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Single cell data analyst, Genetics

The Kundaje lab at Stanford University is seeking a Single-Cell Data Analyst to organize and lead curation of large-scale multi-omic single cell atlases and to maintain a model zoo called Kipoi for machine learning models in genomics.

Duties include:
  • Collect, analyze and integrate large-scale single cell multiomic datasets from the ENCODE, IGVF, HuBMAP and HCA consortia
  • Identify and curate publicly available single cell datasets of relevance to the IGVF consortium
  • Maintain and improve the Kipoi model zoo for machine learning models in genomics
  • Co-lead and participate in the single cell analysis working group of the IGVF consortium
  • Collaborate closely with graduate students and postdocs in the Kundaje lab with curation and analysis of single cell datasets.
  • Create and participate in presentations of research and tools at conferences and workshops.

* - Other duties may also be assigned.

Bachelor’s degree in Computer Science or Bioinformatics or related scientific field and one year of related experience analyzing single cell RNA or ATAC-seq data, or combination of relevant experience.

  • Strong programming skills in Python
  • Strong software engineering skills
  • Strong experience working with single cell analysis tools such as Seurat, ScanPy, scVerse, scVI
  • Strong experience working with deep learning framework such as Keras/TensorFlow and/or Pytorch
  • Working knowledge of single cell assays and technologies
  • Working knowledge of genomics and genetics
  • Experience working with model zoos such as HuggingFaces.
  • Solid analytical skills.
  • Strong written and oral English communication skills
  • Strong team player in interdisciplinary teams
  • Ability to understand scientific literature, experimental procedures and their limitations, and current needs of the research community.

  • Frequently perform desk based computer tasks, seated work and use light/ fine grasping.
  • Occasionally stand, walk, and write by hand, 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.

  • May work extended hours based on project needs

  • 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,

The expected pay range for this position is $68,000 to $89,000 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.

As an organization that receives federal funding, Stanford University has a COVID-19 vaccination requirement that will apply to all university employees, including those working remotely in the United States and applicable subcontractors. To learn more about COVID policies and guidelines for Stanford University Staff, please visit