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Andrzej Pułka and Adam Milik

References GenBank (2010). [PUBMED] Pułka, A., Milik, A. (2008). A New Hardware Algorithm for Searching Genome Patterns. Proceedings of IEEE ICSES 2008 , Kraków, Poland, 177-180. Milik, A., Pułka, A. (2011). On Efficient Implementation of Search for Genome Patterns. PAK , 57(1), 15-18. (in Polish) Gusfield, D. (1997). Algorithms on strings, trees and sequences. Cambridge University Press . Smith, T. F., Waterman, M. S. (1981

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Andrzej Pułka and Adam Milik

, pp. 145-152. B. Phoophakdee and M. J. Zaki, "Genome-scale disk-based suffix tree indexing," in Proceedings of the 2007 ACM SIGMOD International Conference on Management of Data. New York, USA: ACM, 2007, pp. 833-844.

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Małgorzata Białka

References T. A. Brown: Genomes 3. Wydawnictwo Naukowe PWN, Warszawa, 2009, (in Polish). R. Kordek and J. Bartkowiak: Microsatellite instability in human carcinomas. Onkol. Pol , 22 , (1999), 109-112 (in Polish). M. Kimmel, A. Ňwierniak and A. Polañski: Infinite-dimensional model of evolution of drug resistance of cancer cells. J. of Mathematical Systems, Estimation and Control , 8 (1), (1998). W. Mitkowski: Dynamic properties of chain systems with

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Cheng-Hong Yang, Sin-Hua Moi, Yu-Da Lin and Li-Yeh Chuang

of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in Taiwan, Journal of Oral Pathology & Medicine, vol. 37, pp. 271-277, May 2008. [6] J. H. Moore, A global view of epistasis, Nature Genetics, vol. 37, pp. 13-14, Jan 2005. [7] J. H. Moore, F.W. Asselbergs, and S. M.Williams, Bioinformatics challenges for genome-wide association studies, Bioinformatics, vol. 26, pp. 445-455, Feb 15 2010. [8] S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, D. Bender, et al

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Lech Raczynski, Krzysztof Wozniak, Tymon Rubel and Krzysztof Zaremba

estimating the number of clusters in a dataset," Genome Biol. , vol. 3, p. RESEARCH0036, Jun 2002. M. Ester, H.-P. Kriegel, J. Sander, and X. Xu, "A density-based algorithm for discovering clusters in large spatial databases with noise," in Proceedings of 2nd International Conference on Knowledge Discovery and Data Mining (KDD-96). AAAI Press, 1996, pp. 226-231. T. R. Golub, D. K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J. P. Mesirov, H. Coller, M. L. Loh, J. R. Downing, M. A. Caligiuri, and C. D. Bloomfield

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Saurav Mallik, Anirban Mukhopadhyay and Ujjwal Maulik

References [1] A. Navarro, P. Yin, D. Monsivais, S. M. Lin, P. Du, J. J. Wei, S. E. Bulun, Genome-Wide DNA Methylation Indicates Silencing of Tumor Suppressor Genes in Uterine Leiomyoma, PLoS One, vol. 7, no. 3, pp. e33284, 2012. [2] V. Pihur, S. Datta and S. Datta, RankAggreg, an R Package for Weighted Rank Aggregation, BMC Bioinformatics, vol. 10, pp. 62-72, 2009. [3] K.R.V. Eijk, S.D. Jong, M.P.M. Boks, T. Langeveld, F. Colas, J.H. Veldink, C.G.F.D. Kovel, E. Janson, E. Strengman, P. Langfelder, R. S. Kahn, L

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Roman Jaksik and Joanna Rzeszowska-Wolny

References T. R. Gregory, et al.: Eukaryotic genome size databases. Nucleic Acids Res. , 35 (2007), D332-D338. D. S. Latchman: Transcription factors: an overview. Int. J. Biochem. Cell Biol. , 29 (1997), 1305-1312. M. Karin: Too many transcription factors: positive and negative interactions. New Biol. , 2 (1990), 126-131. R. G. Roeder: The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. , 21 (1996

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W. Frohmberg, M. Kierzynka, J. Blazewicz, P. Gawron and P. Wojciechowski

References [1] J. Blazewicz, M. Bryja, M. Figlerowicz, P. Gawron, M. Kasprzak, E. Kirton, D. Platt, J. Przybytek, A. Swiercz, and L. Szajkowski, “Whole genome assembly from 454 sequencing output via modified DNA graph concept”, Comput. Biol. Chem. 33 (3), 224-230 (2009). [2] J. Blazewicz, W. Frohmberg, P. Gawron, M. Kasprzak, M. Kierzynka, A. Swiercz, and P.Wojciechowski, “DNA sequence assembly involving an acyclic graph model”, FCDS 38, 25-34, doi: 10.2478/v10209-011-0019-4 (2013). [3] Forge Genome

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Corina Rotar and Laszlo Barna Iantovics

, p. 2435-2437. [10] Weber L., Applications of genetic algorithms in molecular diversity, Current Opinion in Chemical Biology 2.3, 1998, p. 381-385. [11] Arnold F. H., Design by directed evolution, Accounts of chemical research 31.3, 1998, p. 125-131. [12] Cadwell R. C., and Gerald F. J., Randomization of genes by PCR mutagenesis, Genome research 2.1, 1992, p. 28-33. [13] Stemmer W. PC., Rapid evolution of a protein in vitro by DNA shuffling, Nature 370.6488, 1994, p. 389-391. [14] Gartner Z. J., Evolutionary approaches for the

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S. Grabowski and M. Raniszewski

. Chan, “Two efficient algorithms for linear time suffix array construction”, IEEE Trans. Comput. 60 (10), 1471–1484 (2011). [13] J. Kärkkäinen, “Suffix cactus: A cross between suffix tree and suffix array”, 6th Int. Symp. Combinatorial Pattern Matching, CPM 1995 , 191–204 (1995). [14] M. I. Abouelhoda, S. Kurtz, and E. Ohlebusch, “The enhanced suffix array and its applications to genome analysis”, 2nd Int. Workshop Algorithms in Bioinformatics, WABI 2002 , 449–463 (2002). [15] N. Grimsmo, On Performance and Cache Effects in Substring Indexes