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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 Senior Computational 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.
Thestudies 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 genome-wide datasets, usually from applied sequencing experiments like CUT&RUN-Seq, RNA-Seq, and Hi-ChIP, as well as some single-cell experiments. 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 characterize the specific core regulatory circuitries driving disease-relevant cells and seek to understand 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 gene expression regulation meaningfully differs 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, HiCPro), 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 the 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 ofprovides access to high-performance computing clusters, a 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 joining 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:.
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre 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:.
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:.
Adetunji MO, Abraham BJ. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics. 2022 Feb 23; PMID: 35193506.
Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-Andre V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Oct 10; PMID: 24119843.
Zimmerman MW, Durbin AD, He S, Oppel F, Shi H, Tao T, Li Z, Berezovskaya A, Liu Y, Zhang J, Young RA, Abraham BJ, Look AT. Retinoic acid rewires the adrenergic core regulatory circuitry of childhood neuroblastoma. Science Advances. 2021 Oct 22; PMID: 34669465.
Minimum Education
Bachelor's degree in Bioinformatics, Molecular Biology, Biochemistry, Computer Science, or related field.
Master's degree or PhD preferred.
Minimum Experience:
Minimum Requirement: Bachelor's degree and 7+ years of relevant experience.
Experience Exception: Master's degree and 5+ years of relevant experience (OR) PhD with 2+ years of relevant experience.
Rough criteria for this position based on publication output: 1-2 first author papers IF > 10 (or equivalent contribution to other research outputs).
Prior experience in computational research techniques and processes.
Proven performance in earlier role/comparable role.
Compensation
In recognition of certain U.S. state and municipal pay transparency laws, St. Jude is including a reasonable estimate of the compensation range for this role. This is an estimate offered in good faith and a specific salary offer takes into account factors that are considered in making compensation decisions including but not limited to skill sets, experience and training, licensure and certifications, and other business and organizational needs. It is not typical for an individual to be hired at or near the top of the salary range and compensation decisions are dependent on the facts and circumstances of each case. A reasonable estimate of the current salary range is $104,000 - $186,160 per year for the role of Senior Computational Research Scientist.Explore our exceptional !
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St. Jude Children's Research Hospital has a diverse, global patient population and workforce, built on the principles of diversity, equity and inclusion. Our founder Danny Thomas envisioned a hospital that would treat children of the world-regardless of race, religion or a family's ability to pay. .
Today, we continue the mission to advance cures and means of prevention for pediatric catastrophic diseases through research and treatment. As we accelerate this progress globally, we believe our legacy of diversity, equity and inclusion is foundational to success. With the commitment of leaders at all levels of the organization, we strive to ensure the St. Jude culture, leadership approaches and talent processes are equitable and culturally responsive. View our to learn about the hospital's roots in diversity, equity and inclusion, where we are today and our aspirations for an even better future.
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