New York, New York Research Institute – Research Full Time

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

The (Associate) Staff Scientist, Bioinformatics is responsible for building custom tools to organize and analyze biological data within the NYSCF Research Institute. We are looking for someone who has a knowledge of molecular biology/genomics as well as experience in data science and scientific programming. The successful candidate will have demonstrated a solid understanding of biology and genomics, programming skills, and experience with high-throughput molecular sequencing technologies. Preference will be given to candidates who have significant experience with genome wide CRISPR screens and construction of computational pipelines for RNA-seq data from single-cell platforms such as 10x.

What you'll do:

• Prototype, 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
• Benchmark and evaluate individual bioinformatics tools and components of the analysis pipelines to ensure best performance and correctness
• 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;Develop and implement tools for automatic report generation to be presented both internally and to external collaborators
• Support computational biology groups with scripting, troubleshooting, and automation coding
• Develop stored procedures to store, maintain and query biological data in SQL databases, hosted in AWS EC2 environments
• Communicate and coordinate with external partners to support computational biology projects
• Process and analyze next-generation sequencing (NGS) data generated on Illumina and 10x platforms
• Transform and load sequencing data and results into a SQL database
• Help implement a LIMS system that will store sample and library metadata Perform custom sequence alignment, processing, QC and expression analysis of our novel RNA/DNA-sequencing screens
• Work with teams on requirements for alignment, processing and analysis, and generate appropriate logs and reports of data
• Assist in managing our cloud-computing environment that runs batch jobs to process and analyze our sequencing data at scale

What we're looking for:
• The applicant should have an interest in stem cell research
• A high proficiency with multiple software platforms is required
• Experience with database integration, maintenance, and optimization with LIMS systems are a plus
• Experience programming in R and Python with emphasis on scientific data; experience with programming in Java, C++ or VB.NET is desired.
• M.S. or recent PhD in Biology, Bioinformatics, Genomics, Computational Biology or similar field Grasp of basic molecular biology and genetics - laboratory experience is a plus
• Experience programming in a high-level language such as Python, Ruby or R; Python is preferred
• Basic database skills (SQL) and some experience with LIMS
• 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 DESeq to test for differential expression
• Ability to work in a multi-disciplinary environment of biostatisticians, computational biologists, laboratory biologists and translational scientists
• 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
• Understanding of the biology of gene regulation is a plus (promoters, enhancers, microRNAs, etc)
• Level will be commensurate with experience
NYSCF is an equal opportunity employer and we value diversity at 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.

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