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) and transcriptional networks (mostly in the nervous system). Towards this end, we produce a great deal of small RNA data 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 nature and activity of structurally novel RNA genes, and the mRNA/miRNA networks downstream of key neural transcription factors. We are also part of the NHGRI modENCODE consortium (http://www.modencode.org/) and are working towards integrative analysis with other largescale datasets produced by consortium members.
Relevant candidates should have proficiency in a programming language (Java or C/C++) and a scripting language (Perl or Python), and experience with database design and management. Experience with next-generation sequence data (e.g. 454, Illumina or SOLiD) is recommended.
The position is available immediately and offers competitive salary and benefits. Both 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].
Selected References
Okamura K., J. W. Hagen, H. Duan, D. Tyler and E. C. Lai (2007). The mirtron pathway generates microRNA-like regulatory RNAs in Drosophila. Cell 130: 89-100.
Berezikov, E. W.-J. Chung, J. A. Willis, E. Cuppen and E. C. Lai (2007). Mammalian mirtron genes. Molecular Cell 28:328-336.
Ruby G.J., A. Stark, W. Johnston, M. Kellis, D. P. Bartel and E. C. Lai (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Research 17: 1850-1864.
Okamura, K., M. D. Phillips, D. Tyler, H. Duan, Y.-T. Chou and E. C. Lai (2008). The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nature Structural and Molecular Biology 15: 354-363.
Okamura, K., W.-J. Chung, J. G. Ruby, H. Guo, D. P. Bartel and E. C. Lai (2008). The Drosophila hairpin RNA pathway generates endogenous siRNAs. Nature, 453: 803-806.
Chung, W.-J., K. Okamura, R. Martin and E. C. Lai (2008). Endogenous RNA interference provides a somatic defense against Drosophila transposons. Current Biology 18: 795-802.
Okamura, K., S. Balla, R. Martin, N. Liu and E. C. Lai (2008). Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila. Nature Structural and Molecular Biology 15: 581-590.
Relevant candidates should have proficiency in a programming language (Java or C/C++) and a scripting language (Perl or Python), and experience with database design and management. Experience with next-generation sequence data (e.g. 454, Illumina or SOLiD) is recommended.
The position is available immediately and offers competitive salary and benefits. Both 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].
Selected References
Okamura K., J. W. Hagen, H. Duan, D. Tyler and E. C. Lai (2007). The mirtron pathway generates microRNA-like regulatory RNAs in Drosophila. Cell 130: 89-100.
Berezikov, E. W.-J. Chung, J. A. Willis, E. Cuppen and E. C. Lai (2007). Mammalian mirtron genes. Molecular Cell 28:328-336.
Ruby G.J., A. Stark, W. Johnston, M. Kellis, D. P. Bartel and E. C. Lai (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Research 17: 1850-1864.
Okamura, K., M. D. Phillips, D. Tyler, H. Duan, Y.-T. Chou and E. C. Lai (2008). The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution. Nature Structural and Molecular Biology 15: 354-363.
Okamura, K., W.-J. Chung, J. G. Ruby, H. Guo, D. P. Bartel and E. C. Lai (2008). The Drosophila hairpin RNA pathway generates endogenous siRNAs. Nature, 453: 803-806.
Chung, W.-J., K. Okamura, R. Martin and E. C. Lai (2008). Endogenous RNA interference provides a somatic defense against Drosophila transposons. Current Biology 18: 795-802.
Okamura, K., S. Balla, R. Martin, N. Liu and E. C. Lai (2008). Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila. Nature Structural and Molecular Biology 15: 581-590.