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A Senior Bioinformatics Portal Engineer position is immediately available for a highly motivated candidate to lead the development of cutting-edge web-based applications as part of St. Jude’s groundbreaking platform, St. Jude Cloud. This team member will work directly with world-class researchers at St. Jude to devise novel web applications for working with integrated genomics data for a user base ranging from oncologists to bioinformatics research scientists.   This position requires staying abreast of emerging technologies, platforms, frameworks, and bioinformatics web portals to ensure St. Jude’s web applications exceed industry standards. The successful candidate will have experience in modern back- and front-end technologies such as Node.js/Express, PHP/Laravel, Ruby on Rails, and modern JavaScript such as Vue and React. Experience in database design and programming is preferred. Experience in Bioinformatics is preferred. The candidate is expected to be a creative and critical thinker and a quick learner for new domains and technologies.   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.   St. Jude Children's Research Hospital is an Equal Opportunity Employer. St. Jude does not discriminate on the basis of race, national origin, sex, genetic information, sexual orientation, gender identity, transgender status, age, religion, disability, veteran's status or disabled veteran's status with respect to employment opportunities. All qualified applicants will be considered for employment. St. Jude engages in affirmative action to increase employment opportunities for minorities, women, veterans and individuals with disabilities.  
Job ID
43280
Department
Computational Biology
Company
St. Jude Children's Research Hospital
We are seeking a highly motivated and creative bioinformatics research analyst to join Dr. Martine Roussel's team in the Tumor Cell Biology Department at St. Jude Children's Research Hospital to develop and apply innovative analytical approaches in the area of functional genomics. You will collaborate with St Jude investigators to analyze data such as single cell RNA-seq, single cell ATAC-seq, bulk RNA-seq, DNA methylation, ChIP-seq, to understand the tumor biology, tumor-infiltrating lymphocytes and neurobiology and help the investigators prepare manuscripts and grant applications. Experience with programming languages such as Python and R are preferred. You will also lead the evaluation of published bioinformatics tools and develop the optimized pipeline to share with scientists at St Jude. The department provides a highly interactive environment with collaborative opportunities, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from scientists with deep experience in data analysis, data management and delivery of high-quality results for highly competitive projects. Candidates with a strong background in statistics, computational biology, machine learning, and experience using systems biology approaches to understand the mechanisms of action of disease or experimental intervention are highly encouraged to apply for this position. This position is located in Memphis, TN, and relocation assistance is available.    
Job ID
43342
Department
Tumor Cell Biology
Company
St. Jude Children's Research Hospital
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!   Relevant Papers:   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.    
Job ID
42082
Department
Computational Biology
Company
St. Jude Children's Research Hospital
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.   The department of Computational Biology is seeking a highly motivated and creative Associate Product Owner to serve as a user advocate and key point of contact for the St. Jude Cloud project. The Associate Product Owner will manage the software development lifecycle, oversee and participate in the process of preparation, annotation, and maintenance of genomic data files on St. Jude Cloud, and oversee the process for St. Jude Cloud data access. This position will regularly deal with diverse matters which require extensive knowledge of St. Jude Cloud and the successful candidate will possess the ability to handle sensitive situations in a mature and confidential manner.    
Job ID
42751
Department
Computational Biology
Company
St. Jude Children's Research Hospital

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