Research Software Developer

School of Medicine, Stanford, California, United States

Information Technology Services

Post Date Dec 11, 2023

Requisition # 101712

Stanford University is seeking a Software Developer 1 to join the Kundaje and Bassik labs in the Department of Genetics to lead and assist with collaborative software development, data analysis and research at the intersection of genomics, data science and machine learning. Specifically, the candidate will work on developing and applying cutting edge approaches for modeling massive single cell and bulk multi-omic datasets and CRISPR screen data.

Duties include:

• Collaborate and participate in large consortia to assess needs and requirements.

• Design and develop pipelines and analysis approaches for single cell genomics

• Maintain and update existing software frameworks for regulatory genomics in the Kundaje and Bassik lab

• Troubleshoot and solve technical problems.

• Develop and maintain data processing pipelines for CRISPR screen analysis, sgRNA library design, and data integration from CRISPR screens with other data types

• Develop tutorials and demos for flagship software products in the lab

• Serve as technical resource with respect to applications and assist lab members with software engineering best practices and design

* - Other duties may also be assigned.

DESIRED QUALIFICATIONS:

• PhD degree in relevant field.

• Strong experience with bioinformatics tools and biostatistics for analysis of bulk and single cell RNA-seq and ATAC-seq.

• Familiarity with CRISPR screening approaches.

• Strong data science and software engineering experience in Python, R, Unix scripting.

• Experience leading collaborations between clinicians, wet lab biologists, and computational scientists.

• Experience building community around computational biology, such as hosting conference, meetups, or other events related to machine learning and cloud computing for biological applications.

• Product management experience defining requirements and managing project timelines from early development to broad deployment.

• Project management experience leading small teams to deliver products in a timely fashion.

• Ability to define and solve logical problems for technical applications.

• Solid analytical skills.

• 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.

• Ability to define and solve logical problems for technical applications.

• Knowledge of and ability to select, adapt, and effectively use a variety of programming methods.

• Ability to recognize and recommend needed changes in user and/or operations procedures.

• Basic knowledge of software engineering principles.

• Strong knowledge of at least one programming 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, evening and weekends.

The expected pay range for this position is $80,000 to $135,000 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. 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. The Cardinal at Work website (https://cardinalatwork.stanford.edu/benefits-rewards) 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.

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,http://adminguide.stanford.edu.

Additional Information

• Schedule: Full-time

• Job Code: 4821

• Employee Status: Regular

• Grade: I

• Requisition ID: 101712

• Work Arrangement : Hybrid Eligible