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Group of Computational Biology and Bioinformatics (GC2B)

Computational Biology at GC2B
Bioinformatics at GC2B
Computational resources of GC2B

Group of Computational Biology and Bioinformatics (GC2B)

Group Structure

GROUP LEADER
 
STAFF SCIENTISTS
 
POSTDOCTORAL FELLOWS
 
STUDENTS
Eduardo Lopes da Silva,  PhD Student
Lulu Wu, MSc Student
Daniel Ferreira Silva, Undergraduate Student

Summary

The CeTICS sub-projects rely extensively on a huge amount of biological data that is produced by modern high-throughput omics (e.g., genomics, proteomics, transcriptomics) methods. Hence, there exist demands for biological data organization, retrieval, integration, and analysis to yield scientific knowledge. Bioinformatics is the scientific field that deals with the aforementioned demands, and includes methods to deal with problems that arise in the CeTICS sub-projects, such as: genome and transcriptome assembly, annotation and analysis; computational identification of proteins; taxonomic and phylogeny analysis; computational chemistry and molecular modeling.

On the other hand, the CeTICS sub-projects also rely on investigations that are intrinsically interdisciplinary, since they involve boundary crossing between disciplines such as Molecular Biology, Biochemistry, Mathematics, Statistics, and Computer Science. Those interdisciplinary investigations aim the development of mathematical models and the application of computational simulation techniques to study the behavior of biological systems (e.g., molecular signaling network kinetics), in the context of a scientific field called Computational Biology.

The Group of Computational Biology and Bioinformatics (GC2B) was created in late 2013, just after the CeTICS center itself was established. It has as general objective to develop and to execute scientific projects in Computational Biology and Bioinformatics. Additionally, GC2B has a more specific objective, which is to provide the required assistance to the other sub-projects of this center and, also to other laboratories of the Butantan Institute. To this end, some of the current projects that are carried out by GC2B include the development of the CeTICSdb platform for storage and analyses of heterogeneous omics data [1,5], and the SigNetSim framework for mathematical modeling and computational simulation of signaling network kinetics [2,3,4].


Selected Publications

[1] Reis MS, Nishiyama-Jr MY, Silva DF, Junqueira-de-Azevedo ILM, da Cunha JPC, Barrera J, Iwai LK, Serrano SMT, and Armelin HA. CeTICSdb: a platform for interdisciplinary research that allows quantitative and qualitative -omics analyses and mathematical modeling of signaling networks. RECOMB 2014, Pittsburgh, PA, United States. NSF Poster Session, P-30. Web page:http://f1000.com/posters/browse/summary/1095384.

[2] M.S. Reis, M.H.S. Dias, F. Nakano, J. Barrera, and H.A. Armelin. Mathematical modeling of Ras/MAPK signaling network kinetics provides insights into mechanisms of FGF2-induced cell cycle arrest in the K-Ras-driven mouse Y1 adrenocortical tumor cells. RECOMB 2014, Pittsburgh, PA, United States. NSF Poster Session, P-26. Web page: http://f1000.com/posters/browse/summary/1095383.

[3] Reis MS, Dias MHS, Nakano F, Noël V, Barrera J, and Armelin HA. Modeling the kinetics of Ras/MAPK and PI3K/AKT signaling pathways in the K-Ras-driven mouse Y1 adrenocortical tumor cells: novel insights into the mechanisms of FGF2-driven cell cycle arrest. Challenges and Solutions in Cancer Research and Treatment (CSC) 2014, Mangaratiba, RJ, Brazil. Poster Presentation SIG-09. Web page: http://f1000.com/posters/browse/summary/1095752.

[4] Reis MS, Dias MHS, Albuquerque LL, Nakano F, Noël V, Barrera J, and Armelin HA. Mathematical modeling of the Ras/MAPK and PI3K/Akt signaling networks in the K-Ras-driven mouse Y1 adrenocortical tumor cells. 43rd Brazilian Society for Biochemistry and Molecular Biology (SBBq) Congress 2014, Foz do Iguaçu, PR, Brazil. Poster Presentation C-35. Web page: http://f1000.com/posters/browse/summary/1095753.

[5] Nishiyama Jr MY, Reis MS, Silva DF, Kitano ES, Souza GM, Junqueira-de-Azevedo ILM, da Cunha JPC, Barreira J, Iwai LK, Serrano SMT, Armelin HA. CeTICSdb: an integrated platform for analysis of heterogeneous, high-throughput-omics and mathematical modeling of biochemical reactions.  ISMB 2014 Satellite Meeting - HiTSeq SIG: High Throughput Sequencing Algorithms & Applications, 11 - 12 Jul 2014, P26.Web page: http://f1000.com/posters/browse/summary/1096242.

 

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