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Yonghui Wu, Timothy J. Close, Stefano Lonardi, "Accurate Construction of Consensus Genetic Maps via Integer Linear Programming," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 381394, March/April, 2011.  
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@article{ 10.1109/TCBB.2010.35, author = {Yonghui Wu and Timothy J. Close and Stefano Lonardi}, title = {Accurate Construction of Consensus Genetic Maps via Integer Linear Programming}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {2}, issn = {15455963}, year = {2011}, pages = {381394}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.35}, 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  Accurate Construction of Consensus Genetic Maps via Integer Linear Programming IS  2 SN  15455963 SP381 EP394 EPD  381394 A1  Yonghui Wu, A1  Timothy J. Close, A1  Stefano Lonardi, PY  2011 KW  Linear programming KW  constrained optimization KW  algorithms KW  biology and genetics. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A.H. Sturtevant, "The Linear Arrangement of Six SexLinked Factors in Drosophila, as Shown by Their Mode of Association," J. Experimental Zoology, vol. 14, pp. 4359, 1913.
[2] J. Jansen, A.G. de Jong, and J.W. van Ooijen, "Constructing Dense Genetic Linkage Maps," Theoretical and Applied Genetics, vol. 102, pp. 11131122, 2001.
[3] T. Schiex and C. Gaspin, "CARTHAGENE: Constructing and Joining Maximum Likelihood Genetic Maps," Proc. Int'l Conf. Intelligent Systems for Molecular Biology (ISMB), pp. 258267, 1997.
[4] H. Iwata and S. Ninomiya, "AntMap: Constructing Genetic Linkage Maps Using an Ant Colony Optimization Algorithm," Breeding Science, vol. 56, pp. 371377, 2006.
[5] H.V. Os, P. Stam, R.G.F. Visser, and H.J.V. Eck, "RECORD: A Novel Method for Ordering Loci on a Genetic Linkage Map," Theoretical and Applied Genetics, vol. 112, pp. 3040, 2005.
[6] D.A. Cartwright, M. Troggio, R. Velasco, and A. Gutin, "Genetic Mapping in the Presence of Genotyping Errors," Genetics, vol. 174, pp. 25212527, 2007.
[7] Y. Wu, P.R. Bhat, T.J. Close, and S. Lonardi, "Efficient and Accurate Construction of Genetic Linkage Maps from Noisy and Missing Genotyping," Proc. Workshop Algorithms in Bioinformatics (WABI), pp. 395406, 2007.
[8] Y. Wu, P.R. Bhat, T.J. Close, and S. Lonardi, "Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph," PLoS Genetics, vol. 4, p. e1000212, Oct. 2008.
[9] C. Dib, S. Faure, C. Fizames, D. Samson, N. Drouot, A. Vignal, P. Millasseau, S. Marc, J. Kazan, E. Seboun, M. Lathrop, G. Gyapay, J. Morissette, and J. Weissenbach, "A Comprehensive Genetic Map of the Human Genome Based on 5264 Microsatellites," Nature, vol. 380, pp. 152154, 1996.
[10] N. Ihara, A. Takasuga, K. Mizoshita, H. Takeda, M. Sugimoto, Y. Mizoguchi, T. Hirano, T. Itoh, T. Watanabe, K.M. Reed, W.M. Snelling, S.M. Kappes, C.W. Beattie, G.L. Bennett, and Y. Sugimoto, "A Comprehensive Genetic Map of the Cattle Genome Based on 3802 Microsatellites," Genome Research, vol. 14, pp. 19871998, 2004.
[11] W.F. Dietrich, J.C. Miller, R.G. Steen, M. Merchant, D. Damron, R. Nahf, A. Gross, D.C. Joyce, M. Wessel, R.D. Dredge, A. Marquis, L.D. Stein, N. Goodman, D.C. Page, and E.S. Lander, "A Genetic Map of the Mouse with 4,006 Simple Sequence Length Polymorphisms," Nature Genetics, vol. 7, no. 2S, pp. 220245, 1994.
[12] R.G. Steen, A.E. KwitekBlack, C. Glenn, J. GullingsHandley, W. Van Etten, O.S. Atkinson, D. Appel, S. Twigger, M. Muir, T. Mull, M. Granados, M. Kissebah, K. Russo, R. Crane, M. Popp, M. Peden, T. Matise, D.M. Brown, J. Lu, S. Kingsmore, P.J. Tonellato, S. Rozen, D. Slonim, P. Young, M. Knoblauch, A. Provoost, D. Ganten, S.D. Colman, J. Rothberg, E.S. Lander, and H.J. Jacob, "A HighDensity Integrated Genetic Linkage and Radiation Hybrid Map of the Laboratory Rat," Genome Research, vol. 9, no. 6, pp. AP18, 1999.
[13] B.N. Jackson, S. Aluru, and P.S. Schnable, "Consensus Genetic Maps: A Graph Theoretic Approach," Proc. Computational Systems Bioinformatics Conf. (CSB), pp. 3543, 2005.
[14] B.N. Jackson, P.S. Schnable, and S. Aluru, "Consensus Genetic Maps as Median Orders from Inconsistent Sources," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 5, no. 2, pp. 161171, Apr.June 2008.
[15] W.D. Beavis and D. Grant, "A Linkage Map Based on Information from Four $f_2$ Populations of Maize (Zea Mays L.)," Theoretical and Applied Genetics, vol. 82, pp. 636644, Oct. 1991.
[16] P. Stam, "Construction of Integrated Genetic Linkage Maps by Means of a New Computer Package: Joinmap," The Plant J., vol. 3, pp. 739744, 1993.
[17] D.I. Mester, Y.I. Ronin, M.A. Korostishevsky, V.L. Pikus, A.E. Glazman, and A.B. Korol, "Multilocus Consensus Genetic Maps (mcgm): Formulation, Algorithms, and Results," Computational Biology and Chemistry, vol. 30, no. 1, pp. 1220, 2006.
[18] I.V. Yap, D. Schneider, J. Kleinberg, D. Matthews, S. Cartinhour, and S.R. McCouch, "A GraphTheoretic Approach to Comparing and Integrating Genetic, Physical and SequenceBased Maps," Genetics, vol. 165, pp. 22352247, Dec. 2003.
[19] P. Wenzl, H. Li, J. Carling, M. Zhou, H. Raman, E. Paul, P. Hearnden, C. Maier, L. Xia, V. Caig, J. Ovesn, M. Cakir, D. Poulsen, J. Wang, R. Raman, K.P. Smith, G.J. Muehlbauer, K.J. Chalmers, A. Kleinhofs, and E.H.A. Kilian, "A HighDensity Consensus Map of Barley Linking DArT Markers to SSR, RFLP and STS Loci and Agricultural Traits," BMC Genomics, vol. 7, 2006.
[20] S.A. Plotkin, D.B. Shmoys, and E. Tardos, "Fast Approximation Algorithms for Fractional Packing and Covering Problems," Proc. Ann. Symp. Foundations of Computer Science (FOCS), pp. 495504, 1991.
[21] M. Girvan and M.E.J. Newman, "Community Structure in Social and Biological Networks," Proc. Nat'l Academy of Sciences USA, vol. 99, pp. 78217826, June 2002.
[22] A. Aho, "The Transitive Reduction of a Directed Graph," SIAM J. Computing, vol. 1, no. 2, pp. 131137, 1972.
[23] A.B. Kahn, "Topological Sorting of Large Networks," Comm. ACM, vol. 5, no. 11, pp. 558562, 1962.