NYU Langone Health
Bioinformatics Programmer - Molecular Diagnostics (Onsite position)
NYU Langone Health, New York, New York, us, 10261
Overview
Bioinformatics Programmer - Molecular Diagnostics (Onsite position) at NYU Langone Health. The role focuses on analysis of next-generation sequencing data in a Molecular Pathology setting, supporting clinical genomics and precision medicine initiatives. Position Summary: Bioinformatics Programmer/Analyst in a Molecular Diagnostics environment, working in CLIA/CLEP/FDA-guided clinical genomics workflows, collaborating with laboratory and informatics scientists in the Molecular Pathology Laboratory. 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
Master’s degree with a minimum of 1 year of work or internship experience in cancer or hereditary disease, next generation sequencing (NGS) analysis or cancer genomics/human genetics with demonstrable biomedical NGS bioinformatics skills Strong programming skills in Python, R and shell scripting Basic understanding of human genetics Experience with FASTQ, BAM, VCF data and tools (e.g., BWA, GATK, Picard, samtools, bcftools) Knowledge of SNV, Indel, CNV and structural variant analysis for somatic and germline disease, and variant annotation Familiarity with NGS QC principles Experience with public genomics datasets (e.g., 1000 Genomes, ExAC, gnomAD, ClinVar, HGMD, CIViCDB, PharmGKB, OncoKB, etc.) Detail-oriented, well-organized, and interested in clinical sequencing and cancer genomics Team-oriented with strong written and verbal communication skills Onsite role for a minimum of 6 months with potential for hybrid work based on performance; no fully remote work at this time Preferred Qualifications
Experience in a CLIA environment Experience with variant calling benchmarking and clinical validation analysis (e.g., concordance, limit of detection, assay reproducibility) Experience in Linux environment and with SGE Experience running workflows on public cloud (GCP / AWS) Experience developing and querying databases using SQL Experience with web development (HTML, CSS, JavaScript, TypeScript) Qualified candidates must be able to effectively communicate with all levels of the organization. NYU Grossman School of Medicine provides its staff with a comprehensive benefits and wellness package and is an equal opportunity employer committed to inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply online. Salary range: $67,771.14 - $75,955.36 annually. Actual salaries depend on experience, education, and hospital need. This range does not include bonuses or other compensation. To view the Pay Transparency Notice, please click here.
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Bioinformatics Programmer - Molecular Diagnostics (Onsite position) at NYU Langone Health. The role focuses on analysis of next-generation sequencing data in a Molecular Pathology setting, supporting clinical genomics and precision medicine initiatives. Position Summary: Bioinformatics Programmer/Analyst in a Molecular Diagnostics environment, working in CLIA/CLEP/FDA-guided clinical genomics workflows, collaborating with laboratory and informatics scientists in the Molecular Pathology Laboratory. 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
Master’s degree with a minimum of 1 year of work or internship experience in cancer or hereditary disease, next generation sequencing (NGS) analysis or cancer genomics/human genetics with demonstrable biomedical NGS bioinformatics skills Strong programming skills in Python, R and shell scripting Basic understanding of human genetics Experience with FASTQ, BAM, VCF data and tools (e.g., BWA, GATK, Picard, samtools, bcftools) Knowledge of SNV, Indel, CNV and structural variant analysis for somatic and germline disease, and variant annotation Familiarity with NGS QC principles Experience with public genomics datasets (e.g., 1000 Genomes, ExAC, gnomAD, ClinVar, HGMD, CIViCDB, PharmGKB, OncoKB, etc.) Detail-oriented, well-organized, and interested in clinical sequencing and cancer genomics Team-oriented with strong written and verbal communication skills Onsite role for a minimum of 6 months with potential for hybrid work based on performance; no fully remote work at this time Preferred Qualifications
Experience in a CLIA environment Experience with variant calling benchmarking and clinical validation analysis (e.g., concordance, limit of detection, assay reproducibility) Experience in Linux environment and with SGE Experience running workflows on public cloud (GCP / AWS) Experience developing and querying databases using SQL Experience with web development (HTML, CSS, JavaScript, TypeScript) Qualified candidates must be able to effectively communicate with all levels of the organization. NYU Grossman School of Medicine provides its staff with a comprehensive benefits and wellness package and is an equal opportunity employer committed to inclusion in all aspects of recruiting and employment. All qualified individuals are encouraged to apply online. Salary range: $67,771.14 - $75,955.36 annually. Actual salaries depend on experience, education, and hospital need. This range does not include bonuses or other compensation. To view the Pay Transparency Notice, please click here.
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