Senior Staff Associate I

Position Summary

Columbia University JP Sulzberger Genome Center, within the Department of Systems Biology, is seeking a highly motivated Senior Staff Associate I with strong expertise in bioinformatics, high-throughput sequencing, 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 bulk and single-cell RNA sequencing data, focusing on custom bioinformatics projects from Core users.

The successful applicant would join the Next-Generation Sequencing Lab and Single Cell Analysis Core bioinformatics teams, which are located in the Department of Systems Biology, a vibrant hub for interdisciplinary research. This position will specifically involve the application and development of computational methods for analyzing bulk and single-cell RNA sequencing data, focusing on custom bioinformatics projects from Core users.

Duties

• 25%: Process bulk RNA-seq samples using standard pipelines. This includes basic analysis and data release, updating reference genomes and transcriptomes and syncing differential expression annotation databases. Additionally, the Senior Staff Associate I will communicate with researchers and assist in troubleshooting any issues with the Director and bench scientists.
• 25%: Process single cell samples using standard pipelines (3' and 5' gene expression, T- and B- cell receptor repertoire profiling, ATAC-Seq, multiome, and Visium samples). This includes basic analysis, cellranger, and data release, updating reference genomes and transcriptomes, and analysis package versions. Additionally, the Senior Staff Associate I will communicate with researchers and assist in troubleshooting any issues with the Director and bench scientists.
• 20%: Carry out custom 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.
• 10%: Update bulk RNA-seq pipelines to accommodate new non-Illumina sequencing data (Element AVITI). Work with programmer to integrate this into new pipelines, including advising on best approaches.
• 10%: System administration, including monitoring the running processes; tracking capacity and throughput; architect storage platform; upgrade and install software when necessary.
• 10%: Provide specialized services to GECO core (Xenium data release, CRISPR analysis). Work with programmer to eventually implement a pipeline for analysis.
  
  

Functional Knowledge

• Knowledge and understanding of the field of next-generation sequencing, in particular how this field supports the broader research of the Columbia scientific community.
• Uses that knowledge to solve moderately complex problems and find new perspectives.
• Interacts daily with scientists to provide bioinformatic expertise.
  
  

Problem Solving

• Able to apply analytical skills to help problem solve with other wet lab members, other bioinformaticians, and Director.
• Judgement must be informed by analysis of multiple sources of information, including experience.
• May require new perspective on existing programs or problems.
  
  

Decision Making/Autonomy

• Works independently to design and execute routine projects with minimal supervision.
• Expected to show a high level of initiative.
• Works independently to execute routine experiments while working in a collaborative research environment.
• Requires a high degree of independent judgement.
  
  

Leadership

• Able to identify and recommend improvements to processes and best practices for the core and its needs.
• May provide guidance to more junior bioinformaticians.
  
  

Technical Expertise

• Required to implement protocols to support projects, using a comprehensive understanding of research techniques, software and instruments.
• May develop new protocols or pipelines.
  
  

Communication Skills

• Assist collaboratively research groups, explain complex information.
• Contributing in preparation of publications (manuscripts, funding proposals).
• Contributes to scientific manuscripts.

Master's degree in Computational Biology, Bioinformatics, Genetics, or equivalent in education and experience, plus 4 years of related experience.