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Bioinformatics Analyst

Columbia University

United States

June 4, 2022

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Description

Bioinformatics Analyst

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  • Requisition no: 525394
  • Work type: Full Time
  • Location: Medical Center
  • School/Department: Systems Biology
  • Grade: Grade 104
  • Categories: Information Technology, Other, Research (Lab and Non-Lab)

    • Position Summary

    Columbia University's JP Sulzberger Genome Center is seeking a highly motivated Bioinformatics Analyst with strong expertise in bioinformatics and single-cell RNA sequencing. The Genome Center is equipped with state-of- the-art high-throughput sequencing instruments and a Single Cell Analysis Core with equipment for gene expression profiling in individual cells. It has extensive collaborations with investigators at Columbia University in studies on biology, human diseases, and precision medicine. This position will specifically involve the application and development of computational methods for analyzing single-cell RNA sequencing data, focusing on custom bioinformatics projects from Core users.

    More information can be found at https: // systemsbiology.columbia.edu/genome- center/single-cell-analysis-core.

    The successful applicant would join the Single Cell Analysis Core bioinformatics team, which is located in the Department of Systems Biology, a vibrant hub for interdisciplinary research.

    Responsibilities

  • Maintain and improve robust and highly automated computational pipelines for analyzing and storing single cell RNA-Seq, single nuclei ATAC-Seq, and supporting data.
  • Analyze and integrate newly reported computational tools. This includes recently described computational methods for regulatory network inference and analysis (e.g. VIPER, metaVIPER, ARACNE), matrix factorization methods (e.g. scHPF), and trajectory analysis tools (e.g. topological data analysis, Monocle3).
  • Work with sequencing team to improve Standard Operating Procedures and troubleshoot experiments. This includes both 3'- and 5'-end implementations of single-cell RNA-seq with the 10x Genomics Chromium platform, T cell receptor repertoire profiling with the 10x Genomics Chromium platform, single-cell RNA-seq with plate-based whole transcriptome amplification, and single-cell ATAC-seq with the 10x Genomics Chromium platform.
  • Lead a custom bioinformatics service to provide Core users with access to project-specific computational tools on a fee-for-service basis. This responsibility will involve meeting with faculty and other researchers who use the Core, identifying computational tools to help answer their scientific questions, and executing custom bioinformatics analyses in collaboration with Core users.
  • Provide advice in study design and analytical approaches to existing or new users. Interact with core users to explain the experimental results and to develop further analyses based on user feedback.
  • Carry out data analysis in strategic research projects, including new technology development and collaborations; participate manuscript writing.
  • Develop software for new single-cell RNA-Seq applications. This includes analytical tools for unsupervised clustering, data visualization, differential gene expression analysis, batch effect correction, and dimensionality reduction.
  • System administration for the pipeline computing environment by monitoring the running processes; tracking capacity and throughput; architect storage platform; upgrade and install software when necessary.
  • Develop and automate analytics pipeline for spatial transcriptomics analyses, including integration of imaging data with sequencing data and analytical tools as described above.
  • Perform related duties & responsibilities as assigned/requested.

    • Minimum Qualifications

  • Bachelor's degree in Computational Biology, Bioinformatics, Genetics, or equivalent in education and experience; plus three years of related experience.
  • Demonstrated experience in high-throughput sequencing data analysis or method development.
  • Excellent communication skills and teamwork.
  • Programming: Fluency with Python, R, and UNIX. Experience with source code version control systems. Experience with AWS.
  • Strong creative thinking and problem-solving skills.

    • Preferred Qualifications

  • Graduate degree in Computational Biology, Bioinformatics, Genetics, or equivalent.
  • Experience with pipeline development or automation using Python.

    • Equal Opportunity Employer / Disability / Veteran

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

    Applications open: May 04 2022 Eastern Daylight Time Applications close:

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