Bioinformatics Analyst I

*A Cover Letter is strongly encouraged to be considered for this role

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 Cell Science is to create multi-scale visual models of cell organization, dynamics, and activities. Our approach encompasses large scale data collection, observation, theory, and predictions to understand cellular behavior in normal and pathological contexts. As a division within the Allen Institute, the Allen Institute for Cell Science uses a team-oriented approach, focusing on accelerating foundational research, developing standards and models, and cultivating new ideas to make a transformational impact on science.

We seek an innovative and team-oriented Bioinformaticist to join the Allen Institute for Cell Science to build a multimodal system to analyze cell states. The Bioinformaticist will analyze and integrate single cell transcriptomic data generated from differentiated human induced pluripotent stem cells with imaging information obtained from time-lapse microscopy. A successful candidate will use this dataset to design and test probes for multiplexed RNA-FISH, and subsequently, investigate the spatial transcript and protein localization. This work will generate novel datasets to elucidate cellular states that directly impact the AICS mission and goals. The ideal candidate will possess a background in biology, computational biology/bioinformatics and an interest in working closely with an interdisciplinary team to support institute goals. They will also have an interest in developing a range of robust tools for cell biology research both within and outside AICS.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality, high-impact science can only be produced when it includes different perspectives. We are committed to increasing diversity across each team and strongly encourage people from all backgrounds to apply for this role.

Essential Functions

• Analyze single cell transcriptomics (scRNA-Seq) data from FASTQ through alignment and subsequent downstream analyses
• Build and support bioinformatic tools and reproducible pipelines to support team-based scientific programs
• Assist with creating workflows to enable data sharing internally and externally
• Work across teams to integrate scRNAseq data with imaging data including RNA-FISH to support scientific projects and programs
• Work in an collaborative interdiscplinary scientific environment
• Effectively communicate the impact of the work through presentations, dissemination and research papers within and outside the AICS community

Required Education and Experience

• Bachelor’s Degree in biology, computational biology, bioinformatics, computer science, biostatistics, physics or applied math

Preferred Education and Experience

• Master’s Degree in biology, computational biology, bioinformatics, computer science, biostatistics, physics or applied math
• Experience with computational analysis of biological data sets
• Expertise with bash and at least one programing language (eg. Python, R)
• Experience analyzing RNA-seq, exome, whole genome or related sequencing data types in population and/or single cells
• Knowledge of concepts in genomic experimental, and analytical methods (including different sequencing technologies)
• Knowledge of common Next-generation sequencing analysis tools and workflow managers (eg. STAR, scater, Seurat, Monocle, snakemake etc)
• Experience with git version control and Jupyter and/or Rstudio
• Expertise with Linux environment, high-performance cluster computing, and command line interfaces
• Knowledge of open source genomics database and resources (ex. UCSC genome browser, Ensembl, OMIM, etc)
• Knowledge of multiplexed RNA-FISH methods (spatial transcriptomics)

Work Environment

• May enter laboratory environment, including potential exposure to lasers, biohazards

Position Type/Expected Hours of Work

• This role is currently working onsite and remotely when possible, due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees.

Additional Eligibility Qualifications

• In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

Additional Comments

• **Please note, this opportunity does not offer relocation assistance**
• **Please note, this opportunity does not offer work visa sponsorship**

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.