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Staff Scientist, Transcriptomics/Bioinformatics


New York Stem Cell Foundation

Job Location

619 West 54th Street
New York, NY 10019
United States


Yearly Salary

Job Description

The New York Stem Cell Foundation (NYSCF) Research Institute is a growing and successful nonprofit whose mission is to accelerate cures through stem cell research.

NYSCF is seeking a Staff Scientist, Transcriptomics/Bioinformatics is responsible for building custom pipelines to analyze and interpret biological data generated by teams within the NYSCF Research Institute. You are a skilled bioinformatician who has knowledge and experience in working with a wide range of human transcriptomic based datasets, including single-cell platforms, bulk RNA-seq, as well as CRISPR screens. You will have demonstrated a solid understanding of biology and genomics, programming skills, and experience with high-throughput molecular sequencing technologies.

What you'll do

  • Develop, deploy, and document software that supports the analysis, annotation, and quality control pipelines for data
  • Automate, benchmark and test data analysis pipelines and support transition of these pipelines into a workflow management system
  • Work with teams on requirements for alignment, processing and analysis, and generate appropriate logs and reports of data
  • Process and analyze next-generation sequencing (NGS) data generated on (primarily) Illumina and 10x platforms
  • Perform custom sequence alignment, processing, QC and expression analysis of our novel RNA/DNA-sequencing screens
  • Find novel ways to translate scientific concepts, as published in the literature, into computational context and standard analysis pipelines
  • Develop and implement novel data visualization strategies to summarize results and QC features
  • Assist in managing our cloud-computing environment that runs batch jobs to process and analyze our sequencing data at scale
  • Generate reports and data summaries to be presented both internally and to external collaborators
  • Support research terms in developing analysis pipelines including script writing/coding and troubleshooting


What we're looking for

  • M.S. or recent PhD in Biology, Bioinformatics, Genomics, Computational Biology or similar field
  • An interest in stem cell research
  • Knowledge of sequencing technologies such as RNA-Seq, ChIP-Seq, ATAC-Seq, Single Cell Seq
  • Understanding of whole-genome or transcriptome alignment programs such as Bowtie, Trinity, RNA-STAR, GSNAP, Salmon, Kallisto
  • Experience with statistical analysis of biological data - e.g., using DESeq2 to test for differential expression
  • Experience programming in a high-level language such as Python or R
  • Experience with additional languages such as Java, .NETCore and C# is a plus
  • Experience with database integration (including SQL), maintenance, and optimization with LIMS systems are a pluGrasp of basic molecular biology and genetics - wet-lab laboratory experience is a plus
  • Familiarity with cloud computing infrastructures on AWS and working with cloud-based tools such as AWS Batch, Data Pipeline, RDS/Redshift is a plus
  • Experience with visualization tools such as Tableau, Matplotlib, ggplot2 or TIBCO Spotfire is a plus
  • Level will be commensurate with experience

We offer all full-time employees a comprehensive benefits package that goes into effect on the first of the month following your start date.

In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and complete the required employment eligibility verification upon hire. The position is located onsite on a full-time basis at our location in Manhattan.

NYSCF is an equal opportunity employer, and we value diversity in our company. It ensures equal employment opportunity without discrimination or harassment based on race, color, religion, sex (including pregnancy, childbirth, or related medical conditions), sexual orientation, gender identity or expression, age, disability, national origin, marital or domestic/civil partnership status, genetic information, citizenship status, veteran status, or any other characteristic protected by law.

Our Research Institute facility is a fully COVID-19 vaccinated workplace.

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