Computational Biology Scientist II
Kaleido Biosciences
 Lexington, MA

Computational Biology Scientist II

Kaleido Biosciences is a clinical-stage healthcare company with a differentiated, chemistry-driven approach to leveraging the potential of the microbiome organ to treat disease and improve human health. The Company’s Microbiome Metabolic Therapies (MMT™) are designed to modulate the metabolic output and profile of the microbiome by driving the function and distribution of the organ’s existing microbes. Kaleido is advancing a broad pipeline of MMT candidates to address a variety of diseases and conditions with significant unmet patient needs. The Company’s human-centric discovery and development offers the potential to be faster and more cost-efficient than traditional drug development. We also have an exceptional team that is committed to scientific innovation, transforming lives and building a strong culture.


This Computational Biology Scientist II position is an exciting opportunity for a doctoral level computational scientist to join the growing Computational Biology and Integrated Data Sciences (IDS) team in the Discovery Department of Kaleido Biosciences R&D. IDS plays a key role in enabling the company’s efforts to bring current and future MMTs to patients in-need and improve human health. The successful candidate will lead and execute computational biology analysis projects in collaboration with interdisciplinary teams of biologists, chemists and clinicians, who are focused on developing novel therapeutics that modulate the microbiome for the treatment of various infectious and chronic diseases. This position offers the opportunity to join a high-performing, collaborative computational biology team which embraces innovative and transformative science. Our company culture encourages professional development, engagement with the wider scientific community and personal growth. Individuals with significant experience in using computational biology and biostatistical approaches to analyze multi-omics datasets in the context of the human microbiome and host immunology are strongly encouraged to apply.

Summary of Key Responsibilities:

  • Be the computational biology expert on multi-disciplinary project teams and contribute to pre-clinical and clinical studies for microbiome modulators in multiple disease areas.
  • Deliver timely, in-depth and start-of-the-art analyses of next generation DNA sequencing (NGS) data sets of the microbiome, whole bacterial genomes and human transcriptomics along with other occasional data-types (i.e. metabolomics), that are obtained from pre-clinical studies and clinical trials
  • Provide innovative analyses of public and proprietary human and microbial ‘omics datasets for insights into disease indication, mechanism of action and/or biomarker identification
  • Engage with software development teams working on critical platform projects such as specialized databases and data analysis pipelines
  • Contribute to the strategic direction of the IDS team through your knowledge of new and innovative developments in the microbiome field with potential applications to drug discovery
  • Prepare reports, peer-reviewed publications and oral presentations for both internal and external scientific audiences
  • Ensure on-time and complete compliance with mandatory corporate training, best practices and regulatory requirements


Core qualifications

  • Ph.D. in bioinformatics, computational biology, computer or data science with an emphasis on the microbiome, microbial ecology, molecular immunology, and/or host-microbiome interactions
  • Expert programming skills in the core bioinformatics languages: R, Python and Linux
  • Experience in the analyses of next generation sequencing (NGS) data pertaining to the microbiome (i.e. metagenomics and 16S rRNA gene amplicons) and bacterial whole genomes
  • Experience in the analysis of human NGS (RNA-seq and/or scRNA) and metabolomics data
  • Experience in the integrative analysis of large, multi-dimensional datasets using network analyses, machine learning and other approaches
  • Good knowledge of the microbiome and/or human molecular immunology
  • Innovation scientist with a strong record of scientific publications and presentations
  • Excellent oral and written communication skills.
  • Evidence of effectively interacting and contributing to collaborative research teams

Additional qualifications

  • Experience with drug discovery in biotech, pharma, academic and/or government sectors
  • Applied experience in analyzing microbiome and human disease datasets
  • Experience with basic chemo-informatics tools for compound similarity searches and ligand-based virtual screening
  • Familiarity using AWS cloud computing and cluster deployment
  • Knowledge of database design and query languages (i.e. SQL)


Kaleido Biosciences is an EEO employer committed to an exciting, diverse, and enriching work environment.