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SOFTWARE ENGINEERING PRINCIPLES FOR CREATING A WEB-ORIENTED DATABASE OF GENES

Tundrea, Emanuel

First published: 2015https://doi.org/10.5593/sgem2015/b21/s7.038View metrics

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Title
SOFTWARE ENGINEERING PRINCIPLES FOR CREATING A WEB-ORIENTED DATABASE OF GENES
Authors
Tundrea, Emanuel
Proceedings
SGEM International Multidisciplinary Scientific GeoConference EXPO Proceedings; 15th International Multidisciplinary Scientific GeoConference SGEM2015, INFORMATICS, GEOINFORMATICS AND REMOTE SENSING
Publisher
Stef92 Technology
Year
2015
Pages
307-314
ISSN
1314-2704
ISBN
978-619-7105-34-6
Language
en
Publication type
Conference Paper
References26

  1. D. a. E. D. Fischer, "Finding families for genomic ORFans," Bioinformatics, vol. 15, September 1999.

  2. G. H. S. F. R. A. T. B. Khalturin K., "More than just orphans: are taxonomically-restricted genes important in evolution ," Trends in Genetics, vol. 25, no. 9, pp. 404-413, September 2009.

  3. F. E. L. A. F. D. Wilson GA, "Large-Scale Comparative Genomic Ranking of Taxonomically Restricted Genes (TRGs) in Bacterial and Archaeal Genomes," Fairhead, 2007.

  4. D. R. Z. M. V. a. E. B. Marcel H. Schulz, "Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels," Bioinformatics, vol. 28, no. 8, 2012.

  5. 1. K. W. S. D. J. J. E. S. S. J. J. a. İ. B. Jared T. Simpson, "ABySS: A parallel assembler for short read sequence data," Genome Research, pp. 1117-1123, 2009.

  6. G. G. S. S. J. M. J. a. R. A. H. René L. Warren, "Assembling millions of short DNA sequences using SSAKE," Bioinformatics, vol. 23, no. 4, 2006.

  7. M. P. S. A. W. C. S. E. P. G. G. T. M. Wan-Ping Lee, "MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping," vol. 9, no. 3, March 2014.

  8. C. Y. Y. L. T.-W. L. S.-M. Y. K. K. a. J. W. Ruiqiang Li, "SOAP2: an improved ultrafast tool for short read alignment," Boiinformatics, vol. 25, no. 15, pp. 1966-1967, 2009.

  9. L. F. a. B. L. Li Song, "Lighter: fast and memory-efficient sequencing error correction without counting," Genome Biology, vol. 15, no. 11, 15 November 2014.

  10. E. Tundrea, "SmartModels – An MDE Platform for the Management of Software Product Lines," in Proceedings of 2008 IEEE International Conference on Automation, Quality and Testing, Robotics (AQTR 2008), Cluj-Napoca, Romania, 2008.

  11. E. Tundrea, "SmartModels - A Framework for Generating On-line Assessment Systems," in The Ninth International Conference on Systems – ICONS 2014, Nice, 2014.

  12. R. L. W. J. D. F. L. D. M. K. J. S. R. B. P. W. E. A.-V. R. A. M. a. R. A. H. Mauro Castellarin, "Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma," July 2011.

  13. D. a. D.-L. T. Tautz, "The evolutionary origin of orphan genes," Nature Reviews Genetics, pp. 692-702, August 2011. 7 http://www.i3s.unice.fr/ International Multidisciplinary Scientific GeoConfenferences SGEM 2015 www.sgem.org

  14. D. a. E. D. Fischer, "Finding families for genomic ORFans," Bioinformatics, vol. 15, September 1999.

  15. G. H. S. F. R. A. T. B. Khalturin K., "More than just orphans: are taxonomically-restricted genes important in evolution ," Trends in Genetics, vol. 25, no. 9, pp. 404-413, September 2009.

  16. F. E. L. A. F. D. Wilson GA, "Large-Scale Comparative Genomic Ranking of Taxonomically Restricted Genes (TRGs) in Bacterial and Archaeal Genomes," Fairhead, 2007.

  17. D. R. Z. M. V. a. E. B. Marcel H. Schulz, "Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels," Bioinformatics, vol. 28, no. 8, 2012.

  18. 1. K. W. S. D. J. J. E. S. S. J. J. a. İ. B. Jared T. Simpson, "ABySS: A parallel assembler for short read sequence data," Genome Research, pp. 1117-1123, 2009.

  19. G. G. S. S. J. M. J. a. R. A. H. René L. Warren, "Assembling millions of short DNA sequences using SSAKE," Bioinformatics, vol. 23, no. 4, 2006.

  20. M. P. S. A. W. C. S. E. P. G. G. T. M. Wan-Ping Lee, "MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping," vol. 9, no. 3, March 2014.

  21. C. Y. Y. L. T.-W. L. S.-M. Y. K. K. a. J. W. Ruiqiang Li, "SOAP2: an improved ultrafast tool for short read alignment," Boiinformatics, vol. 25, no. 15, pp. 1966-1967, 2009.

  22. L. F. a. B. L. Li Song, "Lighter: fast and memory-efficient sequencing error correction without counting," Genome Biology, vol. 15, no. 11, 15 November 2014.

  23. E. Tundrea, "SmartModels – An MDE Platform for the Management of Software Product Lines," in Proceedings of 2008 IEEE International Conference on Automation, Quality and Testing, Robotics (AQTR 2008), Cluj-Napoca, Romania, 2008.

  24. E. Tundrea, "SmartModels - A Framework for Generating On-line Assessment Systems," in The Ninth International Conference on Systems – ICONS 2014, Nice, 2014.

  25. R. L. W. J. D. F. L. D. M. K. J. S. R. B. P. W. E. A.-V. R. A. M. a. R. A. H. Mauro Castellarin, "Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma," July 2011.

  26. D. a. D.-L. T. Tautz, "The evolutionary origin of orphan genes," Nature Reviews Genetics, pp. 692-702, August 2011. 7 http://www.i3s.unice.fr/ International Multidisciplinary Scientific GeoConfenferences SGEM 2015 www.sgem.org

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