Software Engineer; Computer Science

Whiting School of Engineering's Computer Science Department is seeking a Software Engineer to assist the Phillippy lab in the development of bioinformatics methods for the analysis of long-read DNA sequencing data and personalized genomes. Assigned projects may include methods development for DNA sequencing, comparative genomics, genome assembly, and genome interpretation. The candidate will work closely with other members of the team, including students, postdocs, and senior staff, to advance the lab's research mission.

• Responsible for the creation, implementation, maintenance, performance, production support and documentation of various departmental and enterprise-wide application systems.
• Install, modify, and test new or upgraded applications, operating systems, file structures, hardware, communication devices, and productivity tools.
• Apply analysis techniques and procedures to gather and translate business requirements into functional/technical specifications and designs.
• Produce deliverables based on functional specifications and designs.
• Maintain databases and application system code.
• Manage full life cycle of medium to large complex projects and develop innovative solutions.
• Define complex business problems by meeting with clients to observe and understand current processes.
• Provide written documentation of findings to share with the client and IT colleagues.
• Gather complex system requirements and research existing technology to devise new applications.
• Develop detailed tasks and project plans by analyzing project scope and milestones.
• Write functional and technical specifications for use by programmers and analysts.
• Design data input, files/database structures, data transformation, algorithms, and data output using appropriate tools.
• Document code and processes, adding comments and appropriate documentation to knowledge-base systems.
• Provide monitoring and guidance in application design and development to junior staff.
• Provide thought leadership in designing and developing integrated solutions.
• Create and document complex test scenarios using appropriate tools.
• Test all changes using complex test scenarios and ensure functionality and error handling.
• Author and maintain audience-appropriate documentation for technical and end-user references.
• Mentor junior staff in testing tools and technologies.
• Implement changes in accordance with change management policies and procedures.
• Monitor changes, resolve complex problems, and ensure a smooth transition to new solutions.
• Provide support by investigating and resolving issues promptly and effectively.
• Develop robust computational methods to advance comparative and personalized genomics.
• Analyze data to contribute to biological discovery of previously inaccessible genome regions.
• Maintain software engineering best practices and disseminate results and software.
• Read scientific literature to stay current in the field.
• Meet with supervisor to report on progress.
• Present at internal lab meetings and engage in all other lab activities.
• Author scientific publications reporting on results and methods.
• Support teaching activities as requested.

• Bachelor's Degree (or foreign equivalent) in Computer Science, Computer Information Systems, Information Technology, Electronic Engineering, or a related field.
• Five years of related work experience with computer systems and applications.
• Additional education may substitute for required experience, to the extent permitted by the JHU equivalency formula.

• Knowledge in the assigned application and the platform it runs on.
• Bachelor's Degree in Computer Science or related field with broad coursework in sciences and math; advanced computing topics such as algorithms, graph theory, machine learning, ethics, and specialized topics in computational biology.
• Strong practical computational skills, particularly in Python, R, and shell scripting (also C, Java, JavaScript, Go, React, SQL).
• Experience in a research computing environment, including version control, pipeline development, and high‑performance computing systems.
• Two or more years of experience working with genomic data, including knowledge and use of common file formats (sam/bam, fastq, vcf, paf, bed) and software (samtools, bedtools, deepvariant, modkit, minimap), pipelines and skills such as alignment, variant calling, and methylation data analysis.
• Effective written and verbal communication skills and ability to read and interpret scientific literature.
• Interest in developing and applying computational methods for genome assembly, sequence alignment, variant detection, variant annotation, and information visualization.

• Agile Methodology - Intermediate
• Algorithms - Intermediate
• Application Programming Interface (API) - Intermediate
• CI/CD - Intermediate
• Cloud Serverless Computing Architecture - Intermediate
• Code Review - Intermediate
• Data Architecture and Design - Intermediate
• Data Structures - Intermediate
• Debugging - Intermediate
• Dev Ops -…