Senior Software Engineer

Stanford University is seeking a Software Developer 1 to join the Kundaje lab in the Department of Genetics to lead and assist with large-scale software development efforts at the interface of machine learning and genomics. Specifically, the candidate will work on developing and applying cutting edge deep learning frameworks for modeling massive single cell and bulk multi-omic datasets.

Duties include:

• Collaborate and participate in large consortia to assess needs and requirements
• Design and develop machine learning models for genomics applications
• Maintain and update existing deep learning frameworks for regulatory genomics
• Troubleshoot and solve technical problems
• Develop and maintain data processing pipelines
• Develop tutorials and demos for flagship software products from the lab
• Serve as technical resource with respect to applications and assist lab members with software engineering best practices

* - Other duties may also be assigned

DESIRED QUALIFICATIONS:

• Strong experience writing software tools and developing pipelines for production-level biological data analysis in Python or R.
• Strong bioinformatics and/or computational biology experience, including machine learning, statistical analysis and data visualization.
• Strong experience leading and executing collaborative computational biology projects from inception to completion, including leading project meetings and setting timelines.
• Experience with bioinformatics command line tools (SAMtools, BEDtools) and genomics data types (fastq, BAM, bed, vcf).
• Experience analyzing GWAS variants.
• Current knowledge of latest software and design standards.
• Ability to define and solve logical problems for technical applications.
• Excellent written and oral English communication and interpersonal skills.
• Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community.

EDUCATION & EXPERIENCE (REQUIRED):

Bachelor's degree and three years of relevant experience or a combination of education and relevant experience.

KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):

• Current knowledge of latest software and design standards
• Broad knowledge of fundamental biological and genomics concepts.
• Ability to define and solve logical problems for technical applications.
• Ability to communicate effectively and with a diverse set of audiences.
• Knowledge of and ability to select, adapt, and effectively use a variety of programming methods and analysis tools.
• Ability to recognize and recommend needed changes in user and/or operations procedures.
• Basic knowledge of software engineering principles.
• Strong knowledge of Python and at least one workflow development language.

CERTIFICATIONS & LICENSES:

None.

PHYSICAL REQUIREMENTS*:

• Constantly perform desk-based computer tasks.
• Frequently sit, grasp lightly/fine manipulation.
• Occasionally stand/walk, writing by hand.
• Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds

* - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.

WORKING CONDITIONS:

• May work extended hours based on project needs

The expected pay range for this position is $113,148 to $137,516 per annum. Stanford University provides pay ranges representing its good faith estimate of the salary wage the university reasonably expects to pay for a position upon hire. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location, and external market pay for comparable jobs.

At Stanford University, base pay represents only one aspect of the comprehensive rewards package.

At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website ( provides detailed information on Stanford's extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process.

The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.

Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources at For all other inquiries, please submit a contact form.

Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

WORK STANDARDS (from JDL):

• Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
• Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
• Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, ;/li>

Additional Information

• Schedule: Full-time
• Job Code: 4821
• Employee Status: Regular
• Grade: I
• Requisition ID: 108541
• Work Arrangement : On Site