Senior Bioinformatics Programmer

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)NYU Langone Health, a world-class, patient-centered, integrated, academic medical center, and one of the nation’s 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 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. We have an exciting opportunity to join our team as a Senior Bioinformatics Programmer. The successful candidate will be primarily responsible for the development and maintenance of computational pipelines and work closely with clinicians to develop bioinformatic tools for clinical Next Generation Sequencing (NGS) based diagnostics. In addition, bioinformatics analysis of various types of patient genomic, epigenomic and transcriptomic data is 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.Job

Responsibilities:
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� Enhance or develop new automated workflows/pipelines within a nextflow environment for bioinformatic tools utilizing next generation sequencing data in clinical diagnostic assays�
� Use existing bioinformatics pipelines to analyze the molecular patient data generated in the clinical lab�
� Oversee systems support for existing bioinformatics pipelines and develop new pipelines to support new molecular assays�
� Support the team in its common clinical genomics and precision medicine goals�
� Perform quality control of the generated sequencing data and develop solutions to enhance future performance�
� Perform 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 integration�
� Work with bioinformatics scientists and clinical pathologists to analyze and interpret patient NGS results for better potential treatment options�
� Work with lab users to analyze biomedical data and address clinical needs using bioinformatics techniques and tools�
� Work with MCIIT and HPC team to provide current and future solutions for server, storage and other requirements.Preferred

Qualifications:
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� 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 ( 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:
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� To qualify you must have a plus a minimum of 3 years’ experience in Bioinformatics, Computer Science, Programming, Software Development, or related fieldPrevious 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 (, 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 writ