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Position Summary

The Center for Infection and Immunity at Columbia University Irving Medical Center (CUIMC) and the Mailman School of Public Health is hiring for the position of Sr. Programmer Analyst, in Bioinformatics, to join one of the world???s largest and most advanced center for basic and translational science, with a global network of researchers, focused on microbial surveillance, discovery and diagnosis in humans and wildlife.  The successful candidate will be part of a team that works on development and maintenance of pipelines for New York State CLIA certification of microbial diagnostic assays, microbiome analysis, large-scale studies on autism and chronic fatigue syndrome/myalgic encephalomyelitis with focus on understanding host response mechanisms using high-throughput protein arrays, RNA-Seq, proteomics and metabolomics platforms, and data integration of multi-omics platforms.

The candidate will participate in the Global Alliance for Pandemic Prevention program and help with development of a secure cloud-based system, using AWS, for data processing, analysis and sharing with global researchers. The scientist will analyze next generation sequencing (NGS) data using on-site high-performance clusters (HPC) and AWS and help with migration of pipelines on Amazon Cloud. The candidate will work closely with statisticians and contribute to the publications and proposal writing.

The candidate is expected to demonstrate the following skills and experience:

• Advanced knowledge of commonly used bioinformatics tools and algorithms, writing pipelines for analysis of NGS datasets, generated using Illumina sequencing platform, along with strong programming and analytical skills.
• Thorough knowledge of NGS experimental design, data quality control, mapping software such as Bowtie and STAR, genome annotations from major bioinformatics resources (EMBL, NCBI). Count generation using featureCounts, normalization and downstream analysis with DESeq2. Experience with tools such as Salmon, Kallisto etc. would be considered a plus.
• High proficiency in scripting languages, such as Shell, Python, Perl and R in an academic or industrial environment.
• Ability to work in Linux environments consisting of high-performance clusters or Amazon Cloud. Familiarity with SGE or Slurm schedulers, resource management, multi-threading tools.
• Familiarity with Gene Set Enrichment Analysis or Ingenuity Pathway analysis

Responsibilities

• Provide bioinformatics support for multi-omics analysis in a large and dynamic laboratory - 50%
• Provide support for projects related to microbial detection and discovery - 30%
• Manage databases and data - 10%
• Contribute to publications and research grants - 5%

Minimum Qualifications

• Bachelor's degree in computer science, bioinformatics, related field or equivalent in training and education with at least four (4) years of related experience.

Preferred Qualifications

• Master???s degree or PhD degree in computer science, bioinformatics, or related field with at least 2 years of related experience. Knowledge of statistical and machine learning techniques is a plus.

Equal Opportunity Employer / Disability / Veteran

Columbia University is committed to the hiring of qualified local residents.

About Columbia University

Columbia University is one of the world's most important centers of research and at the same time a distinctive and distinguished learning environment for undergraduates and graduate students in many scholarly and professional fields. The University recognizes the importance of its location in New York City and seeks to link its research and teaching to the vast resources of a great metropolis. It seeks to attract a diverse and international faculty and student body, to support research and teaching on global issues, and to create academic relationships with many countries and regions. It expects all areas of the university to advance knowledge and learning at the highest level and to convey the products of its efforts to the world.

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