Senior Scientist, Causal Inference Specialist

Company Summary:

Each day, the lives of more than 2 billion people across the globe are impacted by chronic diseases. Moreover, the economic burden on society of treating chronic disease is spinning out of control. Today, this dire situation appears unlikely to change as >95% of global healthcare costs are spent on treating rather than preventing chronic diseases. FL84, Inc. is a privately held early-stage company that is applying advanced biological and computational platforms to discover breakthroughs in detection of and intervention against the etiologies that drive progression from health to disease. Our goal is to leverage our proprietary platforms to disrupt the current approach of treating chronic disease too late. We endeavor to provide true health care rather than sick care to individuals that are at risk of progressing to disease.

About Flagship:

Flagship Pioneering is a biotechnology company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Position Summary:

We are seeking a Sr. Scientist of Computational Biology who is enthusiastic about developing, learning and applying computational skills to understand complex biological systems and their relationship to clinical state changes. The candidate will design and implement causal models that link molecular datasets, including single-cell/nuclei RNAseq, proteomics, and spatial transcriptomics to clinical outcomes.  The role will focus on two main areas: (1) application of machine learning to uncover causal disease mechanisms and identify novel therapeutic targets; and (2) exploration and processing of large, multimodal datasets to expand FL84’s platform to new disease areas.  An ideal candidate will pride themselves on their ability to craft scientifically logical and creative stories out of complex data and convert them into executable experiments. The position will provide a unique opportunity to play a foundational role in the development of FL84’s preclinical platform and treat diseases before they become a burden to the patient or the healthcare system.

Key Responsibilities:

• Develop and apply bioinformatics, computational biology, and machine learning tools to generate causal hypotheses from high-dimensional molecular datasets.
• Work with FL84’s biology team to test causal hypotheses in vitro and interpret the output of computational tools in the context of specific disease areas.
• Identify and incorporate internal and external datasets to augment computational disease models with further evidence of causality.
• Link causal inference made on biological data with clinically relevant data from electronic health records, clinical trials, or other sources.
• Establish pipelines to process large-scale molecular datasets and prioritize targets for biological validation.
• Develop clear, intuitive visualizations and communicate analysis results via presentations to a multi-disciplinary audience.
• Cultivate a data-centric company philosophy by helping to maintain best practices for software development, data management, and infrastructure.
• Monitor and evaluate new and emerging technologies and models and identify opportunities for collaboration within Flagship Pioneering companies, academia, and third parties.

Basic Requirements:

• PhD in computer science, computational biology, bioinformatics, or related field with 5+ years of related experience
• Strong background in causal inference methodology.
• Deep understanding of biology and ability to formulate and test relevant hypotheses using large-scale -omics datasets.
• Extensive Python programming experience, including performance tuning, debugging, and familiarity with standard scientific packages for single-cell data analysis.
• Proficiency with git, Docker and AWS.
• Ability to independently lead and run research projects, while maintaining close communication with team members.
• Excellent communication and presentation skills. Must be able to speak and ideate with multi-disciplinary team including biologists. Must be able to think independently, work collaboratively and contribute to an active intellectual environment.

Preferred Requirements:

• Experience with time series analysis, domain adaptation, transfer learning, multi-modal deep learning, and geometric deep learning
• Familiarity with R/Bioconductor and Nextflow
• Experience with using CMAP, or other perturbagen (e.g., small molecule, CRISPR, etc.) induced transcriptomic databases for causal inference.
• Experience with genetic data and Mendelian Randomization.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.