Frederick National Laboratory for Cancer Research

Bioinformatics Analyst III

Location
Bethesda, MD, USA
Posted
Sep 15, 2020
Ref
req1372
Hotbed
BioCapital
Required Education
Bachelors Degree
Position Type
Full time
The Frederick National Laboratory is dedicated to improving human health through the discovery and innovation in the biomedical sciences, focusing on cancer, AIDS and emerging infectious diseases.

The Biomedical Informatics and Data Science (BIDS) directorate works collaboratively and helps to fulfill the mission of Frederick National Laboratory in the areas of biomedical informatics and data science by developing and applying world leading data science and computing technologies to basic and applied biomedical research challenges, supporting critical operations, developing and delivering national data resources, and employing leading-edge software and data science to effectively enable and advance clinical trials.

The Advanced Biomedical Computing Sciences (ABCS) is a part of the Biomedical Informatics and Data Science (BIDS) Program at Leidos Biomedical Research, Inc. The ABCS provides technology development, scientific consultation, collaboration and training, and high-performance computing support to the NCI and NIH scientists and staff.

The mission of the Oncogenomics Section (Genetics Branch, NCI) is to harness the power of high throughput genomic and proteomic methods to improve the outcome of children with high-risk metastatic, refractory and recurrent cancers. The research goals are to integrate the data, decipher the biology of these cancers and to identify and validate biomarkers and novel therapeutic targets and to rapidly translate findings to the clinic. The section has next generation sequencing data for over 12,000 patients from samples generated both in-house and public data relevant to ongoing research efforts. This includes approximately 400 patients analyzed on their CLIA ClinOmics platform and are enrolled on NIH clinical protocols.

KEY ROLES/RESPONSIBILITIES

The Bioinformatics Analyst III is responsible for providing collaborative bioinformatics support to the investigators in the Oncogenomics section (Genetics Branch) at the National Cancer Institute (NCI). Key responsibilities include:
  • Develop, manage and maintain Data Management pipelines for next-generation sequencing data (eg genomics, transcriptomics, proteomics, epigenetic data, microbiome 16S RNA)
  • Maintain detailed documentation of pipeline runs and validation/benchmarking projects
  • Collect and review data from multiple sources; analyze and interpret data and results; provide reports based on analysis of scientific data, and report research outcomes to make recommendations for future work
  • Assist PIs in submitting data to public genomic databases, such as GEO, and dbGaP, in compliance with the NIH Genomic Data Sharing Policy
  • Work with staff to utilize NIH Biowulf computer clusters to process data streamed off the next generation sequencers (NGS); process data in a batch mode
  • Train fellows and other staff to use NGS and other genomic analysis tools
  • Develop other bioinformatic pipelines for processing molecular data such as ChIP-seq, DNAse-seq, single-cell sequencing, flow cytometry, etc.
  • Advise section researchers about available data analysis pipelines
  • Attend branch and lab meetings, and provide guidance and inputs on expt. design and accurate statistical inference
  • Design and implement state-of-the-art computational methods; use existing open-source algorithms and develop custom algorithms to answer key cancer genomics questions using Next-generation sequencing
  • Create generalizable code bases to improve and support development of pipelines for the analysis, interpretation and visualization of next-generation sequencing data. Develop interactive & shareable code solution using technologies like Jupyter & KnitR for collaborators and actively maintain them in a centralized version controlled repository in Github
  • Incorporating RNAseq data, somatic mutations, translocations, amplifications, deletions and other druggable genomic alterations into the existing platform
  • Coordinate, plan, and at times lead Bioinformatics lab meetings and journal clubs 4-6 weekly, including article presentation. Maintenance and updating of Confluence site
  • Manuscript writing, presentation of scientific projects at lab, local, and national scientific meetings
  • Ensuring that Github is maintained for all codes developed by incumbent
  • Collaboration with biologists, clinicians and core facility members to understand their experimental and technical goals and suggest. statistical and bioinformatics solutions for target discovery, drug mechanism elucidation and patient stratification efforts
  • The Bioinformatics Analyst III is expected to work effectively as a member of a team; coordinate activities among other groups located at the Bethesda, Frederick, Rockville and Gaithersburg NCI campuses; follow sound scientific practices and maintain effective documentation of activities and analyses. Majority of time will be spent on the main NIH campus in Bethesda.

BASIC QUALIFICATIONS

To be considered for this position, you must minimally meet the knowledge, skills, and abilities listed below:
  • Possession of a Bachelors degree from an accredited college or university according to the Council for Higher Education Accreditation. (Additional qualifying experience may be substituted for the required education)
  • In addition to the educational requirements, a minimum of four (4) years of progressively responsible relevant experience is required
  • Foreign degrees must be evaluated for U.S. equivalency
  • Must be able to obtain and maintain a clearance.

PREFERRED QUALIFICATIONS

Candidates with these desired skills will be given preferential consideration:
  • A Masters' or PhD degree in any quantitative science is preferred
  • Commitment to solving biological problems and communicating these solutions
  • Ability to multi-task across projects
  • Experience in submitting data sets to public repositories
  • Management of large genomic data sets including integration with data available from public sources
  • Prior customer-facing role
  • Record of scientific achievements including journal publications and conference presentations
  • Ability and experience in designing and creating bioinformatics pipelines for cancer genomics
  • Ability and experience in creating and optimizing computational framework for clinical genomics
  • Understanding and experience for multiple bioinformatics options and setups for clinical genomics
  • Understanding and experience in creating platforms for pathologist sign out of genomic data
  • Experience in creating clinical grade databases for gene annotation for cancer on a large scale
  • Experience evaluating and comparing different computational pipelines for alignment, variant calling, and functional annotation

EXPECTED COMPETENCIES
  • Deep understanding of and experience in processing high throughput biomedical data: data cleaning, normalization, analysis, interpretation and visualization
  • Ability to understand and analyze data from complex experimental designs
  • Proficiency in at least two of the following programming languages: Python, R, Perl, Java and C/C++
  • Experience in at least two of the following areas: Exome sequencing, metagenomics, ChIPSeq, RNASeq, DHS-Seq, microarray analysis, DNA methylation analysis
  • Familiarity with public databases: NCBI, Ensembl, TCGA, cBioPortal, Broad FireHose
  • Knowledge of working in a cluster environment


Equal Opportunity Employer (EOE) | Minority/Female/Disabled/Veteran (M/F/D/V) | Drug Free Workplace (DFW)

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