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St. Jude Children’s Research Hospital is seeking a Bioinformatics Research Scientist in Epigenetics Group in the Center for Applied Bioinformatics (CAB). CAB is a newly established center to provide centralized genomic and bioinformatic analytic services and collaborations for investigators (PIs) at St. Jude Children's Research Hospital. You will have the opportunity to work on diverse projects together with different PIs and contribute to pediatric cancer patient curation and survival, explore new methods, develop pipelines, in addition to the routine analysis tasks. We encourage you to be a first author on high profile publication with opportunities to cross-train and collaborate with the Transcriptomics and Genetics Groups in the CAB.
Good candidates will have experience building, optimizing analysis pipelines using available software or installing pipelines for high-throughput next generation sequence data analysis (such as ChIP-Seq, ATAC-Seq, RNA-Seq, Hi-C/HI-CHIP/CaptureC) under Linux/Unix environment. The successful candidate is expected to have good programming skills in Bash, Python and R, have an understanding of basic epigenetics gene regulation mechanisms (e.g. Histone Modification, Chromatin Accessibility, DNA Methylation, 3D Genome). Experience with deep learning or C++ or CWL is a plus.
St. Jude has been consistently ranked in Fortune magazine’s “100 Best Places to Work” list and is exceptionally positively reviewed on GlassDoor. Salary is highly competitive (comparable to industry) and employee benefits are outstanding. This position is located at Memphis, TN, and relocation assistance is available.
The Department of Global Pediatric Medicine (GPM) is a new and growing department looking for professionals who are eager to help implement the mission of taking St. Jude to the world by training the clinical workforce, developing and strengthening health systems and patient-centered initiatives, and advancing knowledge to sustain continuous improvement through research.
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.
Salary is highly competitive (comparable to industry) and employee benefits are outstanding. Relocation assistance is available. Working at St. Jude provides the opportunity to make a tangible difference to pediatric cancer patient care and survival and St. Jude has been consistently ranked in Fortune magazine’s “100 Best Places to Work” list and is exceptionally positively reviewed on GlassDoor.
St. Jude Children’s Research Hospital is seeking multiple Bioinformatics Research Scientists to study the role of genome and other nuclear organization in pediatric cancers. 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 that interrogate a broad range of human gene regulatory biology.
The Abraham lab studies gene expression-regulation mechanisms in healthy and diseased mammalian cells. We are recruiting computational biologists to collaboratively develop computational 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.
The successful candidate will become a fundamental component of a multidisciplinary, inter-institutional team assembled to study how genome structures meaningfully differ between normal and pediatric cancer cells.
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!
Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT, Mansour MR, Young RA. Small genomic insertions form enhancers that misregulate oncogenes. Nat Commun. 2017 Feb 9;8:14385. doi: 10.1038/ncomms14385. PubMed PMID: 28181482; PubMed Central PMCID: PMC5309821.
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10. PubMed PMID: 24119843; PubMed Central PMCID: PMC3841062.
Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell. 2014 Oct 9;159(2):374-387. doi: 10.1016/j.cell.2014.09.030. PubMed PMID: 25303531; PubMed Central PMCID: PMC4197132.
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