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Opportunity: Senior Bioinformatics Research Scientist / Bioinformatics Research Scientist @ St. Jude Children's Research Hospital -- Memphis, TN (US)
Submitted by Kirt Woodruff; posted on Thursday, January 07, 2021
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BACKGROUND
St. Jude Children's Research Hospital has a unified mission to use cutting-edge research to discover the origins of disease, especially cancer, in order to facilitate advances in the treatment of disease that improve the lives of patients. The Blanchard Lab in the Department of Structural Biology at St. Jude is seeking a highly motivated and creative Bioinformatician to lead our genomics initiatives, using both existing and novel algorithms, to reveal insights into the role of translational control (using genomics and next-generation sequencing methods including RNA-Seq, ribosome profiling, Pro-Seq, etc.) in regulating physiological events related to cancer metastasis. Particular emphasis will be given to interrogating the role of non-coding RNAs from multi-copy gene families. The successful applicant will be an integral part of an interdisciplinary team of scientists, collaborating directly with team members to expertly solve challenges and empower them to make powerful quantitative insights.
The ideal candidate will have the following:
- Thorough knowledge of statistics, probability theory, machine learning algorithms, maximum likelihood optimization, Bayesian methods, and linear algebra.
- Proficient with R and associated bioinformatics packages (e.g., Bioconductor), MATLAB, and shell scripting.
- Ability to create compelling graphics, including interactive data visualization tools (e.g. R-Shiny, D3.js) and communicate research findings.
- Experience with distributed computing bioinformatics workflows on Unix/Linux and cloud environments.
- Thorough knowledge of software engineering and capability to produce robust, well-documented software with polished user interfaces.
- Expert ability to distill complex information in a clear and concise manner both verbally and in writing.
Relevant Publications:
Implications of sequence variation on the evolution of rRNA.
MM Parks, CM Kurylo, JE Batchelder, CT Vincent, SC Blanchard.
Chromosome Research 27 (1-2), 89-93, 2019.
Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease.
V Prakash, BB Carson, JM Feenstra, RA Dass, P Sekyrova, A Hoshino,..., SC Blanchard, CT Vincent.
Nature communications 10 (1), 1-16, 2019.
Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression.
MM Parks, CM Kurylo, RA Dass, L Bojmar, D Lyden, CT Vincent, SC Blanchard.
Science Advances 4 (2), eaao0665, 2018.
Endogenous rRNA sequence variation can regulate stress response gene expression and phenotype.
CM Kurylo, MM Parks, MF Juette, B Zinshteyn, RB Altman, JK Thibado, CT Vincent, SC Blanchard.
Cell reports 25 (1), 236-248. e6, 2018.
RESPONSIBILITIES
- Perform analysis on clinically relevant biological problems using a variety of bioinformatics workflows, including both genomics and time-series data (hidden Markov modeling).
- Uncover DNA sequence variation in high copy number genes utilizing both existing and novel algorithms for the analysis of RNA-Seq (Illumina) and next-generation DNA sequencing (NGS; e.g., PacBio) data.
- Characterize genome-wide modulation of the transcriptome and translatome using RNA-Seq and ribosome profiling during cellular differentiation events related to cancer metastasis.
- Uncover changes in the expression of gene isoforms with highly similar sequences (e.g., PacBio Iso-Seq; Illumina 10X).
- Collaborate with biologists to provide expertise in the statistical analysis of a variety of data types.
- Present results at group meetings and conferences.
- Publish results in peer-reviewed journals.
REQUIREMENTS
- Ph.D. in Molecular Biology, Biochemistry, Computer Science, Statistics, Mathematics, Bioinformatics or related field required.
- Sr. Bioinformatics Research Scientist
- Three (3) years of postdoctoral and/or job experience in Computational Biology or Bioinformatics research required with analytical experience in the following areas: sequencing data, microarrays, SNPs, proteomics data or biological pathways.
- Experience with programming languages such as Perl, C, C++, SQL, PHP or Java required.
- Experience in development of algorithms, statistical methods or scientific software is preferred.
- Bioinformatics Research Scientist
- Ph.D which must include research related to bioinformatics (such as analysis of sequence data, microarrays, SNPs, image data, proteomics data, or biological pathways; development of algorithms, statistical methods, or scientific software); OR If Ph.D with no bioinformatics research, then two (2) years of pre-or postdoctoral experience in Computational Biology or Bioinformatics research is required.
- Experience with programming languages such as Perl, C, or Java required.
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