Large-scale-single-cell methylome profiling is the current state-of-art for studies that require the DNA methylation profiles at base resolution in heterogenous tissues. Single cell DNA methylation profiling offers the advantage of obtaining uniform genome wide coverage at cellular resolution. snmC-seq3 is an improved version of snmC-seq that provides better throughput, library complexity, coverage uniformity, and read mapping. This method is being used routinely in various projects including the DARPA-funded ECHO and MBA projects and several other projects for identifying DNA methylation patterns and their effects in samples such as blood cells and the brain.
The Bioinformatics Analyst II will work closely with other members of the project and the Ecker laboratory to advance the computational approaches involved in data analysis of snmC-seq datasets. The analyst will contribute directly to research projects by implementing, optimizing and executing the currently available pipelines that include mapping, QC, visualization, and reporting. The analyst will be required to develop advanced computational and statistical methods for big-data analysis. The analyst will be expected to create and implement machine learning algorithms for identifying patterns and signatures relevant to biological datasets. Finally, the analyst will play part in administrating shared computer resources, such as compute and storage servers.
Bioinformatics Analysis (85%)
Work independently to develop advanced computational and statistical methods for big-data analysis.
Work independently to create and implement machine learning algorithms for identifying patterns and signatures relevant to biological datasets.
Work independently or with limited supervision on informatics research projects under direction from senior staff or with research collaborators.
Work with Institute researchers and contribute to scientific discovery by implementing, optimizing and executing computational approaches for DNA methylation analysis, mapping, genome sequence analysis, transcriptome analysis, and data visualization.
Use published and available pipelines, scripts, and tools to prepare and process large datasets.
Work in a high-performance computing environment.
Keep informed of new developments and technical advances in the bioinformatics, image processing, visualization, genomics and biological fields related to current projects.
Research, implement, and test, and present on new tools and pipelines for high-throughput data analysis.
Independent design and coding of analysis pipelines and cutting-edge bioinformatics analysis algorithms.
Participate in the design, coding, and presentation of novel analysis tools for cutting-edge bioinformatics analysis.
Present advanced analysis results, tools, and pipelines at group meetings and contribute to publications in scientific journals.
Research Design and Presentation (5%)
Contribute and assist with project inception, experimental design, analysis and manuscript presentation.
Work on the preparation of data for, manuscripts, publications, grant applications, posters and other presentations.
Present results verbally and with visual aids in one-on-one meetings, group meetings, or conferences.
Maintain lab notebook, online code-share repositories such as GitHub, GitLab, BitBucket, etc including experimental design, time, methods, materials and results.
Maintain code in shareable IDEs such as Jupyter to enable easy reproducibility of results
Maintenance and Management of Bioinformatics Resources (10%)
Prepare allocation requests, benchmarks, progress reports etc. for HPC resources
Help maintain scripts, software, website, tools, wiki, and pipelines used in the lab.
Help ensure that lab servers and hardware are operating properly and report all possible problems.
Help users of lab software and servers to troubleshoot potential problems.
Liaise with IT department and manufacturers with regard to hardware maintenance.
Typically requires a minimum of 3 years of relevant bioinformatics experience after a Master’s degree. If PhD, experience acquired through PhD program may be considered in lieu of professional experience.
Hands-on work experience in statistics and machine learning.
Minimum of 2 years analysis experience with NGS / High-throughput sequencing data analysis
Relevant experience acquired through education and/or profession must include: proficiency in Python programming; fluency in at least 2 common programming languages (Bash, AWK, or R); next-generation sequencing technologies and assays; and high performance computing (e.g., SGE environment)
Experience with making presentations to and communicating effectively with various levels of staff.
Minimum of 1 year analysis experience on DNA methylation datasets and/or single cell datasets
Experience in biology
MS degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline
PhD degree in bioinformatics, computational biology, computer science, biological sciences, bioengineering, mathematics, statistics or related discipline.
SKILLS AND ABILITIES
Proven organizational and time management skills to successfully set priorities, meet established deadlines and recognize new problems with constantly changing priorities and frequent interruptions.
Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment. Ability to read, comprehend, and discuss research materials. Proven ability to write, edit and proofread research results. Skill at explaining difficult concepts and training users and students.
Ability to interact diplomatically and professionally with all levels of Institute staff and external contacts.
Ability to identify, download, install, troubleshoot and assess new analysis tools.
Demonstrated knowledge and experience with MAC or Linux/UNIX operating systems.
Experience applying machine learning approaches for data integration and data mining.
Theoretical and practical knowledge of biological sciences (particularly genetic and molecular biology).
SPECIAL CONDITIONS OF EMPLOYMENT
Satisfactory completion of the Institute’s background investigation.
Must be willing to sign confidentiality agreement
Must be willing to work in an animal-related research environment.
Must be a U.S. Person to work on certain DoD-funded programs.
This position requires constant adjusting focus, grasping, handling, hearing, keying, seeing, sitting, talking, touching/feeling, analyzing, calculating, communicating, reading, reasoning, writing, and working inside.
Equal Opportunity Employer/Protected Veterans/Individuals with Disabilities
The contractor will not discharge or in any other manner discriminate against employees or applicants because they have inquired about, discussed, or disclosed their own pay or the pay of another employee or applicant. However, employees who have access to the compensation information of other employees or applicants as a part of their essential job functions cannot disclose the pay of other employees or applicants to individuals who do not otherwise have access to compensation information, unless the disclosure is (a) in response to a formal complaint or charge, (b) in furtherance of an investigation, proceeding, hearing, or action, including an investigation conducted by the employer, or (c) consistent with the contractor’s legal duty to furnish information. 41 CFR 60-1.35(c)
Salk scientists are dedicated to innovative biological research. The Salk Institute consistently ranks among the leading research institutions in the world for its faculty's contributions and the impact of their findings. Focused both on discovery and on mentoring future generations of researchers, Salk scientists make groundbreaking contributions to our understanding of cancer, aging, Alzheimer's, diabetes and infectious diseases by studying neuroscience, genetics, cell and plant biology, and related disciplines. "We lead biological research. We prize discovery. Salk is where cures begin."Overlooking the Pacific Ocean in La Jolla, the Salk Institute offers a warm, collegial and collaborative work environment, where employees enjoy a generous benefits program. Social activities on campus encourage interaction as a community.