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Biochemistry Department, Institute of Chemistry, Sao Paulo University

Postdoctoral position: Sugarcane regulatory network analysis using ChIP-Seq


Summary


sugarcane stalkx

Sugarcane is a C4 grass used for centuries as the main source of sugar and more recently for ethanol production. We have seen an increasing interest in recent years to understand sugarcane to improve yield and supply the increasing world demand. Sugarcane genomics started with the project SUCEST [1] and continues to expand in activities of the project SUCEST-FUN [2-4] and the ongoing sugarcane genome project [5]. However, as known from other organisms, sequencing will solve only part of a larger problem, and we will need to unravel the complex regulatory networks of sugarcane. This project fits into this context and aims to analyze the data generated by ChIP-Seq using 454 sequencing (Roche) to establish the architecture of regulatory networks and identify gene promoters in sugarcane. The post-doc research will focus on the application and development of computational and statistical methods for inference of gene regulatory networks and development of tools to map regulatory elements. The post-doc position is part of the project Sugarcane Signaling and Regulatory Networks (08/52146-0) which aims to establish the architecture of regulatory networks that control gene expression in sugarcane and produce tools that will allow the scientific community to associate agronomic traits to regulatory regions.

 

Requirements


- Candidates should hold a PhD degree in bioinformatics, biology, engineering, computer science or similar.

- The candidate must have strong computational skills and prior experience with Unix/Linux command line environments, SQL, as well as either Perl, Python or a comparable scripting language.

- The applicant must have experience with Statistical and Computational methods

- Knowledge of Next Generation Sequencing and analysis and large-scale data mining is considered a plus.

 

Person to contact: Dr. Glaucia Souza

Email address: This email address is being protected from spambots. You need JavaScript enabled to view it.


References


1.         Vettore, A.L., et al., Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res, 2003. 13(12): p. 2725-35.

2.         Rocha, F.R., et al., Signal transduction-related responses to phytohormones and environmental challenges in sugarcane. BMC Genomics, 2007. 8: p. 71.

3.         Papini-Terzi, F.S., et al., Sugarcane genes associated with sucrose content. BMC Genomics, 2009. 10: p. 120.

4.         Papini-Terzi, F.S., et al., Transcription profiling of signal transduction-related genes in sugarcane tissues. DNA Res, 2005. 12(1): p. 27-38.

5.         Souza, G.M., et al., The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome. Trop Plant Biol, 2011.