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 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.

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

• 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.