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 (e.g. miRNAs, siRNAs and piRNAs), mRNA processing pathways (e.g. alternative polyadenylation and circularization), and transcription factor networks (mostly regarding neural specification). Towards this end, we produce a great deal of small RNA, RNA-seq 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. Questions of ongoing interest include the mechanics of small RNA biogenesis, the evolution of small RNA genes and their function, the control of 3′UTR formation, how RNA circularization occurs and is regulated, and the mRNA/miRNA networks downstream of key neural transcription factors. We were also a core group of the NHGRI modENCODE consortium (http://www.modencode.org/) and continue with integrative analysis with other largescale datasets produced by consortium members.
Relevant candidates should have proficiency in a programming language (e.g. Java or C/C++) and a scripting language (e.g. Perl or Python), and experience with R and database systems. Strong experience with deep-sequencing data (e.g. Illumina, SOLiD, and/or third-generation methods) is essential. 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 protected]. Position is available immediately.
Recent Selected References
Dai, Q., A. Ren, J. O. Westholm, A. Serganov, D. J. Patel and E. C. Lai (2013). The BEN domain is a novel sequence-specific DNA binding domain conserved in neural transcriptional repressors. Genes and Development 27: 602-14.
Miura, P., S. Shenker, J. O. Westholm, C. Andreu-Agullo and E. C. Lai (2013). Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome Research 23: 812-825.
Okamura K., E. Ladewig, L. Zhou and E. C. Lai (2013). Regulatory RNAs are generated from select miRNA hairpin loops in flies and mammals. Genes and Development 27: 778-792.
Smibert, P., J.-S. Yang, G. Azzam, J.-L. Liu and E. C. Lai (2013). Homeostatic control of Argonaute stability by microRNAs. Nature Structural and Molecular Biology 20: 789-795.
Mohammed, J., D. Bortolamiol-Becet, A. S. Flynt, I. Gronau, A. Siepel and E. C. Lai (2014). Adaptive evolution of testis-specific, recently-evolved, clustered miRNAs in Drosophila. RNA 20: 1195-1209.
Garaulet, D. L., M. Castellanos, F. Bejarano, P. Sanfilippo, D. M. Tyler, D. Allan, E. Sanchez-Herrero and E. C. Lai (2014). Homeotic function of Drosophila Bithorax-Complex miRNAs mediates fertility by restricting multiple Hox genes and TALE cofactors in the central nervous system. Developmental Cell 29: 635-48.
Wen, J., J. Mohammed, D. Bortolamiol-Becet, H. Tsai, N. Robine, J. O. Westholm, E. Ladewig, Q. Dai, K. Okamura, A. S. Flynt, D. Zhang, J. Andrews, L. Cherbas, T. C. Kaufman, P. Cherbas, A. Siepel, and Eric C. Lai (2014). Diversity of miRNAs, siRNAs and piRNAs across 25 Drosophila cell lines. Genome Research 24: 1236-50.