Bioinformatics Research Scientist

Employer
St. Jude Children's Research Hospital
Location
Bo Bo, IN
Closing date
May 22, 2022

View more

Sector
Science
Organization Type
Corporate
The laboratory of Dr. Xiaotu Ma in the department of Computational Biology is seeking a Bioinformatics Research Scientist/Lead Bioinformatics Analyst to join the team with a target start date of July 1, 2022. The Ma lab tackles the cancer initiating events through studying intra-tumor heterogeneity and clonal evolution, which have been demonstrated to be driving mechanisms of relapsed ALL as well as metastatic solid tumors. Mechanistic insights gained from our study can provide novel insights into the development of drug-resistance during cancer treatment which in turn will lead to innovative therapeutic strategies to the clinical management of cancers and improved cure rate.

The candidate will develop and apply novel computational approaches to uncover the intra-tumor heterogeneity at diagnosis and to track the clonal evolution during treatment, by integrating the state-of-art high-throughput deep sequencing technologies on the genome, epigenome and transcriptome of patient samples at both bulk tumor level and single cell level.

PhD in Bioinformatics, Cancer Biology, Molecular Biology, Genetics, Computer Science, Mathematics or related field are encouraged to apply. Prior experience in high-throughput next generation sequence data analysis under high performance computing (HPC) environment is preferred. The successful candidate is expected to have good programming skills in [python or perl or C] and R.

Relevant papers

Davis E, Sun Y, Liu Y, Kolekar P, Shao Y, Szlachta K, Mulder H, Ren D, Rice S, Wang Z, Nakitandwe J, Gout A, Shaner B, Hall S, Robison L, Pounds S, Klco J, Easton J, Ma X. SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data. Genome Biol. 2021 Jan 25. PubMed PMID: 33487172

Ma X, Shao Y, Tian L, Flasch D, Mulder H, Edmonson M, Liu Y, Chen X, Newman S, Nakiwandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison L, Levy S, Easton J, Zhang J. Analysis of error profiles in deep next-generation sequencing data. Genome Biol. 2019 Mar 14. PubMed PMID: 30867008

Brady SW, Ma X, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam DK, Mulder HL, Yergeau D, Edmonson MN, Easton J, Alexandrov LB, Chen X, Mardis ER, Wilson RK, Downing JR, Pappo AS, Raphael BJ, Dyer MA, Zhang J. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Mol Cancer Res. 2019 Jan 16. PubMed PMID: 30651371

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. PubMed PMID: 29489755

Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni H, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen IM, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Guidry Auvil JM, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun. 2015 Mar 19. PubMed PMID: 25790293

Minimum Education

• Bachelors degree is required.

• Masters degree or PHD is preferred

Minimum Experience

Lead Bioinformatics Analyst

• Six (6) years of relevant experience is required.

• Four (4) years of relevant experience may be acceptable with a Masters degree.

• No experience may be acceptable with a PHD in Computer Science or Bioinformatics, with a background in the biological sciences.

• Experience in programming (Python, Java, C/C++, perl or other programming/scripting languages) under linux/unix environment is required.

• Experience with and the ability to deal with a wide range of users is required.

• Experience of independent data analyses and project management is required.

• End user support and training experience is required.

Bioinformatics Research Scientist

• Seven (7) years of relevant post-degree work experience is required

• Five (5) years of relevant post-degree work experience is required with a Masters degree

• Two (2) years of relevant post-degree work experience is required with a PhD

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