Computational Sciences Intern - Cancer and Deep Learning
Posted on Indeed on Mar 18, 2021

Summary

The Computational Sciences Department at The Jackson Laboratory is looking for motivated students interested in spending significant time, during the summer, working remotely at JAX in advanced bioinformatics and biomedical software development for cutting-edge research focused on improving human health. Our internships have the potential to rapidly transform the knowledge and skills gained through education into practical, real-world experiences that make an impact on the world of science.

About Your JAX Internship Experience

Join peers selected from educational institutions across the country for a summer of professional growth and career exploration. As a JAX Intern you will receive a dedicated mentor in your department and connect with your fellow interns through JAX-sponsored activities.

Responsibilities

This internship will focus on characterizing tumor heterogeneity through deep learning. Deep learning approaches are capable of effectively differentiating patients with cancer from healthy controls based on tissue images. We are interested in understanding what regions of the tissue (represented by deep learning features) are associated with cancer. In particular, we seek to delineate regions common to all (or many) cancer types, regions unique to one cancer type, and regions linked to more aggressive forms of disease. By focusing on these regions we believe we can improve the detection limit of these algorithms - e.g., to discern cancer when only a small fraction of the image is malignant. Further, biological interpretation of these prioritized regions may elucidate novel aspects of disease initiation or progression. Such interpretation might involve (1) spatially-resolved expression sequencing (i.e., spatial transcriptomics) to determine genes and pathways active within regions or (2) computational prediction of cell types present within the regions.

Expected Outcomes

As a result of the internship, you will gain:

  • Insight into the fast-moving field of deep learning-based image analysis for cancer detection
  • An introduction to the biological and immune mechanisms underlying cancer
  • Practical skills in applying statistical and machine learning techniques (e.g., regression and clustering) to link image features to patient outcome
  • Experience working in a highly productive, integrated team data science environment,
  • Exposure to leading-edge methods and technologies utilized in advanced biotech enterprises, and
  • An understanding of the potential career opportunities at JAX and in the field.

Desired Qualifications

JAX encourages application from a diverse mix of educational experiences and backgrounds. Preferred qualifications for this project include:

  • Required: experience with Python (numpy, scikit-learn, matplotlib), clustering
  • Preferred: experience with tensorflow, basic image analysis/visualization (e.g., opencv), some understanding of biology fundamentals (e.g., gene expression)

Applicants should be:

  • Able to demonstrate successful completion of coursework in the related field(s),
  • Enthusiastic and willing to learn
  • Experienced in working on projects with a team
  • Responsible, reliable, accountable, and attentive to detail and quality.

About JAX:

The Jackson Laboratory (JAX) is an independent, nonprofit biomedical research institution with more than 2,400 employees. Headquartered in Bar Harbor, Maine, it has a National Cancer Institute-designated Cancer Center in Augusta, Maine, a genomic medicine institute in Farmington, Connecticut, and facilities in Ellsworth, Maine, Sacramento, California, and Shanghai, China. Its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health.

JAX employees work in a collaborative, value-driven, and team-based environment where the focus is on advancing science and improving patients’ lives. Researchers apply genetics to increase the understanding of human disease and advance treatments and cures for cancer, neurological and immune disorders, diabetes, aging, and heart disease. JAX was voted among the top 15 “Best Places to Work in Academia” in the United States in a poll conducted by The Scientist magazine!

EEO Statement:

The Jackson Laboratory provides equal employment opportunities to all employees and applicants for employment in all job classifications without regard to race, color, religion, age, mental disability, physical disability, medical condition, gender, sexual orientation, genetic information, ancestry, marital status, national origin, veteran status, and other classifications protected by applicable state and local non-discrimination laws.

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