Computational Research Jobs (NOW HIRING)

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The Ma laboratory in the Department of Computational Biology is seeking an experienced Senior Computational Research Scientist for the Pediatric Cancer Dependency (PedDep) project, a joint initiative between St. Jude, Dana Farber Cancer Institute, and the Broad Institute.
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 investigate the representativeness of cell models against the mutations observed in primary tumors. 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.
Highly motivated candidates with an MD/PhD in molecular biology, computational biology, computer science, or a closely related field are encouraged to apply. The candidate would ideally have ample experience with genome and transcriptome sequencing data analysis, in particular mutation detection and functional interpretation, as well as extensive computational skills to accurately and efficiently handle large amounts of data. Candidates should be scientifically curious, rigorous, and capable of working independently.
Position Responsibilities:

• Lead computationally focused scientific research projects with little supervision from their PI.
• Initiate and execute research strategies in partnership with the Principal Investigator, collaborator, 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:

• Training in Bioinformatics, Molecular Biology, Computer Science, or related fields.

Minimum Experience:

• 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).
• Substantial experience in own technical area including advanced research techniques.
• Experience leading complex research studies in a technical capacity preferred.
• Experience training and guiding early-career researchers preferred.
• Proven performance in earlier role/ comparable role.

Special Skills, Knowledge, and Abilities:
Ideal candidate should have:

• 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)

About the lab and St. Jude:
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.
The Ma laboratory has extensive experience in the analysis of whole genome, exome, and transcriptome data to detect mutations responsible for tumorigenesis and therapeutic resistance using primary tumor data. We are particularly experienced in developing novel analytical methods for DNA/RNA sequencing analysis, including cancer-early detection where signal-to-noise ratio can be very low and present as a significant challenge for the community, and the general patterns of cancer driver mutations with the aim of understanding why cancer happens. We also pay special attention to novel biotechnologies including long read sequencing to solve challenging problems related to childhood cancers.
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 this element of discovery. Take the first step to joining our team by applying now!
Relevant Papers:
Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, 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. PMID: 29489755; PubMed Central PMCID: PMC5854542.
Ma X*#, Shao Y, Tian L, Flasch DA, Mulder HL, Edmonson MN, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison LL, Levy S, Easton J, 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. PMID: 30867008; PubMed Central PMCID: PMC6417284.
Li B, Brady SW, Ma X*, Shen S, Zhang Y, Li Y, Szlachta K, Dong L, Liu Y, Yang F, Wang N, Flasch DA, Myers MA, Mulder HL, Ding L, Liu Y, Tian L, Hagiwara K, Xu K, Zhou X, Sioson E, Wang T, Yang L, Zhao J, Zhang H, Shao Y, Sun H, Sun L, Cai J, Sun HY, Lin TN, Du L, Li H, Rusch M, Edmonson MN, Easton J, Zhu X, Zhang J, Cheng C, Raphael BJ, Tang J, Downing JR, Alexandrov LB, Zhou BS, Pui CH, Yang JJ, 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. PMID: 31697823; PubMed Central PMCID: PMC6940198.
Davis EM, Sun Y, Liu YL, Kolekar P, Shao Y, Szlachta K, Mulder HL, Ren DR, Rice SV, Wang Z, Nakitandwe J, Gout AM, Shaner B, Hall S, Robison LL, Pounds S, Klco JM, Easton J, 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. PMID: 33487172
Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, 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
Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey A, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco J, Ma X#. SJPedPanel: A Pan-Cancer Gene Panel for Childhood Malignancies to Enhance Cancer Monitoring and Early Detection. Clin Cancer Res. 2024 Sep 13;30(18):4100-4114. doi: 10.1158/1078-0432.CCR-24-1063. PMID: 39047169
Shao Y, Tran Q, Feng Y, Kolekar P, Liu Y, Liang Z, Fan L, McBride A, Jones T, Cameron A, Mulder H, Ji L, Huang BJ, Klco JM, Meshinchi S, Zhang J, Carroll WL, Loh ML, Easton J, Brown PA, Ma X#. Analysis of error profiles of indels and structural variants in deep-sequencing data. Cell Genom. 2026 Feb 11;6(2):101082. doi: 10.1016/j.xgen.2025.101082. Epub 2025 Dec 2. PubMed PMID: 41338220; PubMed Central PMCID: PMC12903382.
Liu Y, Ju B, Dong L, Loyd M, Brady SW, Ries R, Feng Y, Mulder H, Plyler E, Deardorff C, McBride A, Jones T, Eckert A, Kolekar P, Fan L, Li H, Briviba M, Zhao H, Bennett D, Neale G, Chang TC, Chen W, Pounds S, Wu G, Mullighan C, Geeleher P, Ji L, Yang JJ, Meshinchi S, Brown PA, Carroll WL, Zhang J, Loh ML, Easton J, Ma X#. Uncovering the genomic complexity of PAX5 intragenic tandem multiplication via long-read and short-read sequencing. Blood. 2026 Mar 26;147(13):1498-1502. doi: 10.1182/blood.2025031289. PubMed PMID: 41587071.
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 Sr Computational Research Scientist- MA's Lab.
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