
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Alexander Schliep, Roland Krause, "Efficient Algorithms for the Computational Design of Optimal Tiling Arrays," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, no. 4, pp. 557567, OctoberDecember, 2008.  
BibTex  x  
@article{ 10.1109/TCBB.2008.50, author = {Alexander Schliep and Roland Krause}, title = {Efficient Algorithms for the Computational Design of Optimal Tiling Arrays}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {5}, number = {4}, issn = {15455963}, year = {2008}, pages = {557567}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.50}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Efficient Algorithms for the Computational Design of Optimal Tiling Arrays IS  4 SN  15455963 SP557 EP567 EPD  557567 A1  Alexander Schliep, A1  Roland Krause, PY  2008 KW  Biology and genetics KW  Graph Theory VL  5 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] M.J. Buck and J.D. Lieb, “ChipChip: Considerations for the Design, Analysis, and Application of GenomeWide Chromatin Immunoprecipitation Experiments,” Genomics, vol. 83, no. 3, pp.349360, Mar. 2004.
[2] M. Barrett et al., “Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA,” Proc. Nat'l Academy of Sciences USA, vol. 101, no. 51, pp.1776517770, 2004.
[3] J. Mattick, “The Functional Genomics of Noncoding RNA,” Science, pp. 15271528, 2005.
[4] E. Birney et al., “Identification and Analysis of Functional Elements in 1 Percent of the Human Genome by the ENCODE Pilot Project,” Nature, vol. 447, no. 7146, pp. 799816, 2007.
[5] G. Yuan, Y. Liu, M. Dion, M. Slack, L. Wu, S. Altschuler, and O. Rando, “GenomeScale Identification of Nucleosome Positions in S.cerevisiae,” Science, pp. 626630, 2005.
[6] P. Sabo et al., “GenomeScale Mapping of DNase I Sensitivity In Vivo Using Tiling DNA Microarrays,” Nature Methods, vol. 3, pp.511518, 2006.
[7] D. Okou, K. Steinberg, C. Middle, D. Cutler, T. Albert, and M. Zwick, “MicroarrayBased Genomic Selection for HighThroughput Resequencing,” Nature Methods, vol. 4, pp. 907909, 2007.
[8] T. Albert et al., “Direct Selection of Human Genomic Loci by Microarray Hybridization,” Nature Methods, vol. 4, pp. 903905, 2007.
[9] T. Mockler and J. Ecker, “Applications of DNA Tiling Arrays for WholeGenome Analysis,” Genomics, vol. 85, no. 1, pp. 115, 2005.
[10] K. Breslauer, R. Frank, H. Blocker, and L. Marky, “Predicting DNA Duplex Stability from the Base Sequence,” Proc. Nat'l Academy of Sciences USA, vol. 83, no. 11, pp. 37463750, 1986.
[11] M.D. Kane, T.A. Jatkoe, C.R. Stumpf, J. Lu, J.D. Thomas, and S.J. Madore, “Assessment of the Sensitivity and Specificity of Oligonucleotide (50mer) Microarrays,” Nucleic Acids Research, vol. 28, no. 22, pp. 45524557, Nov. 2000.
[12] D.W. Selinger, K.J. Cheung, R. Mei, E.M. Johansson, C.S. Richmond, F.R. Blattner, D.J. Lockhart, and G.M. Church, “RNA Expression Analysis Using a 30 Base Pair Resolution Escherichia coli Genome Array,” Nature Biotechnology, vol. 18, no. 12, pp. 12621268, Dec. 2000.
[13] P. Kapranov, S. Cawley, J. Drenkow, S. Bekiranov, R. Strausberg, S. Fodor, and T. Gingeras, “LargeScale Transcriptional Activity in Chromosomes 21 and 22,” Science, vol. 296, no. 5569, p. 916, 2002.
[14] P. Kapranov etal., “RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription,” Science, vol. 316, no. 5830, p. 1484, 2007.
[15] D. Lipson, Z. Yakhini, and Y. Aumann, “Optimization of Probe Coverage for HighResolution Oligonucleotide ACGH,” Bioinformatics, vol. 23, no. 2, pp. 7783, Jan. 2007.
[16] E. Prak and H. Kazazian Jr., “Mobile Elements and the Human Genome,” Nature Rev. Genetics, vol. 1, no. 2, pp. 134144, 2000.
[17] A. Smit, R. Hubley, and P. Green, RepeatMasker Open3.0. Inst. for Systems Biology, http:/www.repeatmasker.org, 2004.
[18] E. Ryder, R. Jackson, A. FergusonSmith, and S. Russell, MAMMOT—a Set of Tools for the Design, Management and Visualization of Genomic Tiling Arrays, pp. 883884, 2006.
[19] E. Lander et al., “Initial Sequencing and Analysis of the Human Genome,” Nature, vol. 409, no. 6822, pp. 860921, 2001.
[20] R. Brosch et al., “Genome Plasticity of BCG and Impact on Vaccine Efficacy,” Proc. Nat'l Academy of Sciences USA, vol. 104, no. 13, p. 5596, 2007.
[21] P. Bertone, V. Trifonov, J.S. Rozowsky, F. Schubert, O. Emanuelsson, J. Karro, M.Y. Kao, M. Snyder, and M. Gerstein, “Design Optimization Methods for Genomic DNA Tiling Arrays,” Genome Research, vol. 16, no. 2, pp. 271281, Feb. 2006.
[22] S. Gräf, F.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek, “Optimized Design and Assessment of Whole Genome Tiling Arrays,” Bioinformatics, vol. 23, no. 13, pp. 195204, July 2007.
[23] A. Schliep, D. Torney, and S. Rahmann, “Group Testing with DNA Chips: Generating Designs and Decoding Experiments,” Proc. Second IEEE CS Bioinformatics Conf. (CSB '03), pp. 8493, 2003.
[24] O. Shai, Q. Morris, B. Blencowe, and B. Frey, “Inferring Global Levels of Alternative Splicing Isoforms Using a Generative Model of Microarray Data,” Bioinformatics, vol. 22, no. 5, p. 606, 2006.
[25] Z. Galil and K. Park, “Dynamic Programming with Convexity, Concavity, and Sparsity,” Theoretical Computer Science, vol. 92, no. 1, pp. 4976, , 1992.
[26] R.E. Burkard, B. Klinz, and R. Rudolf, “Perspectives of Monge Properties in Optimization,” Discrete Applied Math., vol. 70, no. 2, pp. 95161, 1996.
[27] R. Wilber, “The Concave LeastWeight Subsequence Problem Revisited,” J. Algorithms, vol. 9, no. 3, pp. 418425, 1988.
[28] D. Eppstein, “Sequence Comparison with Mixed Convex and Concave Costs,” J. Algorithms, vol. 11, no. 1, pp. 85101, 1990.
[29] Z. Galil, K. Park, “A LinearTime Algorithm for Concave OneDimensional Dynamic Programming,” Information Processing Letters, vol. 33, no. 6, pp. 309311, 1990.
[30] A. Aggarwal, M. Klawe, S. Moran, P. Shor, and R. Wilber, “Geometric Applications of a Matrix Searching Algorithm,” Proc. Second Ann. Symp. Computational Geometry (SCG '86), pp. 285292, 1986.
[31] A. Aggarwal, B. Schieber, and T. Tokuyama, “Finding a Minimum Weight KLink Path in Graphs with Monge Property and Applications,” Proc. Ninth Ann. Symp. Computational Geometry (SCG '93), pp. 189197, 1993.
[32] E.W. Dijkstra, “A Note on Two Problems in Connexion with Graphs,” Numerische Mathematik, vol. 1, Mathematisch Centrum, pp. 269271, 1959.
[33] M.L. Fredman and R.E. Tarjan, “Fibonacci Heaps and Their Uses in Improved Network Optimization Algorithms,” J. ACM, vol. 34, no. 3, pp. 596615, 1987.
[34] T.H. Cormen, C.E. Leiserson, R.L. Rivest, and C. Stein, Introduction to Algorithms, second ed. MIT Press, Sept. 2001.
[35] Leda, citeseer.ist.psu.edu/galil92dynamic.htmlhttp:/ www.algorithmicsolutions.com/, 2008.
[36] A. Schliep, “The Software GADAR and Its Application to Extremal Graph Theory,” Proc. 25th Southeastern Int'l Conf. Combinatorics, Graph Theory and Computing, vol. 104, pp. 193203, 1994.
[37] S. Kurtz, “The Vmatch Large Scale Sequence Analysis Software,” Ref Type: Computer Program, pp. 412, 2003.
[38] S. Bienert, “Flexible Combination of Filters for Oligodesign,” Diplomathesis, Center for Bioinformatics, Universität Hamburg, 2006.
[39] M. Abouelhoda, S. Kurtz, and E. Ohlebusch, “Replacing Suffix Trees with Enhanced Suffix Arrays,” J. Discrete Algorithms, vol. 2, no. 1, pp. 5386, 2004.
[40] Z. Ning, A.J. Cox, and J.C. Mullikin, “SSAHA: A Fast Search Method for Large DNA Databases,” Genome Research, vol. 11, no. 10, pp. 17251729, Oct. 2001.
[41] P. Rice, I. Longden, and A. Bleasby, “EMBOSS: The European Molecular Biology Open Software Suite,” Trends in Genetics, vol. 16, no. 6, pp. 276277, 2000.
[42] C. Garnis, W. Lockwood, E. Vucic, Y. Ge, L. Girard, J. Minna, A. Gazdar, S. Lam, C. MacAulay, and W. Lam, “High Resolution Analysis of NonSmall Cell Lung Cancer Cell Lines by Whole Genome Tiling Path Array CGH,” Int'l J. Cancer, vol. 118, pp. 15561564, 2006.
[43] A. Schliep and R. Krause, “Efficient Computational Design of Tiling Arrays Using a Shortest Path Approach,” Lecture Notes in Computer Science, vol. 4645, p. 383, 2007.
[44] Boost c++ Libraries, http:/www.boost.org/, 2008.
[45] Automatically Tuned Linear Algebra Software (ATLAS), http:/mathatlas.sourceforge.net/, 2008.
[46] Python, http:/www.python.org/, 2008.
[47] Numpy, http:/numpy.scipy.org/, 2008.
[48] A. Pozhitkov, P.A. Noble, T. DomazetLoso, A.W. Nolte, R. Sonnenberg, P. Staehler, M. Beier, and D. Tautz, “Tests of rRNA Hybridization to Microarrays Suggest that Hybridization Characteristics of Oligonucleotide Probes for Species Discrimination Cannot Be Predicted,” Nucleic Acids Research, vol. 34, no. 9, 2006.
[49] Z. He, L. Wu, X. Li, M. Fields, and J. Zhou, “Empirical Establishment of Oligonucleotide Probe Design Criteria,” Applied and Environmental Microbiology, vol. 71, no. 7, pp. 37533760, 2004.
[50] O. Matveeva, S. Shabalina, V. Nemtsov, A. Tsodikov, R. Gesteland, J. Atkins, and O. Journals, “Thermodynamic Calculations and Statistical Correlations for OligoProbes Design,” Nucleic Acids Research, vol. 31, no. 14, pp. 42114217, 2003.
[51] S. Cole et al., “Deciphering the Biology of Mycobacterium Tuberculosis from the Complete Genome Sequence,” Nature, vol. 393, pp. 537544, 1998.
[52] J. SantaLucia Jr., H. Allawi, and P. Seneviratne, “Improved NearestNeighbor Parameters for Predicting DNA Duplex Stability,” Biochemistry, vol. 35, no. 11, pp. 35553562, 1996.