Publications

  1. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpaa MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F. (2004). The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36:1133- 7.
  2. Flint, J., Valdar, W., Shifman, S., and Mott, R. (2005). Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev Genet, 6(4):271–86.
  3. Liu, Y. and Dean, A. (2004). K-circulant supersaturated designs. Technometrics, 46, 1, 32-43.
  4. Liu, Y., Shen, X., and Doss, H. (2005). Multicategory psi-learning and support vector machine: computational tools. Journal of Computational and Graphical Statistics,14, 1, 219-236.
  5. Bell,T.A., Casa-Esperon,E., Doherty,H.E., Ideraabdullah,F., Kim,K., Wang,Y., Lange,L.A., Wilhemsen,K., Lange,E.M., Sapienza,C., and de Villena,F.P. (2006). The paternal gene of the DDK syndrome maps to the Schlafen gene cluster on mouse chromosome 11. Genetics 172, 411-423.
  6. Liu, Y. and Wu, Y. (2006). Optimizing psi-learning via mixed integer programming. Statistica Sinica, 16, 2, 441-457.
  7. Liu, Y. and Shen, X. (2006). Multicategory psi-learning. Journal of the American Statistical Association, 101, 474, 500-509.
  8. Yang T., Liu J., McMillan L., Wang W. (2006). A fast approximation to multidimensional scaling. Proceedings of the ECCV Workshop on Computation Intensive Methods for Computer Vision (CIMCV).
  9. Liu, J., Paulsen, S., Xu, X., Wang, W., Nobel, A., and Prins, J. (2006a). Mining Approximate frequent itemset in the presence of noise: algorithm and analysis. Proceedings of the 6th SIAM Conference on Data Mining (SDM).
  10. Liu, J., Zhang, Q., Wang, W., McMillan, L, and Prins, J. (2006b). Clustering pair-wise dissimilarity data into partially ordered sets. Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD), 637-642.
  11. Valdar W, Flint J, Mott R. (2006). Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172:1783-97.
  12. Valdar,W., Solberg,L.C., Gauguier,D., Burnett,S., Klenerman,P., Cookson,W.O., Taylor,M.S., Rawlins,J.N., Mott,R., and Flint,J. (2006). Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet 38, 879-887.
  13. Valdar W, Solberg LC, Gaugier D, Cookson WO, Rawlins JNP, Mott R, Flint J (2006). Genetic and environmental effects on complex traits in mice. Genetics 174(2):959-84
  14. Liu, J., Zhang, Q., Wang, W., McMillan, L, and Prins, J. (2007). Poclustering: lossless clustering of dissimilarity data. Proceedings of the 7th SIAM Conference on Data Mining (SDM).
  15. Taylor M, Valdar W, Kumar A, Flint J, Mott R (2007). Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 15;23(12):1545-9.
  16. Yang, H.,  Bell, T., Churchill, G., and de Pardo-Manuel Villena, F. (2007). On the subspecific origin of the laboratory mouse. Nature Genetics Jul 22, 39, 1100-1107.
  17. Pan, F., Roberts, A., McMillan, L., Pardo Manuel de Villena, F., Threadgill, D., and Wang, W. (2007). Sample selection for maximal diversity. Proceedings of the 7th IEEE International Conference on Data Mining (ICDM), 262-271.
  18. Ideraabdullah F., Kim K., Pomp D., Morin J., Beier D., Pardo-Manuel de Villena, F. (2007). Rescue of the mouse DDK syndrome by parent-of-origin-dependent modifiers. Biology of Reproduction, 76, 286-293.
  19. Roberts, A., Pardo-Manuel de Villena, F., Wang, W., McMillan, L., and Threadgill, D. (2007a). Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows. Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics, vol. 23, no. 13, i401-i407.
  20. Roberts, A., Pardo-Manuel de Villena, F., Wang, W., McMillan, L., and Threadgill, D. (2007b). The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics. Mammalian Genome, vol. 18, no. 6, 473-481.
  21. Liu, Y., & Wu, Y. (2007). Variable selection via a combination of the L0 and L1 penalties. Journal of Computational and Graphical Statistics, 16, 4, 782-798.
  22. Wu, Y. & Liu, Y. (2007). Robust truncated-hinge-loss support vector machines. Journal of the American Statistical Association,102, 479, 974-983.
  23. Liu, Y., Zhang, H., Park, C., & Ahn, J. (2007). Support Vector Machines with adaptive Lq penalties. Computational Statistics and Data Analysis, 51, 12, 6380-6394.
  24. Li, Y., Liu, Y., & Zhu, J. (2007). Quantile regression in Reproducing Kernel Hilbert Spaces. Journal of the American Statistical Association, 102, 477, 255-268.
  25. Liu, Y., Ruan, S., & Dean, A. (2007). Construction and analysis of Es2 efficient. Journal of Statistical Planning and Inference,137, 5, 1516-1529.
  26. Alcorta, D. A., Barnes, D. A., Dooley, M. A., Sullivan, P., Jonas, B., Liu, Y., Lionaki, S., Reddy, C. B., Chin, H., Dempsey, A. A., Jennette, J. C., & Falk, R. J. (2007). Leukocyte Gene Expression Signatures in Antineutrophil Cytoplasmic Autoantibody (ANCA) and Lupus Glomerulonephritis.. Kidney International, 72, 853-864.
  27. Liu, Y. (2007). Fisher consistency of multicategory support vector machines. Eleventh International Conference on Artificial Intelligence and Statistics, 289-296.
  28. Wu, Y., & Liu, Y. (2007).On Multicategory Truncated-Hinge-Loss Support Vector Machines. Contemporary Mathematics, 443, 49-58.
  29. Liu, Y., Zhang, H., Park, C., & Ahn, J. (2007). The Lq support vector machine. Contemporary Mathematics, 443, 35-48.
  30. Wright, F.A., Huang, H., Guan, X., Gamiel, K., Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., & Zou, F. (2007). Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics. 23, 2581-2588.
  31. Gordon, R., Hunter, K., La Merrill, M., Sørensen, P., Threadgill, D., & Pomp, D. (2008). Genotype X diet interactions in mice predisposed to mammary cancer: II. Tumors and metastasis. Mammalian Genome, 19, 179-189.
  32. Szatkiewicz, JP., Beane, GL., Ding, Y., Hutchins, L., Pardo Manuel de Villena, F., & Churchill, GA. (2008). An imputed genotype resource for the laboratory mouse. Mammalian Genome, 19, 199-208.
  33. Zhang, X., Pan, F., & Wang, W. (2008). CARE: Finding Local Linear Correlations in High Dimensional Data. Proceedings of 2008 International Conference on Data Engineering (ICDE’08), 130-139.
  34. Pan, F., Zhang, X., & Wang, W. (2008). CRD: Fast Co-clustering on Large Datasets Utilizing Smapling-Based Matrix Decomposition. Proceedings of 2008 SIGMOD/PODS Conference (SIGMOD’08), 173-184.
  35. Zhang, X., Zou, F., & Wang, W. (2008). FastANOVA: an efficient algorithm for genome-wide association study. Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD’08), 821-829.
  36. Zhang, X., Pan, F., Wang, W., & Nobel, A. (2008). Mining non-redundant high order correlations in binary data. Proceedings of the 34th International Conference on Very Large Data Bases (VLDB’08), 1178-1188.
  37. Zhang, X., Pan, F., & Wang, W. (2008). REDUS: finding reducible subspaces in high dimensional data. Proceedings of the 17th ACM Conference on Information and Knowledge Management (CIKM’08), 961-970.
  38. Pan, F., Yang, L., McMillan, L., Pardo-Manuel de Villena, F., Threadgill, D., & Wang, W. (2008). 8th IEEE International Conference on Data Mining. 971-976.
  39. Zhang, Q., Wang, W., McMillan, L., Prins, J., Pardo-Manuel de Villena, F., & Threadgill, D. (2008). Genotype sequence segmentation: handling constraints and noise. Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI), 271-283.
  40. Liu, Y., Hayes, D.N., Nobel, A., & Marron, J. S. (2008). Statistical significance of clustering for high dimension low sample size data. Journal of the American Statistical Association, 103, 483, 1281-1293.
  41. Zhang, H., Liu, Y., Wu, Y., & Zhu, J. (2008). Variable selection for the multicategory SVM via sup-norm regularization. Electronic Journal of Statistics, 2, 149-167.
  42. Wang, J., Shen, X., & Liu, Y. (2008). Probability estimation for large margin classifiers. Biometrika, 95, 1, 149-167.
  43. Moore, K., Zhang, Q., McMillan, L., Pardo-Manuel de Villena, F. & Wang, W. (2008). Genome-wide compatible SNP intervals and their properties. UNC Technical Report, Jun 08.
  44. Pan, F., McMillan, L., Pardo-Manuel de Villena, F., Threadgill, D., & Wang, W. (2009). TreeQA: Quantitative genome wide association mapping using local perfect phylogeny trees. Pacific Symposium on Biocomputing (PSB), 415-426.
  45. Zhang, X., Zou, F., & Wang, W. (2009). FastChi: an efficient algorithm for analyzing gene-gene interactions. Pacific Symposium on Biocomputing (PSB), 528-539.
  46. Zhang, X., Pan, F., Xie, Y., Zou, F., & Wang, W. (2009). COE: a general approach for efficient genome-wide two-locus epistasis test in disease association study. Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 253-269.
  47. Pomp, D., & Mohlke, K. (2008). Obesity genes: so close and yet so far…. J Biol, 7, 36.
  48. Ankra-Badu, GA., Pomp, D., Shriner, D., Allison, DB., & Yi, N. (2009). Genetic influences on growth and body composition in mice: multilocus interactions. Int J Obes (Lond) 33, 89-95.
  49. Bice P, Valdar W, Zhang L, Liu L, Lai D, Grahame N, Flint J, Li TK, Lumeng L, Foroud T (2009). Genomewide SNP Screen to Detect Quantitative Trait Loci for Alcohol Preference in the High Alcohol Preferring and Low Alcohol Preferring Mice. Alcohol Clin Exp Res 33(3):531-7.
  50. Huang GJ, Shifman S, Valdar W, Johannesson M, Yalcin B, Taylor MS, Taylor JM, Mott R, Flint J (2009). High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. Genome Res 19(6):1133-40.
  51. Johannesson M, Lopez-Aumatell R, Stridh P, Diez M, Tuncel J, Blázquez G, Martinez-Membrives E, Cañete T, Vicens-Costa E, Graham D, Copley RR, Hernandez-Pliego P, Beyeen AD, Ockinger J, Fernández-Santamaría C, Gulko PS, Brenner M, Tobeña A, Guitart-Masip M, Giménez-Llort L, Dominiczak A, Holmdahl R, Gauguier D, Olsson T, Mott R, Valdar W, Redei EE, Fernández-Teruel A, Flint J. (2009). A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: the NIH heterogeneous stock.. Genome Res 19(1):150-8.
  52. La Merrill, M., Baston, D., Denison, M., Birnbaum, L., Pomp, D., & Threadgill, DW. (2009). Mouse breast cancer model-dependent changes in metabolic syndrome-associated phenotypes caused by maternal dioxin exposure and dietary fat. Am J Physiol Endocrinol Metab. 296:E203-10.
  53. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R. (2009). A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5(7)
  54. Nehrenberg, DL., Hua, K., Estrada-Smith, D., Garland, Jr T., & Pomp, D. (2009). Voluntary Exercise and its Effects On Body Composition Depend On Genetic Selection History. Obesity (Silver Spring).
  55. Valdar W, Holmes C, Mott R, Flint J (2009). Mapping in structured populations by resample model averaging. Genetics 182(4):1263-77
  56. Wu, Y., & Liu, Y. (2009). Variable selection in quantile regression. Statistica Sinica, 19, 801-817.
  57. Qiao, X., & Liu, Y. (2009). Adaptive weighted learning for unbalanced ulticategory classification. Biometrics, 65(1), 159-68.
  58. Kwangbom Choi and Shawn M. Gomez. (2009). Comparison of phylogenetic trees through alignment of embedded evolutionary distances.. BMC Bioinformatics,10:423.