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Research Bioinformatician II performs general bioinformatics analysis and software support for projects involving in omics, and interact with investigators to identify research problems, find appropriate software tools, and recognize national biological databases and online resources for omic data. The RBII will manage omic data including loading and querying data from database system and public repositories, and transform and merge multilevel omic data into user-friendly formats, assist in development, test, provide bioinformatics data analysis, preliminary interpretation of the data, and reports of the results for possible publications.
Research Bioinformatician II will also work 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. Demonstrate continuous self-improvement, make effective contributions to the section, and adhere to CSHS compliance plan, code of conduct, and hospital and departmental policies and procedures.
Primary Duties and Responsibilities
Provides support for omic projects and responsible for data analysis, 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 conducts preliminary interpretation of data.
Develop, test, and maintain modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences
Work with groups of various scientific background to determine appropriate experimental designs, sequencing techniques, and analysis frameworks.
Manipulate next-generation sequencing data for demultiplexing, alignment, quality control, gene expression quantification, variant analysis, and/or other downstream analyses with minimal supervision.
Performs standard and sophisticated analyses of RNA-seq (bulk and single-cell), spatial transcriptomics, ATAC seq (bulk and single cell), whole-genome/exome sequencing, ChIP-seq, and CROSPR mutagenesis experiments.
Summarize and interpret results for clients in formal/informal presentations, grants, and manuscripts.
Maintain and develop robust and modular pipelines for next-generation sequencing analysis.
Master of Science Degree in Computer Science, Electric Engineering, Computational biology, or Bioinformatics, or Master of Science/ Engineering in relevant fields (e.g. Biology with strong quantitative training, biostatistics with concentration in bioinformatics)
3 years in research environment. Knowledge in algorithms, scientific computing, and machine learning or statistics
Preferred - PhD in Computer Science, Electric Engineering, Computational biology, or Bioinformatics, or Engineering in relevant fields (e.g. Biology with strong quantitative training, biostatistics with concentration in bioinformatics)
Applicants in consideration will be asked to complete a coding test prior to first day to include some of the following:
Familiar with C/C++, Java, Perl, python, and the Unix (Linux) environment. Fluency with a scripting/programming language, preferably R or python.
Experience analyzing, and annotating genomic (e.g. NGS) data sets both in exploratory and pipelined fashions.
Proficiency working in a linux environment, preferably HPC/Cloud based systems.
Basic familiarity with one or more other following programs/pipelines is necessary: STAR, GATK, Seurat, CellRanger, Scanpy, samtools, RSEM, macs2, and/or MultiQC.
Knowledge of Docker, Singularity, Git, and/or Nextflow is a strong plus!
Working Title: Research Bioinformatician II - Applied Genomics
Providing healthcare for more than 100 years, Cedars-Sinai has evolved into one of the most dynamic and highly renowned medical centers in the world. Along with caring for patients, Cedars-Sinai is a hub for biomedical research and a training center for future physicians and other healthcare professionals. This attracts exceptional talent to Cedars-Sinai, including world-renowned physician-scientists who seek a place where they can both conduct research and see patients--the ideal formula for discovery and its translation into cures. Our patients benefit from access to doctors at the top of their fields, and our researchers have an ideal community in which to study the impact of healthcare challenges, and reflect that knowledge in their research. The greater Los Angeles area in which Cedars-Sinai resides possesses unparalleled cultural and ethnic diversity which offers outstanding opportunities for translational and clinical research and a dynamic environment for medical education.Although community based, Cedars-Sinai is a major t...eaching hospital affiliated with the David Geffen School of Medicine at the University of California, Los Angeles (UCLA). Cedars-Sinai has highly competitive graduate medical education programs in more than 50 specialty and subspecialty areas, a graduate program in biomedical sciences and translational medicine, a clinical scholars program directed towards junior physicians with aspirations to become clinical scientists, and post graduate training opportunities.There are more than 250 full-time faculty members at Cedars-Sinai. The voluntary medical staff, comprised of more than 2,200 specialty board-certified or board-qualified physicians, represent all of the specialties and subspecialties and collaborate with full-time medical staff in the teaching responsibilities of the graduate medical education programs.