Categories: Information Technology, Other, Research (Lab and Non-Lab)
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-
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.
Maintain and improve robust and highly automated computational pipelines
for analyzing and storing single cell RNA-Seq, single nuclei ATAC-Seq, and
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
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.
Bachelor's degree in Computational Biology, Bioinformatics, Genetics, or
equivalent in education and experience; plus three years of related
Demonstrated experience in high-throughput sequencing data analysis or
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.
Graduate degree in Computational Biology, Bioinformatics, Genetics, or
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
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