What are the responsibilities and job description for the Bioinformatics Intern – Analysis Tool Development position at Allen Institute for Immunology?
The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.
The mission of the Allen Institute for Immunology is to advance the fundamental understanding of human immunology through the study of immune health and diseases where excessive or impaired immune responses drive pathological processes. The Institute will employ a multi-disciplinary team approach in collaboration with academic centers of human immunology to generate novel mechanistic insights into the immune synapse in health and in diseases such as autoimmunity or oncology. The Institute will simultaneously provide a foundational data set and tools for future immunological research as well as a novel collaboration portal for the broader scientific community.
We are seeking an individual to join the Allen Innovation Center, a new effort within the Allen Institute for Immunology, with a goal of enabling non-coding scientists and external partners to take advantage of our robust, industrial-scale wet lab pipelines and our dry lab platform, the Human Immune System Explorer.
There are many opportunities to help improve and standardize the computational approaches we've utilized to date. Examples of the kinds of internship projects available for this initiative include:
Improved doublet detection for scRNA-seq
We have generated single-cell RNA-seq data from over 55 million cells across many immune system conditions. We've found that a key bottleneck in our analysis is in the identification and removal of "doublets", which are generated when two cells are co-encapsulated in a single droplet by microfluidic capture. We now have millions of expert-identified doublets, and believe that this could be a fruitful training set for neural network or gradient descent machine learning approaches to doublet identification. Once optimized, we will work to integrate this updated approach for application to thousands of datasets.
Standardized pseudobulk differential expression analysis
Many projects that utilize many scRNA-seq samples combine single cells into "pseudobulk" data from each cell type for use in comparisons between conditions. Currently, this data is compiled and comparisons are generated by individual analysts using bespoke code for each project. We would like to enable non-coding scientists to perform these comparisons using an interactive tool to select samples, select genes to compare, set parameters, perform analysis, and return visualizations of results to our scientists.
The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.
Educational Objectives
After completing an internship, we hope you will come away with the following experience:
We hope that an intern may be able to bring some of these skills to this position. However, we recognize that this is a learning experience, and will provide training and resources to expand on an intern's existing skillset.
Required Education And Experience
The mission of the Allen Institute for Immunology is to advance the fundamental understanding of human immunology through the study of immune health and diseases where excessive or impaired immune responses drive pathological processes. The Institute will employ a multi-disciplinary team approach in collaboration with academic centers of human immunology to generate novel mechanistic insights into the immune synapse in health and in diseases such as autoimmunity or oncology. The Institute will simultaneously provide a foundational data set and tools for future immunological research as well as a novel collaboration portal for the broader scientific community.
We are seeking an individual to join the Allen Innovation Center, a new effort within the Allen Institute for Immunology, with a goal of enabling non-coding scientists and external partners to take advantage of our robust, industrial-scale wet lab pipelines and our dry lab platform, the Human Immune System Explorer.
There are many opportunities to help improve and standardize the computational approaches we've utilized to date. Examples of the kinds of internship projects available for this initiative include:
Improved doublet detection for scRNA-seq
We have generated single-cell RNA-seq data from over 55 million cells across many immune system conditions. We've found that a key bottleneck in our analysis is in the identification and removal of "doublets", which are generated when two cells are co-encapsulated in a single droplet by microfluidic capture. We now have millions of expert-identified doublets, and believe that this could be a fruitful training set for neural network or gradient descent machine learning approaches to doublet identification. Once optimized, we will work to integrate this updated approach for application to thousands of datasets.
Standardized pseudobulk differential expression analysis
Many projects that utilize many scRNA-seq samples combine single cells into "pseudobulk" data from each cell type for use in comparisons between conditions. Currently, this data is compiled and comparisons are generated by individual analysts using bespoke code for each project. We would like to enable non-coding scientists to perform these comparisons using an interactive tool to select samples, select genes to compare, set parameters, perform analysis, and return visualizations of results to our scientists.
The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.
Educational Objectives
After completing an internship, we hope you will come away with the following experience:
- An understanding of human immune health and disease
- An understanding of the principles behind cutting edge single cell technologies
- Experience working with a cross-functional team structure including scientists, bioinformaticians and software developers
- Development of new data analysis and/or visualization tools within the context of a large, multimodal data analysis platform
We hope that an intern may be able to bring some of these skills to this position. However, we recognize that this is a learning experience, and will provide training and resources to expand on an intern's existing skillset.
- Write scripts in Python or R
- Use Jupyter Notebook environments to perform and explore data analysis methods
- Utilize interactive visualization toolkits (we primarily use Dash)
- Use Git and Github for version control
- Perform analysis with command-line scripting and tools
- Use Linux/Unix-like systems for data analysis
Required Education And Experience
- Currently enrolled in the MS program in Bioinformatics and Genomics, or a related field at University of Oregon, or in an equivalent MS program
- Open office seating
- May enter laboratory environment, including potential exposure to lasers, biohazards
- Working at a computer and using a mouse for extended periods of time
- This is a full time role for the duration of the internship (9 months, April 2025 to January 2026)
- This is a Monday through Friday, regular business hours position
- This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
- **Please note, this opportunity offers relocation assistance**
- $35.58 per hour plus benefits and travel and/or housing stipend
- Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institute Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.
Salary : $36
