Principal Scientist, Computational Biology/Single Cell

Company Summary:

ProFound Therapeutics is discovering proteins hidden within the expanded human proteome to uncover novel drugs and drug targets, producing first-in-class medicines for a multitude of diseases. The company's ProFoundry Platform uses state-of-the-art protein detection technologies to systematically identify and validate proteins and dissect their therapeutic potential. The result is an ever-expanding database of tens of thousands of novel proteins, including their connectivity, functionality, and roles in health and disease. ProFound Therapeutics was founded in 2020 by Flagship Pioneering. For more information, please visit www.profoundtx.com.

Position Summary:

ProFound Therapeutics is seeking a pioneering Principal Scientist, Computational Biology, specialized in analyzing data from single-cell and/or spatial multi-omics technologies to help advance the ProFoundryTM Platform. The genetic, transcriptomic, proteomic, and imaging data in ProFoundry Atlas of novel human proteins is a unique resource for developing new therapeutics. The ideal candidate will thrive in a collaborative fast-paced environment and will provide the hands-on work necessary to use single-cell and spatial multi-omics data to drive forward ProFound's research and development.

Key Responsibilities:

1. Identify and process publicly available and internal generated single-cell and spatial transcriptome/multi-omics datasets using statistical and bioinformatics techniques to create meaningful biological insight.
2. Ensure multi-omics data analysis are documented and reproducible.
3. Develop and implement single-cell and spatial data integration methods and tools to integrate data from proteomics and high-content imaging to identify, prioritize, and characterize novel therapeutic targets.
4. Collaborate in cross-disciplinary teams including wet-lab and data scientists to build bioinformatic modeling, computational pipelines, data summaries, visualization dashboards for high throughput leading-edge multi-omics technologies.
5. Perform integrative and functional analyses to contribute to the understanding of phenotypes of drug perturbation, mechanism of action, and the identification of key response signatures.
6. Lead develop ProFound's multi-omics platform for maximal impact on biological characterization and the drug development pipeline.

Minimum Qualifications:

1. PhD trained in bioinformatics, computational biology or other relevant field with 5+ years of experience post-PhD.
2. Working knowledge of NGS-based genetics, genomics (especially 10X-based single-cell and spatial omics) and other non-NGS-based omics data processing and statistical analyses.
3. Experience in applying single-cell and/or spatial omics approaches in patients' tissues, primary cells or cell lines to identify causal genes involved in disease pathophysiological pathways and to address problems in the life sciences and generate actionable biological insight in diseases relevant to cardio-metabolic, inflammatory, neurodegenerative and/or neuropsychiatry disorders.
4. Ability to conduct statistical modeling and computational analyses on single-cell and/or spatial omics, especially cell type/state clustering, trajectory analysis, cell-cell communication/interaction, spatial cell-cell interactions.
5. Demonstrated industry experience or academic achievement, as evidenced by publications or contribution to widely used codebase.
6. Skilled user of command-line programming languages Python and/or R; 10X single-cell and spatial omics tools, deep learning modeling; publicly available single-cell/spatial omics browsers; as well as commonly used cloud-based platforms (such as Human cell atlas, CZ CELLxGENE Discover, Bioturing, Terra, Seven Bridge, etc.) to access such data.
7. A commitment to reproducible computational research.
8. Excellent communication and presentation skills.

Preferred Qualifications:

1. Solid background in basic biology, disease biology in therapeutic areas, such as cardio-metabolic, inflammatory, neurodegenerative and/or neuropsychiatry disorders.
2. Knowledge of human, primate and mouse cell references with cell signature and markers to cluster and identify cell types, cell sub-types and cell states.
3. Experience with cloud computing, especially AWS.
4. Experience with other multi-omics data, such as genetics, proteomics and high-content imaging data and software platforms.
5. Familiarity with large public domain data sources (i.e. Human cell data atlas, CZ CELLxGENE Discover, GEO/SRA, TCGA, CCLE, functional annotation resources).

Values and Behaviors:

We are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidate.

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.

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.

If your experience is close to what we're looking for, please consider applying. Experience comes in many forms, skills are transferable, and passion goes a long way. We know that diverse backgrounds and experiences make for the best problem-solving and creative thinking, which is why we're dedicated to adding new perspectives to the team and encourage everyone to apply. We look forward to learning more about you.

Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

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.