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We are seeking a highly motivated and creative bioinformatics research analyst to join the team of Dr. Kim Nichols in the Division of Cancer Predispositon at St. Jude Children's Research Hospital. The bioinformatics analyst will develop and apply innovative analytical approaches in the area of cancer genetics and functional genomics and have the unique opportunity to help carry out research studies that focus on known hereditary forms of childhood cancer and discovery of new causes for familial cancers.   You will work closely with research team members to analyze data such as WES, WGS, bulk and single cell RNA seq,Cut&Run seq and ATAC seq data, to identify novel cancer predisposition genes and interrogate their biological function. You will develop, improve, modify, and operate data analysis pipelines, generate and provide analysis results and reports, and perform requested custom analyses.   The department provides a highly interactive environment with collaborative opportunities, access to high performance computing clusters, a cloud computing environment, innovative visualization tools, highly automated analytical pipelines and mentorship from scientists with interests experience in data analysis, data management and delivery of high-quality results. The Division of Cancer Predisposition supports strong teamwork as well as individual and personal growth.    Candidates with a strong background and interest in genetics, cancer biology, hematopoiesis, and experience with use of genetic approaches to understand disease pathogenesis are highly encouraged to apply for this position. Familiarity with statistical genetics/genomics software including MERLIN, PLINK, GATK, EdgeR, samtools is preferred. This position is a forecasted position located in Memphis, TN, and relocation assistance is available.    
Job ID
44054
Department
Oncology
Company
St. Jude Children's Research Hospital
Type
Full Time
M. Madan Babu's Group at the Center of Excellence for Data-Driven Discovery and the Department of Structural Biology is seeking a highly driven, full-time Principal/Senior Bioinformatics Research Scientist to serve as the Web Development and Design lead to support the Kalodimos and Babu Groups on the Blue Sky Initiative "Seeing the Invisible in Protein Kinases." This project is supported by $35 million in institutional funding (more information in the St. Jude Strategic Plan 2022–2027). This is a joint project between the Kalodimos Lab and the Babu Group at St Jude.   The project will extend the ultra-high field NMR spectroscopy and biochemistry approaches developed recently by the Kalodimos lab (Science 370, eabc2754, 2020) to study the human kinome. This is a large-scale project that aims to detect and structurally characterize the distinct conformational states populated by kinases, and to dissect the mechanisms of allosteric regulation and those underpinning oncogenic and drug-resistance mutations. This strategy will be integrated with and complemented by data-science and computational approaches developed by the Babu lab (Nature 587, 650, 2020), to systematically characterize the conformational landscape of the human kinome.    The ideal candidate will be an expert in UX/UI design and back-end development of web applications to help scientists visualize, analyze and understand high-dimensional biological data. You will have a strong background in computer science, web development, bioinformatics, or computational biology and truly exceptional skills in designing visualizations to render complex, multi-dimensional biological data interpretable and understandable. You should be able to present or provide links to a strong work portfolio that demonstrates your expertise in designing, building, and deploying insightful web-based applications. You will be a team player and will work as part of an interdisciplinary team of 40 scientists including biochemists, NMR spectroscopists, data scientists and bioinformaticians. Exceptional communication (written and verbal) and critical thinking skills are a must.     When submitting your application, please include your CV and a cover letter, which includes information or a link to a portfolio of past projects.   Ranked #1 in the U.S. in Pediatric Cancer, St. Jude Children's Research Hospital is a NCI-designated Comprehensive Cancer Center, and home to the Pediatric Cancer Genome Project. The St. Jude campus is a truly unique research environment, encompassing state-of-the-art HPC facilities, world-leading oncology basic research, outstanding Shared Resources and Core Facilities and a dedicated translational Chemical Biology and Therapeutics department. The $412M Advanced Research Center, opened in 2021, doubles the campus’ research space and adds support for an additional 1000 employees. There is a vibrant Data Science community at St. Jude, with opportunities to interact with researchers in the Biostatistics and Computational Biology Departments, and tremendous support from the Center for Applied Bioinformatics.   The Department of Structural Biology is building one of the world’s most comprehensive research center for defining molecular structures to understand health and disease at the molecular level. The Department is home to multiple Technology Core Centers (Cryo-EM and Tomography, X-ray, NMR, Single-Molecule Imaging, and Protein Technologies) ready to characterize Data Driven Discoveries.
Job ID
44690
Department
Structural Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
M. Madan Babu's Group at the Center of Excellence for Data-Driven Discovery and the Department of Structural Biology is seeking a highly driven, full-time Principal Bioinformatics Research Scientist to serve as a Database Engineer to support the Kalodimos and Babu Groups on the Blue Sky Initiative "Seeing the Invisible in Protein Kinases." This project is supported by $35 million in institutional funding (more information in the  St. Jude Strategic Plan 2022–2027 (pp 62-63). This is a joint project between the Kalodimos Lab and the Babu Group at St Jude.   The project will extend the ultra-high field NMR spectroscopy and biochemistry approaches developed recently by the Kalodimos lab (Science 370, eabc2754, 2020) to study the human kinome. This is a large-scale project that aims to detect and structurally characterize the distinct conformational states populated by kinases, and to dissect the mechanisms of allosteric regulation and those underpinning oncogenic and drug-resistance mutations. This strategy will be integrated with and complemented by data-science and computational approaches developed by the Babu lab (Nature 587, 650, 2020), to systematically characterize the conformational landscape of the human kinome.    This position is for a senior-level database engineer who will employ a variety of languages and tools to develop, construct, test and maintain data pipelines to organize multimodal biological information, and work with data scientists and visualization specialists to make biological discoveries and reveal fundamental principles of biological systems. The ideal candidate will have strong experience working in data warehouse environments and developing data marts to help scientists query, visualize and understand high-dimensional biological data.  This role requires a strong background in computer science, data architecture and database management. You will work with an interdisciplinary team of 40 scientists including biochemists, spectroscopists, data scientists and bioinformaticians; exceptional communication (written and verbal), training experience and critical thinking skills are a must. When submitting your application, please include your CVand a cover letter. St Jude offers a well-defined career ladderwith potential for growth and advancement. Industry-competitive salaries are based on your degree and years of experience.   Ranked #1 in the U.S. in Pediatric Cancer, St. Jude Children's Research Hospital is a NCI-designated Comprehensive Cancer Center, and home to the Pediatric Cancer Genome Project. The St. Jude campus is a truly unique research environment, encompassing state-of-the-art HPC facilities, world-leading oncology basic research, outstanding Shared Resources and Core Facilities and a dedicated translational Chemical Biology and Therapeutics department. The $412M Advanced Research Center, opened in 2021, doubles the campus’ research space and adds support for an additional 1000 employees. There is a vibrant Data Science community at St. Jude, with opportunities to interact with researchers in the Biostatistics and Computational Biology Departments, and tremendous support from the Center for Applied Bioinformatics.   The Department of Structural Biology is building one of the world’s most comprehensive research center for defining molecular structures to understand health and disease at the molecular level. The Department is home to multiple Technology Core Centers (Cryo-EM and Tomography, X-ray, NMR, Single-Molecule Imaging, and Protein Technologies) ready to characterize Data Driven Discoveries.   St. Jude Children’s Research Hospital is consistently named as one of Fortune magazine and Glassdoor.com’s “Best Places to Work,” as well as “Best Workplace for Women” and “Best Workplace for Diversity.” We are in the heart of Memphis, Tennessee, a vibrant and friendly city at the historic American crossroads of music, trade, food, and culture. Mild winters and beautiful green outdoor spaces are part of the reasons why Forbes recently named Memphis the 4th happiest city in which to work. Low cost of living and high quality of life are other attractions; Money magazine listed Memphis as one of the least expensive cities in which to raise a child. St. Jude facilities and salaries are highly competitive. The Kalodimos and Babu Groups strive to build and maintain a culture of respect, diversity, and inclusion and we strongly feel these values directly contribute to the dynamic and intellectually stimulating scientific environment we can provide.
Job ID
44976
Department
Structural Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
The department of Computational Biology is seeking a highly motivated Sr. Bioinformatics Research Scientist to serve as the scientific lead for St. Jude Cloud, a cloud-based ecosystem for data sharing, cloud-computing and dynamic visualization of the world’s largest pediatric cancer genomic data set. The candidate will be a part of an interdisciplinary team consisting of scientists and engineers from St. Jude and our external partners at DNAnexus and Microsoft. Specific responsibilities include providing scientific guidance for the engineering team, organizing pilot studies to evaluate collaborative research initiatives, developing prototypes of workflow and designing new concepts for data visualization, performing curation on data releases, and participating in presentation and training of St. Jude Cloud platform to the biomedical community.      Candidates with a strong background in bioinformatics, computational biology, and cancer genomics are highly encouraged to apply for this position. Successful candidates shall have well-established track record in cancer genomic research, in-depth experience in data analysis, excellent critical thinking and communication skills, as the St. Jude Cloud project is an institutional strategic initiative and this position will frequently interact with senior scientists from departments across the institution, as well as external partners and collaborators.   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 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 collaborative projects. This position is located in Memphis, TN, and relocation assistance is available.    
Job ID
44379
Department
Computational Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
M. Madan Babu's Group at the Center of Excellence for Data-Driven Discovery and the Department of Structural Biologyis seeking a highly driven, full-time human geneticist. This post will be part of a newly established Centre for Adipocyte Signaling (ADIPOSIGN) funded by a major grant from the Novo Nordisk Foundation. This position is available immediately with four years of funding. ADIPOSIGN is run by four partners with highly complementary expertise in the fields of adipocyte biology, transcriptional regulation, signal transduction, physiology, and computational systems biology:   Susanne Mandrup, Prof., Dept. Biochemistry and Molecular Biology, SDU, DK Jan-Wilhelm Kornfeld, Prof., Dept. Biochemistry and Molecular Biology, SDU, DK Madan Babu, Member, Dept. of Structural Biology SJCRH, USA Zach Gerhart-Hines, Assoc. Prof., NNF Center for Basic Metabolic Research, University of Copenhagen, DK   The ideal candidate may have extensive expertise and a proven track record in statistical genetics, population genetics, computational analysis of human genetics and large-scale phenotype data and interpreting genome variation data (coding and non-coding variant effects). Your primary role as a computational human geneticist will be to identify, develop, implement and use computational genetics methods to integrate, mine, visualize and analyze multiple large-scale molecular omics and natural variation datasets for hypothesis generation, polygenic risk score calculation, and creation of molecular network models of obesity. You will develop computational pipelines and machine learning approaches to analyse genome sequences in order to quantify obesity risk and predict its effects. When submitting your application, please include a cover letter.   This position requires relocation to Memphis, TN. When possible, it will involve travel for collaborative purposes to Denmark. You will be working in a highly dynamic and collaborative environment, and will be expected to communicate complex informatics principles, methods, analyses and results to scientists from diverse backgrounds in the consortium.Excellent interpersonal and communication skills are a must, as you will interact directly with both Computational Biologists and Experimentalists in a highly interdisciplinary environment.   Ranked #1 in the U.S. in Pediatric Cancer, St. Jude Children's Research Hospital is a NCI-designated Comprehensive Cancer Center, and home to the Pediatric Cancer Genome Project. The St. Jude campus is a truly unique research environment, encompassing state-of-the-art HPC facilities, world-leading oncology basic research, outstanding Shared Resources and Core Facilities and a dedicated translational Chemical Biology and Therapeutics department. The $412M Advanced Research Center, opened in 2021, doubles the campus’ research space and adds support for an additional 1000 employees. There is a vibrant Data Science community at St. Jude, with opportunities to interact with researchers in the Biostatistics and Computational Biology Departments, and tremendous support from the Center for Applied Bioinformatics.   Preferred skills and experience: - Experience with GWAS data analysis, QTL, eQTL analysis, and other methods of linking genotype and epigenetics information to phenotype - Experience with development, implementation and application of Polygenic Risk Score estimation for phenotypes - Experience with diverse statistical data analysis approaches (Bayesian and non-Bayesian statistical methods) - Interest and expertise in adipocyte biology, human physiology, or other areas relevant to the study of obesity - Interest or expertise in GPCR signalling, transcription, metabolic pathways, and/or nuclear receptors is desirable - Experience with writing reports, developing web interfaces for data analysis and/or data dissemination. - Experience with developing and maintaining databases (ideally graph databases) - Experience with novel data visualisation methods
Job ID
45020
Department
Structural Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
The Department of Computational Biology is seeking a highly motivated Bioinformatics Research Scientist to lead genomic variant analysis as part of the pediatric cancer genomic portal development. The candidate will be responsible for developing analytical pipelines to annotate genomic variants including those that are in the non-coding regions for assessing their potential pathogenicity by integrating genetic, transcriptomic, and epigenetic data. This position will be working within the biomedical data visualization team led by Dr. Xin Zhou.   Candidates with a strong background in bioinformatics, computational biology, and cancer genomics are highly encouraged to apply. Successful candidates will have excellent critical thinking, data management and programming skills. Experience in multi-omics analysis including epigenetic data is highly desirable.   Recognized as a world leader in pediatric cancer genomics, the St. Jude Computation Biology department has developed state-of-art computational algorithms, well-established analytical pipelines, and deep data analysis expertise with a track record of high-impact publications in top-tier biomedical journals such as Nature, NEJM, Nature Genetics and Nature Methods. The department provides a highly interactive environment with projects involving basic and clinical research collaborators, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and teamwork with scientists who have 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.
Job ID
44919
Department
Computational Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
The Chi Lab is seeking a Systems Immunology Specialist to work on exciting projects related to immune signaling and metabolism in the St. Jude Deparment of Immunology. One of the premier pediatric research institutions in the world, St. Jude Children’s Research Hospital provides exceptional resources, a collaborative environment, and access to extensive, unique cancer genomics datasets from large-scale research initiatives. In this role you will assist with the curation, integration, and analysis of immunology, oncology, and cancer immunology data using methods from computational and systems biology. She/he will assist in the development, implementation, and maintenance of computational biology and immunology databases. Experience in R programming language preferred.  
Job ID
44412
Department
Immunology
Company
St. Jude Children's Research Hospital
Type
Full Time
The Department of Computational Biology is seeking a highly motivated Bioinformatician to develop and apply computational and systems biology approaches to dissect the molecular circuits that drive tumorigenesis, tumor immune-escape and drug resistance, and identifying novel immunotherapy targets, biomarkers and combination therapies (particularly with immunotherapy) for the treatment of pediatric cancers. This analyst/scientist will analyze and integrate high-throughput omics data, at bulk and single-cell levels, including transcriptomic, genomic, epigenomic, functional genomic, chemical genomic and proteomic data to model context-specific cellular/molecular networks and to identify actionable targets, biomarkers or compounds that could be translated into clinic for the development of precision medicine in pediatric cancer. The scientist will report to Dr. Jiyang Yu and will work closely with our collaborators in the departments of Immunology and Oncology for experiment design and data generation, and with our pipeline and visualization teams to explore novel analysis approaches for single-cell RNA-Seq, NGS-based RNAi/CRISPR screening, immune-profiling and proteomics data for molecular network inference and target identification.   Candidates with a strong interest in cancer immunotherapy, cancer precision medicine and expertise in oncology, immunology, computational biology, bioinformatics are encouraged to apply. The successful candidate will also have an opportunity to participate in research projects involved in the analysis of the cancer genome, epigenome, transcriptome or proteome. Experience with omics data analysis using R or Python and familiarity with linux/unix is required. Experience and knowledge in immunology and/or immuno-oncology is highly desirable. Expertise in systems biology, network biology, parallel computing, web development, visualization and databases is also highly desirable.   The Yu Lab provides a highly interactive environment with projects involving basic and clinical research collaborators, access to high performance computing clusters, cloud computing environment, innovative visualization tools, highly automated analytical pipelines and teamwork with scientists who have 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.    
Job ID
44476
Department
Computational Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
We are seeking a highly motivated, organized, and responsible individual to lead a major component of Dr. Stephen Mack's new cancer genetics and epigenetics lab, as a foundation for their career advancement in academia or industry. Candidates will leverage and analyze cancer genomics and epigenomics data that we have generated in a variety of pediatric and adult brain tumors. Applications include short- and long- read WGS, long-isoform sequencing, ChIP-seq, ATAC-seq, and RNA-seq. This candidate will play an integral role in the functional discovery, validation, as well as the development of integrated large-scale datasets using new genetic technologies. The ideal candidate will have experience in working with genomics datasets, specifically with respect to implementing new algorithms and pipelines, as well as utilizing existing computational software. Knowledge in R, UNIX, Python, and general scripting languages are preferred. He/she will demonstrate a willingness to learn new concepts and technical skills, but most meaningfully harbor an enthusiasm for working in a team-based environment and interfacing with national and international collaborative efforts.  
Job ID
44607
Department
Developmental Neurobiology
Company
St. Jude Children's Research Hospital
Type
Full Time
St. Jude Children’s Research Hospital is seeking a Bioinformatics Research Scientist 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
44390
Department
Computational Biology
Company
St. Jude Children's Research Hospital
Type
Full Time
The Geeleher Lab is seeking a Bioinformatics Research Scientist to work on exciting projects related to cancer genomics, pharmacogenomics, and drug repurposing in the St. Jude Department of Computational Biology. One of the premier pediatric research institutions in the world, St. Jude Children’s Research Hospital provides exceptional resources, a collaborative environment, and access to extensive, unique cancer genomics datasets from large-scale research initiatives.   Positions are available in these broad research areas: - Developing machine learning approaches for integration of pre-clinical, clinical genomics and electronic health record data for drug re-purposing and pharmacogenomics of anticancer agents. Identifying targeted therapies for patients with cancer is a central focus at St. Jude, and genome and RNA sequencing of patients’ tumors is now being performed regularly as part of standard-of-care. A major goal of the Geeleher lab is to explore machine learning approaches to prioritize targetable variants and expand the scope of targeted therapeutics. You will explore, optimize and build on emerging informatics techniques, including integrating somatic variation with transcriptomic variation and with protein-protein interaction networks. The Geeleher lab’s wet-lab component provides a platform for validation of computational predictions and discoveries. Successful completion of the project has the potential for a direct positive impact on patient care and high-impact publications. (Projects funded by our NCI R01 award). - Developing computational methods for single-cell RNA-seq and spatial transcriptomics data. Recent advances have allowed the measurement of genome-wide gene expression directly within tissue sections, using a set of technologies referred to as spatial transcriptomics. These tools allow us to dissect tumor heterogeneity in unprecedented detail and will allow us to study the determinants of drug response at a resolution not previously possible. You will develop new computational and statistical methodologies for analyzing and interpreting these data and develop approaches to integrate spatial transcriptomics with matched single-cell RNA-seq data. You will utilize both Visium and MERFISH data, with a primary focus on neuroblastoma. This work will aim to improve our understanding of tumor heterogeneity and yield computational approaches applicable to a broad variety of complex traits and diseases. (Projects funded by our NIGMS R35 award) The Geeleher Lab is recognized for developing innovative computational approaches and has led drug re-purposing efforts, spearheaded publications in Nature, Genome Research, Genome Biology, Journal of the National Cancer Institute (JNCI) and Bioinformatics in the last five years, and is funded by the NIH. St. Jude offers an exceptional research environment, including state-of-the-art high-performance computing facilities, robust analytical pipelines, the latest wet-lab technology, access to outstanding core facilities and scientific expertise in genomics, cancer biology, statistics, and computer science. The Department of Computational Biology is highly interactive with collaborative opportunities across basic and clinical departments and mentorship from faculty-level scientists with deep experience in data analysis, data management and delivery of high-quality results for highly competitive projects
Job ID
44456
Department
Computational Biology
Company
St. Jude Children's Research Hospital
Type
Full Time

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