Bio-Informatics Analyst

Overview

The National Cancer Institute (NCI) is a leading research institution dedicated to advancing our understanding of cancer and developing innovative approaches for prevention, diagnosis, and treatment. Data Management Services, Inc. (a BRMi company) is currently seeking an experienced and collaborative Bioinformaticist to join our team in support of basic science driven stem cell and regeneration research in the Potency and Developmental Plasticity Section (https://ccr.cancer.gov/staff-directory/erin-l-davies).

This position offers a unique opportunity to contribute to primary research projects and to build public-facing community resources for two new laboratory models, the regenerative flatworms Macrostomum lignano and Schmidtea polychroa. We use these tractable laboratory organisms to study how adult stem cells are specified and regulated in different physiological contexts. We seek to uncover the molecular mechanisms and transcriptional regulatory programs required for the creation and maintenance of form and function during embryogenesis and adult tissue regeneration. Understanding the principles and genetic pathways that confer lifelong regenerative abilities in flatworms will provide paradigms and candidates for reverse-engineering regenerative therapies in mammals.

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Responsibilities

As a Bioinformaticist, you will serve as the lead analyst for ongoing transcriptomic projects employing bulk and single cell RNA-Sequencing. You will work closely with wet bench researchers to discuss analysis priorities and needs, fostering a collaborative environment and mentoring them in bioinformatics techniques. Your role will include regular interactions with the Principal Investigator and lab members, and periodic presentations to the lab, intramural colleagues, and the wider scientific community at society meetings. You will be expected to prepare analyses, code repositories, and necessary documentation for co-authored preprints and peer-reviewed publications. Good communication, documentation, and organizational skills are required.

• Project 1: Postnatal Single Cell Transcriptomic Atlas for the regenerative flatworm Macrostomum lignano
  • Create a comprehensive whole-animal transcriptomic atlas for Macrostomum lignano (Mlig) postnatal development, from newborn hatchlings through sexually mature adults.
  • Characterize the cellular repertoires of the major adult anatomical systems at different levels of resolution, starting with the characterization of major anatomical systems followed by subset analysis to examine heterogeneity within each system. This will involve manual curation and the use of homology-driven approaches.
  • Characterize adult pluripotent stem cell transcriptional heterogeneity and identify highly variable marker genes associated with major lineages. Additionally, identify differentially expressed candidate genes involved in stem cell identity, behavior, and cell type-specific lineage differentiation programs.
  • Determine in silico derived lineage trajectories from adult pluripotent stem cells to terminally differentiated cell types, providing valuable insights into fate determination processes.
  • Characterize the reproductive system, construct differentiation trajectories for male and female germline stem cell lineages, identify differentially expressed marker genes for comprehensive gonad composition characterization, and determine stages in the stepwise reconstruction of the gonads during juvenile development.
  • Contribute to the annotation and characterization of highly variable marker genes for somatic reproductive support structures.
  • Develop interactive, user-friendly apps and databases to facilitate data manipulation and presentation. These resources will initially be for internal use and subsequently web-accessible upon publication.
  • Detailed documentation of code used for analysis, including creation of a github repository.
  • Written accounts of work for Materials and Methods, Results, and Figures for preprinted manuscripts and peer-reviewed publication are required.
  • Other duties as assigned
• Project 2: Embryonic Single Cell Transcriptomic Staging Series for Schmidtea polychroa
  • Create a comprehensive whole-embryo transcriptomic atlas for Schmidtea polychroa embryos.
  • Characterize the cellular repertoires of major embryonic and adult anatomical systems at different levels of resolution, starting with the characterization of major anatomical systems and then examining heterogeneity within each system.
  • Assess which clusters and anatomical components remain constant across stages and which undergo changes during development.
  • Identify highly variable marker genes restricted to different cell types and/or developmental time points.
  • Determine in silico derived lineage trajectories and identify differentially expressed candidate genes involved in cell type-specific lineage differentiation programs.
  • Develop interactive, user-friendly apps and databases to facilitate data manipulation and presentation. These resources will initially be for internal use and subsequently web-accessible upon publication.
  • Detailed documentation of code used for analysis, including creation of a github repository.
  • Written accounts of work for Materials and Methods, Results, and Figures for preprinted manuscripts and peer-reviewed publication are required.
  • Other duties as assigned

Qualifications

• A Master's degree or higher in Bioinformatics or a related field, providing a strong foundation in bioinformatics techniques and data analysis.
• Relevant experience and training in bioinformatics and/or related fields of data analysis, with a strong emphasis on single cell RNA-Seq data analysis.
• In-depth knowledge of best practices in next-generation sequencing assays, particularly scRNA-Seq and bulk RNA-seq.
• Proficiency in programming languages such as R and Python, with the ability to handle large-scale datasets and implement advanced data analysis methods.
• Experience working in a UNIX environment on a high-performance computing cluster.
• Demonstrated experience in creating clear, interpretable graphics for publication and expertise in data visualization techniques.
• Strong desire and ability to develop interactive and user-friendly apps for data manipulation and presentation, such as RShiny apps.
• Excellent communication skills and the ability to work collaboratively in a team setting.
• Mentoring skills to guide wet bench researchers in acquiring competency in bioinformatics techniques.

EOE/Minorities/Females/Vet/Disabled 

We are an equal opportunity employer that values diversity and commitment at all levels. All individuals, regardless of personal characteristics, are encouraged to apply. Employment policies and decisions on employment and promotion are based on merit, qualifications, performance, and business needs. The decisions and criteria governing the employment relationship with all employees are made in a nondiscriminatory manner, without regard to race, religion, color, national origin, sex, age, marital status, physical or mental disability, medical condition, veteran status, or any other factor determined to be unlawful by federal, state, or local statutes.