We seek a motivated bioinformatician to be involved in our studies of gene regulatory networks. Our laboratory at Memorial Sloan-Kettering Cancer Center combines computational and experimental approaches to annotate and functionally elucidate small RNA pathways, mRNA processing and modification pathways, and transcription factor networks. Towards this end, we produce small RNA, RNA-seq, CLIP-seq, RNA modification and ChIP-seq data, and analyze these with respect to the rich comparative genomic data available for Drosophila and mammals. There is a close exchange of ideas between dry and wet lab members to generate and test biologically-based hypotheses.
The candidate will integrate into several related projects regarding post-transcriptional regulation, including mechanisms of miRNA biogenesis, tissue-specific alternative polyadenylation, and in vivo regulation by m6A/RNA methylation.
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.
Relevant candidates will have strong computational skills and experience with analyzing deep-sequencing data, comparative genomics and statistics. Postdoctoral fellows or BA/MS level candidates seeking experience before graduate school will be considered.
Please send letter of inquiry, CV and references to email@example.com.