Bioinformatics Programmer - Molecular Diagnostics

NYU Langone Health

  • New York
  • $67,771-75,955 per year
  • Training
  • Full-time
  • 9 days ago
NYU Grossman School of Medicine is one of the nation's top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU Langone Health, the Grossman School of Medicine at its core is committed to improving the human condition through medical education, scientific research, and direct patient care. At NYU Langone Health, equity and inclusion are fundamental values. We strive to be a place where our exceptionally talented faculty, staff, and students of all identities can thrive. We embrace inclusion and individual skills, ideas, and knowledge.For more information, go to med.nyu.edu, and interact with us on LinkedIn, Glassdoor, Indeed, Facebook, Twitter and Instagram.Position Summary:We have an exciting opportunity to join our team as a Bioinformatics Programmer/Analyst working in a Molecular Diagnostics environment.NYU Langone Health, a world-class, patient-centered, integrated, academic medical center, and one of the nations premier centers for excellence in clinical care, biomedical research and medical education, is seeking highly motivated, enthusiastic individual to join the Department of Molecular Pathology working in the field of Clinical Genomics and Precision Medicine.The Molecular Pathology Lab at NYU Langone Health with Applied Bioinformatics Laboratories (ABL) are seeking a highly motivated, enthusiastic and creative individual to become a member of our clinical bioinformatics team. Working in the Department of Molecular Pathology as a Bioinformatics Analyst specializing in molecular diagnostics, you will be responsible for the analysis of next-generation sequencing (NGS) data conformant to CLIA / CLEP and FDA guidelines. You will work as part of a team of highly experienced laboratory and informatics scientists at the NYU Langone Health Molecular Pathology Laboratory. The primary responsibilities include and are not limited to end-to-end analysis of next generation sequencing data using established pipelines, data quality control, assisting in validation of new clinical assays, and performing custom case-by-case bioinformatics analyses. You will be part of a clinical lab team of scientists and laboratory personnel taking an active part in generating, developing, and rThis is a great opportunity to quickly acquire high-in-demand bioinformatics programming skills, develop new analysis tools/pipelines, analyze challenging datasets, and be involved in cutting edge NGS based cancer diagnostics, clinical genomics and hands on precision medicine for the benefit of patients.Job Responsibilities:
  • Analyze clinical sequencing data using established workflows
  • Develop and apply novel analysis approaches to aid clinical sample variant prioritization
  • Benchmark new tools for sequencing data analysis and propose improvements
  • Analyze validation experiments for laboratory developed tests (LDT)
  • Implement and execute analysis pipelines and workflows using Nextflow and Singularity Containers
  • Assist CLIA laboratory personnel in preparing data, text and figures for case analysis, LDT validation proposals, manuscripts and external presentations
  • Perform and evaluate appropriate sequencing QC measures
  • Develop and maintain database of variants, curation, and notes.
Minimum Qualifications:
  • To qualify you must have a M.Sc. degree with a minimum of 1 years of work or internship experience in cancer or hereditary disease, next generation sequencing (NGS) analysis or in cancer genomics or human genetics with demonstrable biomedical NGS bioinformatics skills is required
  • Strong programming skills in Python, R and shell scripting
  • Basic understanding of human genetics
  • Work experience and algorithm understanding of standard software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools
  • Knowledge in the analysis of SNV, Indel, CNV and structural variants for both somatic and germline disease, additional understanding of variant annotation
  • Familiarity with various NGS QC principles
  • Work experience with commonly used public genomics datasets (1000 genomes, ExAC, OMIM, gnomAD, ClinVar, HGMD, CIViCDB, PharmGKB, OncoKB, etc.)
  • Detail-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics
  • Team oriented with excellent written and verbal communication skills
  • This position is an onsite role for a minimum of 6 months with the potential for hybrid role after that based on performance, no fully remote work at this time.
Preferred Qualifications:
  • Prior experience working in CLIA environment is a plus
  • Experience in variant calling benchmarking and clinical validation analysis (e.g. concordance, limit of detection, assay reproducibility)
  • Experience of working in a Linux environment, experience with SGE
  • Experience with running workflows on public cloud (GCP / AWS)
  • Experience with developing and querying databases using SQL queries
  • Experience with web-development (HTML, CSS, JavaScript, TypeScript and related)
Qualified candidates must be able to effectively communicate with all levels of the organization.NYU Grossman School of Medicine provides its staff with far more than just a place to work. Rather, we are an institution you can be proud of, an institution where you'll feel good about devoting your time and your talents. At NYU Langone Health, we are committed to supporting our workforce and their loved ones with a comprehensive benefits and wellness package. Our offerings provide a robust support system for any stage of life, whether it's developing your career, starting a family, or saving for retirement. The support employees receive goes beyond a standard benefit offering, where employees have access to financial security benefits, a generous time-off program and employee resources groups for peer support. Additionally, all employees have access to our holistic employee wellness program, which focuses on seven key areas of well-being: physical, mental, nutritional, sleep, social, financial, and preventive care. The benefits and wellness package is designed to allow you to focus on what truly matters.NYU Grossman School of Medicine is an equal opportunity employer and committed to inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply and will receive consideration. We require applications to be completed online.View Know Your Rights: Workplace discrimination is illegal.NYU Langone Health provides a salary range to comply with the New York state Law on Salary Transparency in Job Advertisements. The salary range for the role is $67,771.14 - $75,955.36 Annually. Actual salaries depend on a variety of factors, including experience, specialty, education, and hospital need. The salary range or contractual rate listed does not include bonuses/incentive, differential pay or other forms of compensation or benefits.To view the Pay Transparency Notice, please click hereRequired SkillsRequired Experience

NYU Langone Health