Job Description

Bioinformatics Scientist I – AI Applications

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.

The Allen Institute for Immunology is seeking a Bioinformatics Scientist II I – AI Applications to train AI models using our enormous multimodal omics data. Reporting to the Director of Informatics & Computational Biology at the Allen Institute for Immunology, the ideal candidate is a self-motivated team player who can work closely with immunologists and bioinformaticians, is an expert in applying AI methodologies for biological/medical research and has a track record of training transformer models. The successful candidate will also have excellent communication skills that can represent our efforts to our stakeholders internally and in external forums.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly. We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Essential Functions

• Train AI models (e.g. transformers and variational autoencoders) based on multimodal OMICS data under minimal supervision, including but not limited to: spatial transcriptomics, scRNA-seq, scATAC-seq, CITE-seq, TEA-seq, flow cytometry, and proteomics
• Apply AI methodologies and work closely with other scientists to generate testable hypotheses for new biological insights, and identify potential biomarkers and/or drug targets for disease of interest
• Write reports, research papers, patent applications, and other documents
• Represent our efforts to our stakeholders internally and in external forums
• Contribute to a rigorously scientific, cohesive and efficient team environment

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.

Required Education and Experience

• PhD in computer science, applied mathematics, bioinformatics, biostatistics, computational biology, or closely related disciplines; or equivalent combination of education and experience

Preferred Education and Experience

• Demonstrated experience in training AI models, including but not limited to: large language models (LLMs), transformers, variational autoencoders, neutral networks, etc.
• Experience in applying AI methodologies for biological/medical research
• Familiar with OMICS technologies
• Foundational knowledge of AI methodologies and bioinformatics
• Experience with R and/or Python
• Strong publication record
• Experience working with outside collaborators to achieve defined objectives
• Familiarity with cloud computing and/or Linux
• Experience using Git or similar version control system
• Excellent written and verbal communication skills and organizational skills
• Good problem-solving skills, curious and eager to take new challenges
• Able to work independently as well as in a collaborative high paced environment
• The successful candidate must be self-motivated, a team player, attentive to details, and able to handle multiple projects simultaneously

Work Environment

• May enter laboratory environment - possible exposure to chemical, biological, or other hazardous substances.

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type/Expected Hours of Work

• Occasional evening and weekend hours required
• 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.

Travel

• Attendance and participation in national and international conferences may be required

Additional Comments

• **Please note, this opportunity offersrelocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

• $90,900 – 112,400

* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outline 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 Institutes 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.

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.

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