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Job Req ID:  13095

Sr. Software Engineer

Classified Title: Sr. Software Engineer 
Working Title: Sr. Software Engineer ​​​​​
Role/Level/Range: ATP/04/PF 
Starting Salary Range: [[$79,864 - $109,782 ]]
Employee group: Full Time 
Schedule: Monday-Friday / 8:30am - 5:00pm 
Exempt Status: Exempt  
Location: [[1812 Ashland Avenue, Suite 200]] 
Department name: 10002884-SOM Genetics Ctr for Inhrtd Dis Res CIDR 
Personnel area: School of Medicine




General Summary:


Johns Hopkins Genomics (JHG) is a partnership between the Department of Pathology and the Institute of Genetic Medicine.JHG is recruiting for a Senior Software Engineer to join an experienced team of bioinformatic specialists.The Sr. Software Engineer will play a prominent role in the support of All of Us Research Program activities as part of our newly funded Genome Center and partner on the development of informatic and analysis pipelines for newly launched high-volume whole genome sequencing services.This position will support both clinical and research projects and services.


Duties and Responsibilities:


  • Performs independent statistical genetic and genomic data science/big data research and activities
  • Provides bioinformatics expertise, specifically informed by deep knowledge of human genetics, to faculty and staff of JH Genomics
  • Uses expertise to lead the development of new services such as; cutting-edge scientific analysis pipelines; cloud-based, big data, computational genomics analysis platforms; data collaboration portals, etc.
  • Responsible for assembling project plans and teamwork assignments and ,  identifying resource needs, Will manage one or more high profile/high impact projects considered to be of medium to high level complexity.
  • Development of cutting-edge scientific analysis pipeline; in the near term with a focus on development, optimization and validation of structural variant calling for whole genome sequencing datasets.
  • Development of cloud-based, big data, computational genomics analysis platforms and portals to support population-scale exome sequencing studies as well as whole genome sequencing studies.
  • Optimization of local compute architecture for production scale whole exome and whole genome sequencing requirements, for both QC of research data and rapid clinical service needs.


Minimum Requirements



Required: Six years of related experience

Required:   Bachelor’s degree in Computer Science, Information Technology or other related field.          

Preferred:  Master’s degree in Statistical Genetics or Human Genetics or related field



Special Knowledge, Skills, and Abilities:


Expert knowledge of statistics and human genetics. Experience with statistical analysis packages such as R, Bioconductor and SAS. Experience with cloud based computing and platforms.  Experience with “Big data” – in particular genomic data.  Experience with statistical genetics software such as Plink, S.A.G.E, FBAT, Impute, Beagle.  Expert knowledge of current NGS analysis software, including Genome Analysis Tookit (GATK), BWA, Bowtie, Picard, SAMtools.  Working knowledge of structural variant detection software like Breakdancer, LUMPY, Pindel; and annotation tools like Annovar. Data visualization skills that enable complex findings to be presented in meaningful formats readily understood by others, using tools like Spotfire and IGV.


Solid functional understanding of the scientific process, molecular biological research and genomic analysis algorithms.  Ability to effectively manipulate, annotate, and format large-scale genomic datasets and to assess data quality.  Fluent in Linux/Unix scripting languages (bash/awk/sed) for file management/parsing, data manipulation and process automation.  Proficiency with one or more programing languages (e.g., Perl, Python, Java) for application development.  Familiarity with database management systems (MySQL, Oracle) and query languages (SQL).  Excellent debugging and troubleshooting skills for complex large-scale open source software; familiarity with package managers (yum, PPM) and software repositories (GitHub, BitBucket). Thorough understanding of cluster/grid computing and associated management software and working knowledge of distributed computing paradigms like map-reduce.


Strong organizational and time management skills to meet project goals and deadlines. Demonstrated ability for self-direction and initiative, and to independently and appropriately prioritize responsibilities. Excellent written and oral communications skills.  Experience working in a fast-paced academic R&D environment.  Must demonstrate strong critical thinking and analytical reasoning skills.  Ability to maintain confidentiality.



Any specific physical requirements for the job: 


Ability to sit in a normal seated position for extended periods of time. Dexterity of hands to operate a computer keyboard, mouse or other office machinery. 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. The incumbent will be required to communicate regularly via telephone and face to face with internal and external customers and must be able to exchange accurate and timely information in these settings.  Ability to see and hear within normal parameters; lift, carry, move supplies, computers, etc. Ability to move about workspace.






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 HR Business Services Office at For TTY users, call via Maryland Relay or dial 711.


The following additional provisions may apply depending on which campus you will work.  Your recruiter will advise accordingly.


During the Influenza ("the flu") season, as a condition of employment, The Johns Hopkins Institutions require all employees who provide ongoing services to patients or work in patient care or clinical care areas to have an annual influenza vaccination or possess an approved medical or religious exception. Failure to meet this requirement may result in termination of employment.


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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