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The primary objective of the Data Integration Engineer position is to create technology solutions that give simple access to curated structured and unstructured data in support of basic science research at St. Jude Children's Research Hospital (SJCRH). The Data Integration Engineer is responsible for the design, development, and implementation of extract, transform, and load (ETL) processes and tools supporting scientific applications and web portal sites that contain research data. The Data Integration Engineer partners with the SJCRH researchers, SMEs, business analysts, and technical leads/architects to lead the implementation of innovative data integration solutions across on-premises and cloud-based environments.
At St. Jude Children’s Research Hospital, we know what can be achieved when the brightest scientific minds face the fewest barriers. The Division of Brain Tumor Research is seeking a highly motivated Sr. Bioinformatics Research Scientist to lead projects to dissect critical connections between development, epigenetics and cancer driving the molecular pathogenesis of pediatric brain tumors. You will work with a highly collaborative team of investigators focusing on pediatric brain tumors including Suzanne Baker, Martine Roussel, Peter McKinnon and Paul Northcott. Projects will involve integrative omics data from primary tumors, human and mouse tumor models, and developing brain to address mechanistic questions. Big datasets will include RNAseq, single cell RNAseq, ChIP-seq, cut and run, ATAC-seq, exome and whole genome sequence and DNA methylation profiling. Candidates with a strong background in bioinformatics, computational biology, epigenetics, gene regulation, and/or cancer genomics are highly encouraged to apply for this position.
St. Jude Children’s Research Hospital is seeking a Bioinformatics Research Scientist who is excited to work in the field of functional genomics and proteomics. This is a forecasted position, available for hire on July 1, 2019.
Recognized for state-of-the-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise, St. Jude offers a work environment where you will directly impact the care of pediatric cancer patients. As a Bioinformatics Research Scientist, your responsibilities include analyzing data generated from a variety of second- and third-generation sequencing applications and mass spectrometry-based proteomics.
The Abraham lab studies gene expression-regulation mechanisms in healthy and diseased mammalian cells. We are recruiting computational biologists to collaboratively develop tools and frameworks to analyze high-throughput sequencing (-omics) data. We build analytical software pipelines to find answers to biological questions about gene regulation in big datasets, usually from applied sequencing experiments like ChIP-Seq, RNA-Seq, and Hi-ChIP. Our interests center on enhancers and super-enhancers. Specifically, we seek to understand how these regulatory elements establish gene expression programs in healthy cells, and how enhancers are altered by mutation, abused by mistargeting, and targetable with drugs in diseased cells. We focus on characterizing the core regulatory circuitries driving disease-relevant cells, and on understanding how mutations in the non-coding DNA of such cells can drive disease, including cancers, through gene misregulation.
Ideal candidates will have experience building, tailoring, and deploying analysis pipelines using widely available genomic analysis toolkits (e.g. bedtools, samtools), as well as experience managing large numbers of datasets. The successful candidate will be tasked with collaborative research within and beyond the lab, so strong communication and interpersonal skills are essential. Additional experience in fundamental understanding of gene expression mechanisms (e.g. transcription factors, enhancers, genome structure, and transcriptional condensates), and experience building succinct, clear figures using R are preferred.
The department of Computational Biology provides access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from faculty scientists with experience in data analysis, data management and delivery of high-quality results for competitive projects. We encourage first author, high profile publications to share this element of discovery. Take the first step to join our team by applying now!
The Data Architect - Analytics will be a key contributor for the design, implementation and optimization of complex enterprise-wide reporting, analytics and data science solutions, utilizing state-of-the-art technologies. The selected candidate will responsible for taking our strong legacy platform to a cloud-based modern BI platform complete with data lakes, big data tools, technologies and machine learning infrastructure. The ideal candidate would have robust implementation experience of security standards, protocols, tools and technologies to ensure compliance with HIPAA and Sarbanes Oxley.
This role will define technical architecture and workflow for analytics solutions, as well as documentation standards and policies. Will have regular interaction with St. Jude executive leadership to determine analytic needs and update strategy and project/roadmap documents. The Data Architect will develop diagrams and other visualizations needed to depict high to low level architecture and workflow for analytics solutions. The ideal candidate will have an understanding of clinical data management, Cerner experience, strong written and verbal skills.
St. Jude is a seeking full-time, senior level IT risk and cybersecurity professional with demonstrated experience in the areas of GRC and IT Risk Management. The St. Jude Risk Management Lead is responsible for maintaining a consistent, repeatable lifecycle process for cybersecurity risk management across the institution. The ideal candidate would have GRC consulting experience or healthcare cybersecurity experience. Candidates must demonstrate strong leadership and communication skills, a positive, can-do attitude and the ability to work well with cross functional teams in a dynamic environment
St. Jude is anticipating the need for several Associate Software Engineers. The department of Computational Biology is seeking highly motivated and creative Associate Software Engineers to develop software used in big data bioinformatics analysis as part of a team of scientists and engineers at the forefront of genomic research into catastrophic childhood diseases. Positions are available in the following focus areas:
- Developing web applications in the St. Jude Cloud project.Primary responsibilities will be designing and developing bioinformatics-related web applications in St. Jude Cloud (https://www.stjude.cloud). Knowledge of at least one of the following middleware technologies is required: NodeJS (leveraging Express, Koa, or comparable), Ruby (leveraging Ruby on Rails or Sinatra), or PHP (leveraging Laravel). Knowledge of at least one of the following frontend frameworks is required: React, Vue, or Angular. Knowledge of Linux, Bash/Zsh, and Git are preferred. Knowledge of containerization (Docker), database technologies (PostgreSQL, MySQL), common software product design processes (Agile/SCRUM), and common cloud computing paradigms is preferred.
- Developing internal web applications to support clinical genomics operations. Primary responsibilities include understanding the needs of scientists and clinicians who review and report clinical genomics results and resolving those needs with web-based interfaces that help to advance their work. Facility with modern web application architecture is a key factor to success. We use PHP Laravel, Vue.js, and PostgreSQL for development. Experience with these technologies, or experience with similar technologies and a willingness to learn, is required. Individuals with a desire to make the work of clinical users easier and who are interested in maintaining and applying broad knowledge of modern web application technologies are encouraged to apply.
- Developing and maintaining HPC Bioinformatics automation systems. Primary responsibilities will be managing large scale Bioinformatics pipelines run with on premise HPC cluster along with development and improvement of automation tools for high throughput analyses. Knowledge of Linux, Bash, Git, Python, and at least one of the following is preferred: Perl, C / C++, CWL, WDL. Previous experience with HPC, knowledge of containerization including Docker and Singularity, and common software product design processes (Agile / SCRUM) are preferred.
- Developing and maintaining data stores for our clinical genomics data. Primary responsibilities include learning and applying the semantics of our data to code extensions to our data store infrastructure, proactively discovering and resolving data errors, and enhancing processes to ensure complete and accurate data capture. This person plays a critical role in accelerating data delivery to scientists and clinicians. Main tools used are databases, SQL, and Python. Analytical thinkers with training in mathematics, logic, statistics, or a related area are encouraged to apply.
All positions listed will require working within a team of software developers to develop software, write and maintain documentation relevant to the position’s scope of work, write and maintain unit tests for software, and assist in preparing and submitting manuscripts. When applying, please include areas of specific interest in cover letter and a portfolio of any school projects or work samples you can provide in your resume. You can upload your cover letter with your resume as the first page of your resume.
Recognized as a world leader in mapping the genetic landscape of pediatric cancers, the St. Jude department of Computational Biology has developed state-of-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise with a track record of high-impact publications in top-tier biomedical journals such as Nature, NEJM, JAMA, Nature Genetics, and Nature Methods. The department provides a highly interactive environment with collaborative opportunities across basic and clinical departments, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from faculty scientists with deep experience in data analysis, data management, and delivery of high-quality results for highly competitive projects. This position is located in Memphis, TN, and relocation assistance is available
Recognized as a world leader in mapping the genetic landscape of pediatric cancers, the St. Jude department of Computational Biology has developed state-of-art computational infrastructure, well-established analytical pipelines, and deep genomic analysis expertise with a track record of high-impact publications in top-tier biomedical journals such as Nature, NEJM, JAMA, Nature Genetics, and Nature Methods. The department of Computational Biology is seeking a highly motivated, analytical thinker for the position of Genomic Data Engineer to develop data stores and accompanying software used in big data bioinformatics analysis. The Genomic Data Engineer plays a key role in delivering highly accurate and timely data to scientists and clinicians at the forefront of genomic research into catastrophic childhood diseases. This position also requires experience working within a team of software and data engineers, writing and maintaining documentation relevant to the position’s scope of work, and assisting with the preparation and submission of manuscripts.
The department provides a highly interactive environment with collaborative opportunities across basic and clinical departments, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from faculty scientists with deep experience in data analysis, data management, and delivery of high-quality results for highly competitive projects. This position is located in Memphis, TN, and relocation assistance is available.