Intern, Regulatory Sequence Machine Learning (PhD)

Key Skills

ATAC-seq, ChIP-Seq, Deep neural networks, JAX framework, Machine learning techniques, Python Programming, PyTorch, R Programming, RNA-seq Data processing, Statistical modeling, TensorFlow

Job Description

Calico is seeking an intern to join the Kelley group. To succeed, you will need to be an enthusiastic team player, detail-oriented, extremely organized and comfortable working on complex problems. In this position you will explore cutting edge techniques for training machine learning models of regulatory sequences and applying them to predict the effect of genetic variants on gene regulation. The successful candidate will work closely with members of the Kelley group on our ongoing research program to understand the sequence basis of gene regulation with deep neural network models (e.g. Avsec 2021). The ML literature suggests several techniques to improve model accuracy or speed that we hope to explore during this internship. These improvements would greatly benefit Calico efforts to determine mechanisms for human genetic associations with aging phenotypes.

Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nat Methods 18, 1196–1203 (2021).

Responsibilities: 

• Build and improve upon current state-of-the-art deep neural network models for biological sequence analysis.
• Develop effective techniques for large-scale genetic variant effect prediction and interpretation.

Position requirements:

• Currently pursuing a PhD degree in computational biology, computer science, or a related field 
• Experience working with deep neural networks.
• Knowledge of gene regulation and genomics assays like RNA-seq, ATAC-seq, and ChIP-seq.
• Detail-oriented and organized
• Strong teamwork and communication skills
• Self-motivated with a “can-do” attitude
• Ability to work on-site in the South San Francisco office (pursuant with Calico’s return-to-site hybrid work policies)

About our Program:

Calico’s internship program is a paid 12-week program over the summer for students interested in understanding the fundamental science of aging and finding treatments for the associated and intractable diseases. Working in a collaborative environment and fully embedded in one of our labs/teams, Calico interns tackle a unique project under the mentorship of at least one of our scientists or engineers. Students from all schools, and students who identify with a demographic that is underrepresented within the technology, data science, and healthcare industries are encouraged to apply. This includes but is not limited to Black, Latinx, Native American, students with disabilities, veterans, and non-binary people.

Program Features:

• 3-month summer timeline
• In-person experience at our offices in South San Francisco
• Matching with at least one Calico mentor
• Group supplemental activities weekly featuring guest speakers, Senior Leadership spotlights, and discussion groups on aging science, our drug development approach, and more
• End-of-summer company-wide project showcase and poster session
• Competitive compensation ($40 - $65/hour) and monthly living expenses stipend