Job Description:
The Center for Brain Development (http://www.cbd.ucsd.edu) project seeks to identify the genetic causes for autism, epilepsy and intellectual disability using high-throughput bioinformatics approaches. Using genomic sequencing data from >5000 patients, consisting of >500 TB of data and growing rapidly, CBD seeks to discover the genetic variants that underlie human diseases. The project utilizes open source software to develop improved methods of genetic variant discovery and annotation to discover new human disease genes and link them to specific neurodevelopmental conditions. Uses whole exome, whole genome, RNAseq, CHIPseq and a variety of other types of nucleic acid profiling to align genotype with phenotype along the spectrum of pediatric brain disease. Candidate will be required to possess knowledge of DNA and RNA sequencing, processing and analysis, and should be able to combine results from varied DNA RNA sequencing technologies, as well as standard DNA and RNA sequence quality assessment, mapping, alignment, splicing and expression. Responsibilities include performing computational studies of sequenced genomes, extracting and integrating data and performing programming and database development and maintenance. Candidate will also use statistical approaches for hypothesis-testing and hypothesis-generating components. Candidate will develop algorithms as well as prepare data analysis and participate in statistical evaluations. The Candidate’s work will be multi-faceted, largely tasked with participating in the analysis of a diverse collection of biological data. Responsibilities will include providing ad-hoc technical support, and benchmarking of newly emerging computational tools for specific projects and system maintenance. Primary tasks revolve around development and maintenance of a variant analysis pipeline that processes sequencing data, integrates internal and external data, and prioritizes genetic variants based on an array of metrics. This pipeline currently relies on a MySQL database, so experience with databasing is a plus. Additional work includes creating new visual summaries of data in R, downloading and piloting new analysis tools, working with the San Diego Super Computer Center for storage and processing needs, integrating with a team of bioinformaticians, collaboration with a team of molecular and cellular biologists, and performing statistics-based analysis to achieve high-impact results. Projects may require some web-based tool development and some minor IT assistance maybe requested. MINIMUM QUALIFICATIONS: -Bachelor's degree in computer science, bioinformatics or related field with some biology background or an equivalent combination of education and experience. -Strong theoretical knowledge and independent experimental ability to perform applied bioinformatics in a molecular biology research laboratory. -Demonstrated conceptual/theoretical experience in bioinformatics analysis of DNA/RNA related data. -Ability to develop, optimize, debug tools and scripts in scientific programming in any of using Java, R, C++, and Python. -Proficiency with computer hardware and software including different operating system environments (such as Mac, Windows and UNIX) and High Performance Computing (HPC) clusters, schedulers and tools. Proven ability to update skills and knowledge as needed. -Knowledge, skill and ability to perform statistical analysis including experience with statistical analyses and data visualization in R. -Demonstrated experience working in a Linux/Unix environment. PREFERRED QUALIFICATIONS: -Demonstrated ability to interpret/coordinate research protocols such as RNASeq, RipSeq and CLIPSeq and the corresponding data requirements. -Knowledge of database development and maintenance and proven experience with biological databases used in biomedical studies. -Prior experience working in an environment where research relates to human diseases and private health. -Master or PhD degree in bioinformatics, computational molecular biology or related field and/or an equivalent combination of education and experience. SPECIAL CONDITIONS: Must be able to work various hours and locations based on business needs.
Additional Info:
UC San Diego career employees who have passed their trial period will have priority consideration for this position. Recruiters will begin to refer qualified internal applicants after the first 7 days of the job posting. Qualified external applicants may be referred to the hiring department, if a qualified pool of internal candidates is not identified and upon the request of the hiring manager. UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. U.S. News and World Report’s annual "America’s Best Hospitals" report has repeatedly ranked UC San Diego Health as the #1 health system in San Diego. We invite you to join our dynamic team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. [Click Here to Access the Original Job Post]
The Center for Brain Development (http://www.cbd.ucsd.edu) project seeks to identify the genetic causes for autism, epilepsy and intellectual disability using high-throughput bioinformatics approaches. Using genomic sequencing data from >5000 patients, consisting of >500 TB of data and growing rapidly, CBD seeks to discover the genetic variants that underlie human diseases. The project utilizes open source software to develop improved methods of genetic variant discovery and annotation to discover new human disease genes and link them to specific neurodevelopmental conditions. Uses whole exome, whole genome, RNAseq, CHIPseq and a variety of other types of nucleic acid profiling to align genotype with phenotype along the spectrum of pediatric brain disease. Candidate will be required to possess knowledge of DNA and RNA sequencing, processing and analysis, and should be able to combine results from varied DNA RNA sequencing technologies, as well as standard DNA and RNA sequence quality assessment, mapping, alignment, splicing and expression. Responsibilities include performing computational studies of sequenced genomes, extracting and integrating data and performing programming and database development and maintenance. Candidate will also use statistical approaches for hypothesis-testing and hypothesis-generating components. Candidate will develop algorithms as well as prepare data analysis and participate in statistical evaluations. The Candidate’s work will be multi-faceted, largely tasked with participating in the analysis of a diverse collection of biological data. Responsibilities will include providing ad-hoc technical support, and benchmarking of newly emerging computational tools for specific projects and system maintenance. Primary tasks revolve around development and maintenance of a variant analysis pipeline that processes sequencing data, integrates internal and external data, and prioritizes genetic variants based on an array of metrics. This pipeline currently relies on a MySQL database, so experience with databasing is a plus. Additional work includes creating new visual summaries of data in R, downloading and piloting new analysis tools, working with the San Diego Super Computer Center for storage and processing needs, integrating with a team of bioinformaticians, collaboration with a team of molecular and cellular biologists, and performing statistics-based analysis to achieve high-impact results. Projects may require some web-based tool development and some minor IT assistance maybe requested. MINIMUM QUALIFICATIONS: -Bachelor's degree in computer science, bioinformatics or related field with some biology background or an equivalent combination of education and experience. -Strong theoretical knowledge and independent experimental ability to perform applied bioinformatics in a molecular biology research laboratory. -Demonstrated conceptual/theoretical experience in bioinformatics analysis of DNA/RNA related data. -Ability to develop, optimize, debug tools and scripts in scientific programming in any of using Java, R, C++, and Python. -Proficiency with computer hardware and software including different operating system environments (such as Mac, Windows and UNIX) and High Performance Computing (HPC) clusters, schedulers and tools. Proven ability to update skills and knowledge as needed. -Knowledge, skill and ability to perform statistical analysis including experience with statistical analyses and data visualization in R. -Demonstrated experience working in a Linux/Unix environment. PREFERRED QUALIFICATIONS: -Demonstrated ability to interpret/coordinate research protocols such as RNASeq, RipSeq and CLIPSeq and the corresponding data requirements. -Knowledge of database development and maintenance and proven experience with biological databases used in biomedical studies. -Prior experience working in an environment where research relates to human diseases and private health. -Master or PhD degree in bioinformatics, computational molecular biology or related field and/or an equivalent combination of education and experience. SPECIAL CONDITIONS: Must be able to work various hours and locations based on business needs.
Requeriments :
Skills :
- Bioinformatics
- Database design
- DNA sequencing
- HPC
- Lunix/Unix
- MySQL
- Programing in C++
- Programing in Python
- Programming in Java
- Programming in R
- RNA-seq
- Statistics
Areas :
Additional Info:
UC San Diego career employees who have passed their trial period will have priority consideration for this position. Recruiters will begin to refer qualified internal applicants after the first 7 days of the job posting. Qualified external applicants may be referred to the hiring department, if a qualified pool of internal candidates is not identified and upon the request of the hiring manager. UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. U.S. News and World Report’s annual "America’s Best Hospitals" report has repeatedly ranked UC San Diego Health as the #1 health system in San Diego. We invite you to join our dynamic team! Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached. UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. [Click Here to Access the Original Job Post]