Bioinformatician: post-transcriptional regulatory networks

Institution/Company:
Memorial Sloan-Kettering Cancer Center
Location:
New York, New York, United States
Job Type:
  • Postdoctoral
Degree Level Required:
Masters, PhD
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Bioinformatician: post-transcriptional regulatory networks

Our laboratory at Memorial Sloan-Kettering Cancer Center combines computational and experimental approaches to discover, annotate and functionally elucidate diverse post-transcriptional regulatory pathways and their biological impacts. Currently, we are particularly interested in non-canonical small RNA pathways, alternative mRNA processing strategies, and RNA methylation. Towards these ends, we produce RNA-seq, 3’-seq, CLIP-seq, small RNA, RNA modification and ChIP-seq data, and analyze these with respect to the rich comparative genomic data available for Drosophila and mammals.

Responsibilities:

The candidate will integrate into projects that seek the mechanistic bases and impact of (1) tissue-specific alternative polyadenylation, and (2) regulation and dysregulation of miRNA biogenesis. There is a close exchange of ideas between dry and wet lab members to generate and test biologically-based hypotheses and interpret genomics data.

Qualifications:

Relevant candidates will have strong computational skills and have demonstrated extensive experienced with analyzing deep-sequencing data, comparative genomics and statistics. Fluency with at least one general purpose programming language (e.g. Perl or Python), a language for statistical computing (e.g. R), proficiency with bash/shell scripting in LINUX/UNIX environments for using high performance clusters, and knowledge of HTML/JavaScript for building web-based data interfaces.

Excellent problem solving, independent thinking, communication skills and scientific curiosity. Working knowledge of how experimental data are generated and teamwork between dry/wet lab.

  • How to Apply

    Please send motivation letter including details of prior research experience, CV, and contact information of three references to laie@mskcc

Additional Information

Recent Studies involving genomics/bioinformatics approaches

Kan, L., A. V. Grozhik, J. Vedanayagam, D. P. Patil, N. Pang, K.-S. Lim, Y.-C. Huang, B. Joseph, C.-J. Lin, V. Despic, J. Guo, D. Yan, S. Kondo, W.-M. Deng, P. C. Dedon, S. R. Jaffrey and E. C. Lai (2017). The m6A pathway facilitates sex determination in Drosophila. Nature Communications 8: 15737, 1-16.

Kondo S., J. Vedanayagam, J. Mohammed, S. Eizadshenass, L. Kan, N. Pang, R. Aradhya, A. Siepel, J. Steinhauer and E. C. Lai (2017). New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes and Development 31: 1841–1846. (Highlighted in Genes and Dev 31: 1825-1826.)

Sanfilippo P., J. Wen and E. C. Lai (2017). Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biology 18: 229 doi: 10.1186/s13059-017-1358-0.

Mohammed, J., A. S. Flynt, A. M. Panzarino, M. Mondal, M. DeCruz, A. Siepel and E. C. Lai (2018). Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Research 28: 52-65.

Jee, D., J.-S. Yang, S. M. Park, D.’J. Farmer, J. Wen, T. Chou, A. Chow, M. T. McManus, M. G. Kharas and E. C. Lai (2018). Dual strategies for Argonaute2 Slicer-dependent miRNA biogenesis of erythroid miRNAs underlie conserved requirements for slicing in mammals. Molecular Cell 69: 265-278.

Lin C.-J., F. Hu, R. Dubruille, J. Vedanayagam, J. Wen, P. Smibert, B. Loppin and E. C. Lai (2018). The hpRNA/RNAi pathway is essential to resolve intragenomic conflict to permit transmission of sons. Developmental Cell 46: 316-326. (Featured in Developmental Cell 46: 251-253).

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