SAMasGC: Sequencing Analysis with a Multiagent System and Grid Computing

1. Mitchelson, K.R., Hawkes, D.B., Turakulov, R., Men, A.E.: Chapter Overview: Developments in DNA Sequencing. Perspectives in Bioanalysis 2, 3–44 (2007)

   Google Scholar 

2. Soo, R.A., Wang, L.Z., Ng, S.S., Chong, P.Y., Yong, W.P., Lee, S.C., Liu, J.J., Choo, T.B., Tham, L.S., Lee, H.S., Goh, B.C., Soong, R.: Distribution of gemcitabine pathway genotypes in ethnic Asians and their association with outcome in non-small cell lung cancer patients. Lung Cancer 63(1), 121–127 (2009)

   Article  Google Scholar 

3. Esteban, F., Royo, J.L., González-Moles, M.A., Gonzalez-Perez, A., Redondo, M., Moreno-Luna, R., Rodríguez-Sola, M., Gonzalez, A., Real, L.M., Ruiz, A., Ramírez-Lorca, R.: CAPN10 alleles modify laryngeal cancer risk in the Spanish population. European Journal of Surgical Oncology (EJSO) 34(1), 94–99 (2008)

   Article  Google Scholar 

4. Zhang, J., Chiodini, R., Badr, A., Zhang, G.: The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics 38(3), 95–109 (2011)

   Article  Google Scholar 

5. Corchado, J.M., De Paz, J.F., Rodríguez, S., Bajo, J.: Model of experts for decision support in the diagnosis of leukemia patients. Artificial Intelligence in Medicine 46(3), 179–200 (2009)

   Article  Google Scholar 

6. Gregoretti, F., Laccetti, G., Murlib, A., Olivaa, G., Scafuri, U.: MGF: A grid-enabled MPI library. Future Generation Computer Systems 24(2), 158–165 (2008)

   Article  Google Scholar 

7. Jin, H., Jespersen, D., Mehrotra, P., Biswas, R., Huang, L., Chapman, B.: High performance computing using MPI and OpenMP on multi-core parallel systems. Parallel Computing (in Press)

   Google Scholar 

8. Rakić, P.S., Milašinović, D.D., Živanov, Ž., Suvajdžin, Z., Nikolić, M., Hajduković, M.: MPI–CUDA parallelization of a finite-strip program for geometric nonlinear analysis: A hybrid approac. Advances in Engineering Software, 42(5), 273–285 (2011)

   Google Scholar 

9. Wooldridge, M.: Introduction to Mult iAgent Systems. John Wiley & Sons (2002)

   Google Scholar 

10. International Human Genome Sequencing Consortium, Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004)

    Google Scholar 

11. Sahua, S.S., Pand, G.: dentification of Protein-Coding Regions DNA Sequences Using A Time-Frequency Filtering Approach. Genomics, Proteomics & Bioinformatics 9(1-2), 45–55 (2011)

    Article  Google Scholar 

12. Khajeh-Saeed, A., Poole, S., Perot, J.B.: Acceleration of the Smith–Waterman algorithm using single and multiple graphics processors. Journal of Computational Physics 229(11), 4247–4258 (2010)

    Article  MathSciNet  MATH  Google Scholar 

13. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215(3), 403–410 (1990)

    Google Scholar 

14. Kent, W.J.: BLAT—the BLAST-like alignment tool. Genome. Res. 12, 656–664 (2002)

    MathSciNet  Google Scholar 

15. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., Rothberg, J.M.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

    Google Scholar 

16. Miller, J.R., Koren, S., Sutton, G.: Assembly algorithms for next-generation sequencing data. Genomics 95(6), 315–327 (2010)

    Article  Google Scholar 

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