Summer Intern – Data-Driven Discovery Center / Integrating genomic and electrophysiological data single cell mouse data

Summer Intern – Data-Driven Discovery Center / Integrating genomic and electrophysiological data single cell mouse data

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 Data-Driven Discovery Center for Biology (D3B) is committed to pioneering the future of bioscience research by leveraging state-of-the-art computational techniques and data analytics. Our mission focuses on driving advancements in neuroscience, cellular biology, and immunology through the integration of computer science and biological research. As part of the Allen Institute, D3B aims to be a global leader in creating actionable insights from complex biological data.

The Allen Institute has provided a unique opportunity by offering access to single-cell RNA transcription data and single-cell electrophysiological recordings for the same set of neurons. This convergence of genomic and electrophysiological measurements within a shared neuronal population presents an unprecedented avenue for unraveling the complexities inherent in the biological neural system. One of the biggest recent advancements is the development of foundational models for cell states. We plan to make use of the hidden states in such foundational models as a predictor for physiology. On the other hand neuronal models predicting the in-vitro electrophysiological responses are also getting better and better. This project will try to link the two using simple statistical models. Due to the availability of physiological data, this project will focus on mouse neurons.

We are seeking a Summer Intern to investigate the relationship between transcriptomic exon and intron information and electrophysiological in vitro data. Specifically, the intern will employ standard machine learning techniques (e.g. Principal component analysis (PCA)), to denoise the transcriptional information, with a focus of including both exon and intron data. This denoising process is needed to unveil latent patterns of genomic information. Subsequently, the intern will analyze the relation between neuronal electrophysiological features and the denoised transcription data. The analysis of this relation will start with generalized linear models and potentially. Depending on the knowledge of the intern and time available, more advanced methods can be used (e.g. Transformer, Variational Autoencoder (VAE)).

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.

Applications must be received by January 7, 2025, to be considered.

Educational Objectives

• Accessing and Analyzing Single-Cell RNA data, understanding the difference between exon and intronic information
• Accessing Single-Cell Electrophysiological Recording Data
• Learning to use PCA and potentially Variational Auto Encoders and/or Transformers
• Learning to use generalized linear models

Applicant Requirements

• Must be enrolled in, or a 2025 graduate of an accredited associate’s, bachelor’s, or master’s degree program
• Must be able to start on either June 9th or June 23rd, 2025 and commit to the full 10-week program
• Must be eligible to work in the United States for the duration of the internship
• Must be 18 years of age or older

Work Environment

• Open Office Environment

Position Type/Expected Hours of Work

• Interns are expected to work 35-40 hours a week throughout the 10-week period
• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with flexibility to work remotely on a limited basis.

Additional Comments

• **Please note, this opportunity requires U.S work authorization and does not sponsor work visas**
• **Travel and/or housing stipend available to qualifying interns**

Compensation

• $21.50 per hour (non-negotiable)

Benefits

• Interns will accrue paid sick days and receive a free Seattle transportation card (ORCA Business Passport)

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities