivalency Formula: 30 undergraduate degree credits (semester hours) or 18 graduate degree credits may substitute for one year of experience.  Additional related experience may substitute for the required education on the same basis. For jobs where equivalency is permitted, up to two years of non-related college course work may be applied towards the total minimum education/experience required for the respective job. 


** Applicants who do not meet the posted requirements but are completing their final academic semester/quarter will be considered eligible for employment and may be asked to provide additional information confirming their academic completion date. 


Preferred Qualifications:

  • Master's Degree in a related field.
  • Minimum of three years paid, collaborative software development experience, using at least one scripting language (e.g., Perl, Python, shell) and at least one object-oriented programming language (e.g., C++, Java).
  • Working knowledge of biology, genomics, and implementation of bioinformatic algorithms. Additional education may substitute for some experience.
  • Database programming experience with a major RDBMS is required; background in biological sciences preferred.
  • Experience configuring and administering application servers (e.g., Apache Tomcat) is helpful, as is proficiency with source code repositories such as git.


Special Knowledge, Skills & Abilities:

  • Able to work in a demanding and dynamic team environment as well as independently, managing and prioritizing projects without input of supervisor.
  • Thorough knowledge of software development methodology, principles of relational database design and user interface design, and familiarity with Unix/Linux and Windows operating systems are essential.
  • Excellent oral and written communication skills, including the ability to present complex technical information clearly.
  • Working knowledge of biology, genomics, and implementation of bioinformatic algorithms.


Physical Requirements:

  • Sitting in a normal seated position for extended periods of time.
  • Reaching by extending hand(s) or arm(s) in any direction.
  • Finger dexterity to manipulate objects with fingers rather than with whole hand or arm, for example, using a keyboard.
  • Communication skills using the spoken word.
  • Ability to see and hear within normal parameters.
  • Ability to move about workspace.
  • Lift, carry, move supplies, computers, etc.


Classified Title: Sr. Programmer Analyst
Role/Level/Range: ATP/04/PD 
Starting Salary Range: $59,870 - $82,250 annually (commensurate with experience)
Employee group: Full Time 
Schedule: Mon- Fri 8:30-5 
Exempt Status: Exempt 
Location: Hybrid/School of Medicine Campus

Department name: SOM Genetics Ctr for Inhrtd Dis Res CIDR 
Personnel area: School of Medicine


The successful candidate(s) for this position will be subject to a pre-employment background check.


If you are interested in applying for employment with The Johns Hopkins University and require special assistance or accommodation during any part of the pre-employment process, please contact the Talent Acquisition Office at For TTY users, call via Maryland Relay or dial 711.


Johns Hopkins has mandated COVID-19 and influenza vaccines, as applicable. Exceptions to the COVID and flu vaccine requirements may be provided to individuals for religious beliefs or medical reasons. Requests for an exception must be submitted to the JHU vaccination registry. For additional information, applicants for SOM positions should visit and all other JHU applicants should visit


The following additional provisions may apply, depending on campus. Your recruiter will advise accordingly.


The pre-employment physical for positions in clinical areas, laboratories, working with research subjects, or involving community contact requires documentation of immune status against Rubella (German measles), Rubeola (Measles), Mumps, Varicella (chickenpox), Hepatitis B and documentation of having received the Tdap (Tetanus, diphtheria, pertussis) vaccination. This may include documentation of having two (2) MMR vaccines; two (2) Varicella vaccines; or antibody status to these diseases from laboratory testing. Blood tests for immunities to these diseases are ordinarily included in the pre-employment physical exam except for those employees who provide results of blood tests or immunization documentation from their own health care providers. Any vaccinations required for these diseases will be given at no cost in our Occupational Health office.


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