Bioinformatics Programmer

Senior Bioinformatics ProgrammerNYU 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 is committed to improving the human condition through medical education, scientific research, and direct patient care.NYU Langone Health, a world-class, patient-centered, integrated, academic medical center, 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 the Applied Bioinformatics Laboratories (ABL) are seeking a highly motivated, enthusiastic and creative individual to become a member of our clinical bioinformatics team. This is a great opportunity to be involved in an innovative environment utilizing and mastering 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.Position Summary:We have an exciting opportunity to join our team as a Sr. Bioinformatics Programmer working in a Molecular Diagnostics environment. This position is an onsite role for a minimum of 6 months with the potential for hybrid role after that based on performance. Ability to be onsite 3 to 5 days a week a must (possibility of full remote work is currently not available).Job Responsibilities:Enhance or develop new automated workflows/pipelines within a nextflow environment for bioinformatic tools utilizing next generation sequencing data in clinical diagnostic assaysUse existing bioinformatics pipelines to analyze the molecular patient data generated in the clinical labOversee systems support for existing bioinformatics pipelines and develop new pipelines to support new molecular assaysSupport the team in its common clinical genomics and precision medicine goalsPerform quality control of the generated sequencing data and develop solutions to enhance future performancePerform different types of data analysis relating to the genomics-based approaches utilized by the lab, in an independent fashion.Develop new methods for multi-omics data analysis and integrationWork with bioinformatics scientists and clinical pathologists to analyze and interpret patient NGS results for better potential treatment optionsWork with lab users to analyze biomedical data and address clinical needs using bioinformatics techniques and toolsWork with MCIIT and HPC team to provide current and future solutions for server, storage and other requirements.Preferred Qualifications:Expert in creating customized sequencing analysis pipelines, in applications for data analysis, and executing standard bioinformatics pipelines (relevant examples in a GitHub repository). Basic knowledge and understanding of software engineering concepts. Knowledge of algorithms, data structures, machine learning. 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 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)Minimum Qualifications:To qualify you must have a M.Sc. plus a minimum of 3 years' experience in Bioinformatics, Computer Science, Programming, Software Development, or related field Previous experience with NGS data and associated bioinformatics tools. Experience in Unix/Linux systems including high-performance computing environments. Strong programming skills in Python, R, shell scripting. Proficiency in Nextflow, Django, Docker and Singularity containers. 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. Knowledge of biology, cancer genomics or an understanding of key and complex biological concepts. Detail-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics. Ability to work independently (e.g., recommend new software or bioinformatic tools, find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results). Team oriented with excellent written and verbal communication skills. Ability to function in a multidisciplinary team including MD's and PhD's. Qualified candidates must be able to effectively communicate with all levels of the organization.