Open Rank: Staff Associate I, Staff Associate II, or Staff Associate III

We are seeking a motivated Research Programmer / Computational Biologist to join the laboratory of Dr. Chaolin Zhang in the Department of Systems Biology at Columbia University Irving Medical Center (CUIMC).

The Zhang Laboratory takes a multidisciplinary approach that integrates biochemistry, molecular biology, genome engineering, high-throughput data analysis, and integrative modeling to study protein-RNA interaction, neuronal alternative splicing regulation and RNA-based precision medicine.

The Zhang Lab is a diverse, collaborative, and creative research environment committed to scientific rigor, innovation, and mentorship. More information can be found at: http://zhanglab.c2b2.columbia.edu

The successful candidate will participate in and lead projects focused on improving, extending, and sustaining genomic research software packages developed by our group, such as:

• CLIP Tool Kit (CTK)
• Quantas
• DeltaSplice

These tools are widely used by the research community for CLIP-seq and RNA-seq data analysis: https://zhanglab.c2b2.columbia.edu/index.php/Resources

The position emphasizes software engineering,user community engagement, and genomic data analysis in a dynamic and collaborative research environment. Strong mentorship will be provided to support the candidate’s scientific and career development.

Specific responsibilities and duties will be as follow for each position title and grade (Staff Associate I, Staff Associate II, and Staff Associate III):

1. Functional Knowledge - For Staff Associate I & Staff Associate II: Algorithm development, software engineering, and computational genomics. For Staff Associate III: Algorithm development, software engineering, and computational genomics to a broader research.
2. Problem Solving - For Staff Associate I: Able to apply computer science and software engineering skills for problem solving. For Staff Associate II: Use computer science/software engineering skills to solve problems in moderate complex situations. For Staff Associate III: Use strong computer science/software engineering skills to solve problems in complex situations.
3. Decision Making/Autonomy - For Staff Associate I & Staff Associate II: Work independently and as part of a collabortive research team. Expected to show medium level of initiative and independent judgement. For Staff Associate III: Work independently and as part of a collabortive research team. Expected to show minimum level of initiative and independent judgement.
4. Technical Expertise - For Staff Associate I, Staff Associate II & Staff Associate III: Strong programming skills (Python and/or Perl preferred). Experience working in Linux/Unix environments, familiarity with version control systems.
5. Communication - For Staff Associate I: Strong communication skills. Collaborate with experimental and computational researchers. For Staff Associate II: Strong communication skills. Collaborate with experimental and computational researchers. may contribute to publications. For Staff Associate III: Able to translate information to general terms and help others understand impact of information. Collaborate with experimental and computational researchers. Assist PI to prepare publications and funding proposals.

Additional Opportunities

The candidate may also contribute to projects involving:

• RNA-binding protein biology
• Splicing regulation
• Transcriptomics and post-transcriptional regulation
• RNA-based therapeutic development

Minimum qualification to be considered for:

1. Staff Associate I: Bachelor's degree in specific research field and 4 years experience preferred.
2. Staff Associate II: Bachelor's degree in specific research field and 4 years experience recommended
3. Staff Associate III: Bachelor's degree in specific research field and 4-6 years experience preferred.

Other preferred qualifications:

1. Experience with genomic data analysis (e.g., CLIP-seq, RNA-seq)
2. Knowledge of NGS pipelines and file formats (FASTQ, BAM, BED, GTF)
3. Experience with Docker, Singularity, or workflow systems
4. Experience or strong interest in software engineering for scientific tools

Interested applicants should submit the following documents with their application AND via email to Dr. Chaolin Zhang (cz2294@columbia.edu):

• A CV
• A brief cover letter describing relevant experience and interests
• Contact information for 3 references