NICHD Data Scientist

Company: Axle Informatics
Location: Bethesda
Posted on: March 18, 2023

Job Description:

Overview
Axle Informatics -is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques to empower decision-making and accelerate research discoveries. We work with some of the top research organizations and facilities in the country including multiple institutes at the National Institutes of Health (NIH). -

Axle is seeking a highly ambitious, adaptable, structured, and detail-oriented NICHD Data Scientist to join our vibrant team at the National Institutes of Health (NIH) supporting the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) located in Bethesda, MD. -

Overall Position Summary and Objectives -The Perinatology Research Branch, DIR/NICHD (PRB) has conducted translational research on the subjects of normal pregnancy, labor, andpregnancy complications. The results of this research need to be disseminated in the form of publications in biomedical journals. The scope of the work is to analyze data previously generated by the Perinatology Research Branch, NICHD which consists of cell free RNA data of maternal plasma in patients who subsequently develop preterm labor/birth and preeclampsia.

Deliverables:

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• Work products, documents, including, but not limited to, the material and methods section as well as the results section of each manuscript and supplementary materials including figures, graphs, tables and relevant references - Ad-Hoc
  
  Work Details:
  
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  • Provides programming and troubleshooting support to the Federal Government in the dissemination of research data.
    
  • Serve as bioinformatics expert and coordinate with teams of biologists to conduct experimental queries and/or perform portions of studies using complex procedures and techniques common to modern bioinformatics. 3
    
  • Performs computations on research data analysis.
    
  • Perform computational analysis of, and interpret results.
    
  • Provide reports based on analysis of scientific data.
    
  • Provide interpretive analyses of data derived from different experimental platforms to generate biological meaning.
    
  • Works with staff on scientific programming and experimental design.
    
  • Collaborate with scientists to design, analyze, manage and interpret all types of data.
    
  • Work with staff to develop specifications for new analysis; design, test and implement solutions.
    
  • Make recommendations to investigators about the correct computational tools for testing scientific hypotheses and reaching valid conclusions.
    
  • Records observations and report results at weekly laboratory meetings.
    
  • Prepare scientific reports and progress reports; assemble data to prepare tables, graphs and slides; conduct scientific and program related information searches and report results.
    
  • Organize laboratory notebook or computer database to record results of calculations. Share results at lab meetings.
    
  • Provides statistical support / analysis on research data.
    
  • Devise novel methods of statistical analysis for collected data.
    
  • Utilize and adapt existing bioinformatics techniques to check for trends and patterns in the data.
    
  • Perform data processing and data analysis with existing computational and statistical methods.
    
  • Assist in evaluating and interpreting results for validity and scientific meaning.
    
  • Provides research / service goals in the context of the laboratory's overall mission. 1
    
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    • Cell free RNA analysis in maternal circulation: development-related changes and predictors of preterm birth and term preeclampsia.
      
    • Preprocess the RNA-Seq data in FASTQ format using established protocols including aligning the paired-end short reads to the genome using STAR and RSubread pipelines
      
    • Perform unsupervised visualization of data using techniques including Principal Coordinates Analysis (PCoA) and Uniform Manifold Approximation and Projection (UMAP)
      
    • Conduct differential expression abundance analysis between study groups using negative binomial models implemented in the DESeq2 and EdgeR package of Bioconductor
      
    • Determine the effect of relevant covariates such as maternal characteristics and obstetrical history on the significance of differences between cases and controls
      
    • Perform functional profiling to identify biological process and other gene ontologies associated with the proteins with significant changes in each contrast of interest (e.g. 24-28 vs 16-20 weeks of gestation in normal pregnancy, preterm preeclampsia vs control; term preeclampsia vs control) using hypergeometric tests implemented in packages such as GOStats, iPathwayGuide
      
    • Use alternative approaches such as Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) and GSEA if there is not a sufficient number of genes that pass significance cut-offs for enrichment analyses
      
    • Explore different pathways and gene sets such as MSigDB and DFLAT in enrichment analyses
      
    • Integrate results with single cell RNA-Seq signatures previously derived by the PRB to identify which placenta and immune cell type could have contributed to the observed changes in cell free RNAs in circulation
      
    • Determine possible tissue-specific contributions to the RNA signatures for preeclampsia based on the Gene Atlas collection
      
    • Evaluate correlations with previously reposted cell free RNA signatures of preeclampsia and preterm birth in maternal blood
      
    • Build network representations of the most relevant RNAs using STRING and other tools
      
    • Use cross-validation to estimate the accuracy, sensitivity and specificity of cell free RNA-based machine learning methods for prediction of preterm and term preeclampsia using longitudinal data
      
    • Apply top performing machine-learning pipelines identified in the DREAM Preterm Birth Prediction Challenge to the prediction of preeclampsia
      
    • Conduct sub-analyses after disaggregation of preeclampsia cases by presence of specific types of lesions in the placenta
      
    • Draft material and methods section and results section for manuscripts
      
    • Assist with the response to the comments of reviewers and editors including but not limited to correspondence such as letters to the editor after the publication of manuscripts
      
      
    • Evaluates new types of experimental approaches to protocols based on knowledge of scientific literature, available facilities and research needs.
      
    • Research and review literature to retrieve targeted clinical or scientific information, including novel statistical methods, from publicly available resources.
      
    • Collaborate with staff to review current and historical procedures for the acquisition, quality control and management of data.
      
    • Analyze and evaluate data cleaning and harmonization needs in the using a variety of descriptive statistics and analytic methods.
      
    • Identify new tools and resources for reaching biologically meaningful conclusions.
      
    • Independently coordinates the training of personnel in the use of scientific software applications, statistical software applications and programmatic software applications. 2
      
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      • Analysis of the amniotic fluid, maternal blood and cord blood proteomes in term parturition.
        
      • Assess the data quality based on specific metrics described by the manufacturer of the SomaScan v 4.1 assays
        
      • Determine inter-platform agreement for specific analytes (e.g. IL6) for which ELISA-based data is available
        
      • Remove the effect of gestational age and maternal characteristics using previously defined proteomic models (e.g. SomaPreg package for maternal blood)
        
      • Perform unsupervised visualization of data using techniques including Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP)
        
      • Identify the biological pathways associated with the proteins contributing the most to principal components
        
      • Conduct differential protein abundance analyses between study groups using linear models with evaluation of significance via moderated t-tests implemented in the limma package of Bioconductor
        
      • Perform a dose-response analysis to identify proteins that are more dysregulated with a higher degree of cervical dilatation among women in the labor group
        
      • Determine the effect of relevant covariates such as maternal characteristics and obstetrical history (for cord blood and amniotic fluid)
        
      • Perform functional profiling to identify biological process and other gene ontologies associated with the proteins with significant changes in each contrast of interest (e.g. TL vs TNL) using hypergeometric tests implemented in packages such as GOStats, iPathwayGuide
        
      • Use alternative approaches such as Pathway Analysis with Down-weighting of Overlapping Genes (PADOG) if not sufficient proteins pass significance cut offs for enrichment analyses
        
      • Explore several collections of pathways and gene sets such as MSigDB and DFLAT in enrichment analyses
        
      • Integrate results with single cell RNA-Seq signatures previously derived by the Perinatology Research Branch to identify which placenta and immune cell type could have contributed to the observed changes in the proteome
        
      • Determine possible tissue specific contributions to the signatures based on the Gene Atlas collection
        
      • Evaluate correlations with previously established RNA signatures of parturition in the uterus, cervix and fetal membranes
        
      • Assess the overlap in proteomic changes among the amniotic fluid, maternal blood and cord blood p.Extract from the literature results from other omics studies to gage overlap in changes with term parturition among different platforms and studies
        
      • Build network representations of the most relevant proteins using STRING and other resources
        
      • Draft material and methods section and results section for manuscripts
        
      • Assist with the response to the comments of reviewers and editors including but not limited to correspondence such as letters to the editor after the publication of manuscripts
        
        
      • Initiates interdisciplinary collaborations with other research centers.
        
      • Work with an interdisciplinary team to apply computational data analysis approaches to make biological discoveries.
        
      • Collaborate with group members in experiments associated with data collection.
        
      • Interact with all levels of staff and communicate with outside collaborators in the US and abroad.
        
      • Deliver at least one presentation per year to audiences outside the Government.
        
        1, 2, 3, 4, 5 represents priority rankings, where 1 is highest priority and 5 is lowest priority of those ranked
        
        
        Minimum Education
        
        Master's
        
        Additional Qualifications:
        
        Certifications & Licenses
        
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        • Minimum of Ph.D. in Statistics or related field.
          
          Field of Study
          
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          • Statistics and Decision Science
            
            Software
            
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            • R
              
            • Powerpoint
              
            • Outlook
              
            • STATA
              
            • SPSS
              
            • Word
              
              Skills
              
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              • Next gen sequencing data analysis: Bulk RNA-Sequencing
                
              • Clinical and/or translational research
                
              • Work with large data set
                
                
                
                
                Benefits
                
                
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                • 100% Medical Dental & Vision Coverage for Employees
                  
                • Educational Benefits for Career Growth
                  
                • Paid Time Off (Including Holidays)
                  
                • Employee Referral Bonus
                  
                • Profit Sharing
                  
                • 401K Matching
                  
                • Flexible Spending Accounts:
                  
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                  • Healthcare (FSA)
                    
                  • Parking Reimbursement Account (PRK)
                    
                  • Dependent Care Assistant Program (DCAP)
                    
                  • Transportation Reimbursement Account (TRN)
                    
                    
                    
                    The diversity of Axle's employees is a tremendous asset. We are firmly committed to providing equal opportunity in all aspects of employment and will not tolerate any illegal discrimination or harassment based on age, race, gender, religion, national origin, disability, marital status, covered veteran status, sexual orientation, status with respect to public assistance, and other characteristics protected under state, federal, or local law and to deter those who aid, abet, or induce discrimination or coerce others to discriminate.
                    
                    Accessibility: If you need an accommodation as part of the employment process please contact: careers@axleinfo.com
                    
                    Disclaimer:The above description is meant to illustrate the general nature of work and level of effort being performed by individual's assigned to this position or job description. This is not restricted as a complete list of all skills, responsibilities, duties, and/or assignments required. Individuals may be required to perform duties outside of their position, job description or responsibilities as needed.

Keywords: Axle Informatics, Bethesda , NICHD Data Scientist, Other , Bethesda, Maryland