Research Bioinformatician III - Knott Lab - Bioinformatics & Functional Genomics
Cedars-Sinai Medical Center
Location: Los Angeles, California
Internal Number: HRC0561259A
Are you passionate about applying genomics, computer science, and probability theory to study cancer progression?
The Knott Lab at is searching for a computational scientist to develop and apply computational tools for digital histopathology! This scientist will lead the data analyses portion of our studies of breast cancer clinical trial materials, where we are studying the cellular relationships and the spatial distributions of distinct cell types within tumors that impact the course of the disease. One of our favored spatial profiling tools it the Co-detection by Indexing (CODEX) platform housed within our laboratory. However, the Knott Lab also utilizes other spatial profiling methodologies paired with traditional single cell sequencing to study tissues.
Ultimately, this role will provide the candidate with an opportunity to leverage their quantitative skillset and apply machine learning, graph theory and statistical inference to improve the lives of patients. To learn more, please visit: Knott Research Lab | Cedars-Sinai
The Bioinformatician III in the Knott Lab works independently but in close cooperation and consultation with Research Scientists, PI, Research Nurses, and Research Coordinators. The RB III will interact with investigators to understand scientific questions, define the scope of work and propose an analytical plan with a time estimate for its completion. In addition, the RB III will develop and maintain software based on current projects and in anticipation of long-term needs.
Primary Job Duties & Responsibilities:
Provides general bioinformatics analysis support for omic projects and mainly 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.
Manages data including loading and querying data from database systems, downloading omic data from public repositories, and transforming data to the necessary formats
Familiar with medical and biological terminologies, bioinformatics resources, and national biological databases. Ready to provide solutions for investigator's problems through data mining and extraction.
Be proficient and maintain proficiency in development, testing, and maintenance of modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms including 454, Illumina, and Pacific Biosciences
Identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology
Provide bioinformatics expertise in the design of experiments and studies, including research proposal development, sample size determination, and plans for interim reviews and final analysis
Develop tools and pipelines as necessary to keep pace with rapid advances in sequencing technology.
Interact with and support other bioinformatics colleagues in pursuing excellence in Research and Education, that is, the generation of new ideas and concepts, and their dissemination.
Educate others about bioinformatics and computational biology through mentoring of and teaching colleagues, investigators, fellows, and graduate students.
Master's 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), required.
Doctorate's Degree in a quantitative field such as Computer Sciences, Mathematics, Statistics or Physics, preferred. First or senior author publications describing development and application of relevant computational tools for studying high-dimensional spatial datatypes is highly desirable.
Experience and Skillset:
Seven (7) years in a research environment with background and working knowledge in algorithms, scientific computing, and machine learning or statistics to study complex multidimensional datasets that have spatial context
Familiar with C/C++, Java, Perl, python, and the Unix (Linux) platforms and comfortable in an HPC or Cloud environment
Prior experience in manipulating, analyzing, and annotating very large genomic (e.g. NGS) data sets both in exploratory and pipelined fashions.
Proven ability of the candidate to develop and apply computational tools to study high-dimensional datatypes where there is a clear spatial context.
Prior experience with single cell sequencing technologies would be looked upon favorably.
Capable of organizing and teaching formal bioinformatics courses, inter-disciplinary courses, continuing education courses, and seminars.
Excellent written/oral communication skills.
Working Title: Research Bioinformatician III - Knott Lab - Bioinformatics & Functional 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.