The Lead-Computational Research Scientist is responsible for leading computational research projects, executes research strategies, and develops new research methods under little supervision. With vast knowledge accumulated from patient tumor data, we are now characterizing cell models (cell lines and PDX models) for childhood cancers to discover novel vulnerabilities that can lead to new therapeutic targets. In this role you will analyze the genomics data from >1,000 cancer cell models to identify their driver alterations and you will investigate the representativeness of cell models against the mutational diversity observed in patient populations. You will also study the similarities and differences of driver alterations between pediatric and adult cancers. Published studies from external and internal cohorts will be compiled for the comparison. In addition to the extensive internal tools we have developed, you will develop novel tools during the investigation to generate novel analyses and to integrate new data types. You are expected to present findings in regular internal/external forums and to draft figures/manuscripts with the help of the PI and the team. 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. The Ma Lab has focused on studying childhood cancer genomics in the past decade and has led or participated numerous projects on various childhood cancers including B-ALL, T-ALL, AML, Wilms Tumor, Neuroblastoma, Osteosarcoma, and various Brain Tumors, in the setting of diagnosis, relapse, and metastatic samples. These works not only provided valuable insights into the precision diagnosis and classification of childhood cancers but also led to the development of powerful tools and computational methods that enabled precise and efficient characterization of cancer relevant mutations, as well as early detection of cancer. The Department of Computational Biology provides 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 our novel discoveries. Take the first step to joining our team by applying now! Relevant Papers: (#: corresponding author) Ma X, …, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015 Mar 19;6:6604. doi: 10.1038/ncomms7604. PubMed PMID: 25790293; PubMed Central PMCID: PMC4377644. Ma X, …, Zhang J. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature. 2018 Mar 15;555(7696):371-376. doi: 10.1038/nature25795. Epub 2018 Feb 28. PubMed PMID: 29489755; PubMed Central PMCID: PMC5854542. Ma X, …, Zhang J. Analysis of error profiles in deep next-generation sequencing data. Genome Biol. 2019 Mar 14;20(1):50. doi: 10.1186/s13059-019-1659-6. PubMed PMID: 30867008; PubMed Central PMCID: PMC6417284. Brady SW, Ma X*, …, Zhang J. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Mol Cancer Res. 2019 Apr;17(4):895-906. doi: 10.1158/1541-7786.MCR-18-0620. Epub 2019 Jan 16. PubMed PMID: 30651371. Li B, Brady SW, Ma X*, …, Zhang J. Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia. Blood. 2020 Jan 2;135(1):41-55. doi: 10.1182/blood.2019002220. PubMed PMID: 31697823; PubMed Central PMCID: PMC6940198. Davis EM, …, Ma X#. SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data. Genome Biol. 2021 Jan 25;22(1):37. doi: 10.1186/s13059-020-02254-2. PubMed PMID: 33487172 Schwartz JR, …, Ma X#, Klco JM#. The acquisition of molecular drivers in pediatric therapy-related myeloid neoplasms. Nat Commun. 2021 Feb 12;12(1):985. doi: 10.1038/s41467-021-21255-8. PubMed PMID: 33579957 Huang BJ, …, Ma X#, Meshinchi S#. CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Adv. 2021 Dec 14;5(23):4963-4968. doi: 10.1182/bloodadvances.2021004965. PMID: 34547772. Umeda M, …, Ma X#, Klco JM#. Integrated genomic analysis identifies UBTF tandem duplications as a recurrent lesion in pediatric acute myeloid leukemia. Blood Cancer Discov. 2022 Feb 16:bloodcandisc.BCD-21-0160-A.2021. doi: 10.1158/2643-3230.BCD-21-0160. Epub ahead of print. PMID: 35176137. Liu Y, …, Ma X#. Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Nat Commun. 2023 Apr 5;14(1):1739. doi: 10.1038/s41467-023-37438-4. PMID: 37019972 Job Responsibilities: Lead computationally focused scientific research projects with little supervision from their PI. Initiate and execute research strategies in partnership with the Principal Investigators and/or more experienced scientists. Explore, identify, and propose adoption of relevant emerging scientific and technical trends in computational research; develop new methods, techniques, and procedures. Identify, process, organize, interpret, review, and report relevant data; generate hypotheses to predict future implications based on the critical evaluation of these data. Direct/monitor data collection. Present research both internally and externally to multi-disciplinary audiences; draft complex manuscripts. Provide ongoing instruction and guidance to junior-level staff and train as needed. Perform other duties as assigned to meet the goals and objectives of the department and institution. Maintains regular and predictable attendance. Minimum Education and/or Training: 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 10+ years of relevant experience. Experience Exception: Master's degree and 8+ years of relevant experience (OR) PhD with 5+ years of relevant experience. Rough criteria for this position based on publication output: 3-4 first author papers IF > 10 (or equivalent contribution to other research outputs). Substantial experience in own technical area including advanced research techniques. Experience leading complex research studies in a technical capacity. Experience training and guiding early-career researchers. Proven performance in earlier role/ comparable role. Special Skills, Knowledge, and Abilities: Strong knowledge in molecular biology, genetics, genomics and statistics. Next generation sequencing: variant calling; IGV-based variant inspection; whole-genome/exome analysis for mutations including copy number, loss of heterozygosity, structural variation, SNV/Indel; RNAseq based fusion analysis; bam/fastq operations including mapping and basic quality control; variant functional interpretation using data collected from patient cohort and molecular biology and genetics principles. Programming: [Python or Perl or C/C++] and R Operating system: High performance computing system, bash scripting Office: Microsoft Excel/Word/PowerPoint Preferred: Adobe Illustrator (no Photoshop) 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 $125,840 - $238,160 per year for the role of Lead-Computational Research Scientist. Explore our exceptional benefits! Diversity, Equity and Inclusion 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. Learn more about our history and commitment. 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 Diversity, Equity and Inclusion Report to learn about the hospital’s roots in diversity, equity and inclusion, where we are today and our aspirations for an even better future. St. Jude is an Equal Opportunity Employer No Search Firms St. Jude Children's Research Hospital does not accept unsolicited assistance from search firms for employment opportunities. Please do not call or email. All resumes submitted by search firms to any employee or other representative at St. Jude via email, the internet or in any form and/or method without a valid written search agreement in place and approved by HR will result in no fee being paid in the event the candidate is hired by St. Jude.