Research Bioinformatician II - Knott Lab

CEDARS-SINAI; West Hollywood (CA); On-site; USD 90,000 - 130,000; Full time

Job summary

Cedars-Sinai is seeking a Research Bioinformatician II to perform general bioinformatics analysis and software support for multi-omic projects. You will interact with investigators to identify problems, select tools, and leverage public databases for omic data, while managing and transforming data for downstream analyses.

The role includes developing modular pipelines, assisting in publications and grants, and mentoring teammates to keep pace with rapid sequencing technology advances in a

Qualifications

• Three years of research experience in algorithms, computing, and ML/statistics.
• Three years handling large genomic (NGS) datasets in exploratory and pipeline modes.
• Familiar with C/C++, Java, Perl, Python and Unix/Linux environments.

Responsibilities

• Provide general bioinformatics analysis support for omic projects and data analysis.
• Develop, test, and maintain modular software pipelines for sequencing data.
• Manage data loading, querying, and transformation from public repositories.
• Collaborate with investigators and assist in grant proposals, publications, and presentations.
• Mentor colleagues and stay current with sequencing tech advances.

Skills

C/C++

Python

Java

Perl

Unix/Linux

Machine learning

Education

Bachelor's of Science in CS/Computational Biology/ Bioinformatics

Master's or Doctorate preferred

Tools

NGS pipelines

Bioinformatics tools

Job description

Job Description

The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II!

The Knott laboratory utilizes human samples and mouse models to generate multi-omic datasets using single-cell RNA- and ATAC-seq, ChIPseq, Proteomics, Spatial Transcriptomics and Functional Genomics. The ultimate goal is to integrate these data to provide deeper knowledge of the interplay between the tumor and its immune microenvironment and how these interactions provide support of tumor evolution via plasticity, metastatic progression, and therapy resistance. The Research Bioinformatician will be a critical team member that provides data that will inform follow-up functional validation experiments that provide an important rationale for the initiation of the first in human clinical trials. To learn more, please visit: Knott Research Lab | Cedars-Sinai.

Are you ready to be a part of breakthrough research?

The Research Bioinformatician II performs general bioinformatics analysis and software support for projects involving in omics, and interacts with investigators to identify research problems, find appropriate software tools, and recognize national biological databases and online resources for omic data. The RBII manages omic data including loading and querying data from database system(s) and public repositories, and transforms and merges multilevel omic data into user-friendly formats. The RBII assists in development, testing, and maintenance of modular software pipelines, provides bioinformatics data analysis, preliminary interpretation of the data, and reports of the results for possible publications. The Research Bioinformatician II also works with bioinformatics faculties to determine future bioinformatics needs, and helps to develop tools and pipelines as necessary to keep pace with rapid advances in sequencing technology. The Bioinformatician II demonstrates continuous self-improvement, makes effective contributions to the section, and adheres to the Cedars-Sinai compliance plan, code of conduct, and hospital and departmental policies and procedures.

Primary Job Duties & Responsibilities:

• Provides general bioinformatics analysis support for omic projects. Responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers.
• Summarizes data analyses results in the form suitable as the basis for the first draft of written reports, and makes preliminary interpretations of the data.
• Develops, tests, and maintains modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences.
• Manages data including loading and querying data from database systems, downloading omic data from public repositories, and transforming data to the necessary formats.
• Provides solutions for investigator’s problems through data mining and extraction.
• Identifies, evaluates, and incorporates relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology.
• Assists and/or collaborates in preparation of grant proposals, publications, and presentations involving omic data.
• Helps develop tools and pipelines as necessary to keep pace with rapid advances in sequencing technology.
• Educates others about bioinformatics through mentoring of and teaching colleagues, investigators, fellows, and graduate students.

Qualifications

Education:

• Bachelor's of Science Degree in Computer Science, Electric Engineering, Computational Biology, or Bioinformatics, or a Master of Science/ Engineering in relevant fields (e.g. Biology with strong quantitative training, biostatistics with a concentration in bioinformatics) is required.
• Master's or Doctorate Degree in Computer Science or a related computational field is preferred.

Experience & Skills:

• Three (3) years of experience in research environment including developing working knowledge in algorithms, scientific computing, and machine learning or statistics.
• Three (3) years of experience in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets both in exploratory and pipelined fashions.
• Familiar with C/C++, Java, Perl, python, and the Unix (Linux) environment.
• Familiar with medical and biological terminologies, bioinformatics resources, and national biological databases.