Publications

Metric learning from relative comparisons by minimizing squared residual, by Eric Yi Liu, Zhishan Guo, Xiang Zhang, Vladimir Jojic, and Wei Wang, Proceedings of ICDM, 2012.

MaCH-Admix: genotype imputation for admixed populations, by Eric Yi Liu, Mingyao Li, Wei Wang, and Yun Li, Genetic Epidemiology, 2012.

Inferring Ancestry in Admixed Populations using Microarray Probe Intensities, by Chen-Ping Fu, Catherine E. Welsh, Leonard McMillan, and Fernando Pardo-Manuel de Villena, ACM-BCB, 2012.

Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias, by John P Didion, Hyuna Yang, Keith Sheppard, Chen-Ping Fu, Leonard McMillan, Fernando Pardo-Manuel de Villena, and Gary A Churchill, BMC Genomics 2012, 13:34

Status and access to the Collaborative Cross Publication, by Catherine E. Welsh, Darla R. Miller, Kenneth F. Manly, Jeremy Wang, Leonard McMillan, Grant Morahan, Richard Mott, Fuad A. Iraqi, David W. Threadgill, and Fernando Pardo-Manuel de Villena, Mammalian Genome 2012: 10.1007/s00335-012-9410-6.

Accelerating the Inbreeding of Multi-Parental Recombinant Inbred Lines Generated By Sibling Matings, by Catherine E. Welsh and Leonard McMillan, G3 2012: 10.1534/g3.111.001784.

High resolution genetic mapping using the mouse Diversity Outbred population, by Svenson, Karen. L., Daniel. M. Gatti, William. Valdar, Catherine. E. Welsh, Riyan. Cheng, Elissa J. Chessler, Abraham A. Palmer, Leonard McMillan, and Gary A. Churchill, Genetics, 2012 190: 437-447.

WikiGWA: an open platform for collaborative utilization of genome-wide association (GWA) findings, by Jie Huang, Eric Yi Liu, Ryan Welch, Cristen Willer, Lucia A. Hindorff, and Yun Li, European Journal of Human Genetics, 2012.

Genotype imputation of Metabochip SNPs using a study specific reference panel, by Eric Yi Liu et al. Genetic Epidemiology, 36(2), 2012.

Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data, by Yun Li, Wei Chen, Eric Yi Liu, and Yi-Hui Zhou, Statistics in Biosciences, 2012.

Hierarchical Co-Clustering Based on Entropy Splitting, by Wei Cheng, Xiang Zhang, Feng Pan, and Wei Wang, Proceedings of the ACM Conference on Information and Knowledge Management (CIKM), 2012.

Inferring Novel Associations between SNP Sets and Gene Sets in eQTL Study using Sparse Graphical Model, by Wei Cheng, Xiang Zhang, Yubao Wu, Xiaolin Yin, Jing Li, David Heckerman, and Wei Wang, Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 2012.

Dual Transfer Learning, by Mingsheng Long, Jianmin Wang, Guiguang Ding, Wei Cheng, Xiang Zhang, and Wei Wang, Proceedings of the SIAM International Conference on Data Mining (SDM), 540-551, 2012.

Learning Transcriptional Regulatory Relationships Using Sparse Graphical Models, by Xiang Zhang, Wei Cheng, Jennifer Listgarten, Carl Kadie, Shunping Huang, Wei Wang, and David Heckerman, PLoS One, 7(5): e35762, 2012.

Imputation of SNPs in inbred mice using local phylogeny, by Jeremy R Wang, Fernando Pardo-Manuel de Villena, Heather A Lawson, James M Cheverud, Gary A Churchill, and Leonard McMillan, Genetics, February 2012 190:449-458.

The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population, by the Collaborative Cross Consortium, Genetics, February 2012 190:389-401.

Transcriptome Atlases Of Mouse Brain Reveals Differential Expression Across Brain Regions And Genetic Backgrounds, by Wei Sun, Seunggeun Lee, Vasyl Zhabotynsky, Fei Zou, Fred Wright, Jim Crowley, Zaining Yun, Ryan Buus, Darla Miller, Jeremy Wang, Leonard McMillan, Fernando Pardo-Manuel de Villena, and Patrick F Sullivan, G3 February 2012 2(2):203-211.

Comparative analysis and visualization of multiple collinear genomes, by Jeremy Wang, Fernando Pardo-Manuel de Villena, and Leonard McMillan, BMC Bioinformatics, 2012 13(Suppl 3):S13.

Measuring Opinion Relevance in Latent Topic Space, by Wei Cheng, Xiaochuan Ni, Jian-Tao Sun, Xiaoming Jin, Hye-Chung Kum,Xiang Zhang, and Wei Wang, Proceedings of the IEEE International Conference on Social Computing (SocialCom),323-330, 2011.

Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data, by Jeremy Wang, Fernando Pardo-Manuel de Villena, and Leonard McMillan, ACM Bioinformatics and Computational Biology, 2011.

Clustering with relative constraints, by Eric Yi Liu, Zhaojun Zhang, and Wei Wang, Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining(KDD), 2011.

Genetic analysis of complex traits in the emerging collaborative cross, by David L Aylor, William Valdar, Wendy Foulds-Mathes, Ryan J Buus, Ricardo A Verdugo, Ralph S Baric, Martin T Ferris, Jeff A Frelinger, Mark Heise, Matt B Frieman, Lisa E Gralinski, Timothy A Bell, John D Didion, Kunjie Hua, Derrick L Nehrenberg, Christine L Powell, Jill Steigerwalt, Yuying Xie, Samir NP Kelada, Francis S Collins, Ivana V Yang, David A Schwartz, Lisa A Branstetter, Elissa J Chesler, Darla R Miller, Jason Spence, Eric Yi Liu, Leonard McMillan, Abhishek Sarkar, Jeremy Wang, Wei Wang, Qi Zhang, Karl W Broman, Ron Korstanje, Caroline Durrant, Richard Mott, Fuad A Iraqi, Daniel Pomp, David Threadgill, Fernando Pardo-Manuel de Villena, and Gary A Churchill, Genome Research, 2011.

Subspecific origin and haplotype diversity in the laboratory mouse, by Hyuna Yang, Jeremy R Wang, John P Didion, Ryan J Buus, Timothy A Bell, Catherine E Welsh, Francois Bonhomme, Alex Hon-Tsen Yu, Michael W Nachman, Jaroslav Pialek, Priscilla Tucker, Pierre Boursot, Leonard McMillan, Gary A Churchill, and Fernando Pardo-Manuel de Villena, Nature Genetics, 2011 43 (7), 648-655.

Efficient genome ancestry inference in complex pedigrees with inbreeding, by Eric Yi Liu, Qi Zhang, Leonard McMillan, Fernando Pardo-Manuel de Villena,  and Wei Wang, Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics, 26(12), 2010.

Genome-wide compatible SNP intervals and their properties, by Jeremy Wang, Kyle J Moore, Qi Zhang, Fernando Pardo-Manuel de Villena, Wei Wang, and Leonard McMillan, ACM Bioinformatics and Computational Biology, 2010.

A fast approximation to multidimensional scaling, by Tynia Yang, Jinze Liu, Leonard McMillan, and Wei Wang, Proceedings of the ECCV Workshop on Computation Intensive Methods for Computer Vision (CIMCV), 2006.

Poclustering: lossless clustering of dissimilarity data, by Jinze Liu, Qi Zhang, Wei Wang, Leonard McMillan, and Jan Prins, Proceedings of 2007 SIAM International Conference on Data Mining (SDM2007), 2007.

Inferring missing genotypes in large SNP panels using fast nearest-neighbor searches over sliding windows, by Adam Roberts, Leonard McMillan, Wei Wang, Joel Parker, Ivan Rusyn, and David Threadgill, Proceedings of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2007.

On the subspecific origin of the laboratory mouse, by Hyuna Yang, Timothy Bell, Gary Churchill, and Fernando Pardo-Manuel de Villena, Nature Genetics Jul 22, 2007.

The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics, by Adam Roberts, Fernando Pardo-Manuel de Villena, Wei Wang, Leonard McMillan, and David Threadgill, Mammalian Genome, Aug 3, 2007.

Sample selection for maximal diversity, by Feng Pan, Adam Roberts, Leonard McMillan, Fernando Pardo Manuel de Villena, David Threadgill, and Wei Wang, 2007 IEEE International Conference on Data Mining (ICDM’07)

An imputed genotype resource for the laboratory mouse, by Jin P. Szatkiewicz, Glen L. Beane, Yueming Ding, Lucie Hutchins, Fernando Pardo Manuel de Villena, and Gary Churchill, Mammalian Genome, 19,3, 199-208.

CARE: Finding Local Linear Correlations in High Dimensional Data, by Xiang Zhang, Feng Pan, and Wei Wang, Proceedings of 2008 International Conference on Data Engineering (ICDE’08).

CRD: Fast Co-clustering on Large Datasets Utilizing Smapling-Based Matrix Decomposition, by Feng Pan, Xiang Zhang and Wei Wang, Proceedings of  2008 SIGMOD/PODS Conference (SIGMOD’08).

FastANOVA: an efficient algorithm for genome-wide association study, by Xiang Zhang, Fei Zou, and Wei Wang. Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (SIGKDD’08).

Mining non-redundant high order correlations in binary data, by Xiang Zhang, Feng Pan, Wei Wang, and Andrew Nobel. Proceedings of the 34th International Conference on Very Large Data Bases (VLDB’08).

Genotype Sequence Segmentation: Handling Constraints and Noise, by Qi Zhang, Wei Wang, Leonard McMillan, Jan Prins, Fernando Pardo-Manuel de Villena, and David Threadgill, Proceedings of 8th Workshop on Algorithms in Bioinformatics (WABI’08), 2008.

REDUS: finding reducible subspaces in high dimensional data, by Xiang Zhang, Feng Pan, and Wei Wang. Proceedings of the 17th ACM Conference on Information and Knowledge Management (CIKM’08).

TreeQA: Quantitative Genome Wide Association Mapping Using Local Perfect Phylogeny Trees, by Feng Pan, Leonard McMillan, Fernando Pardo-Manuel de Villena, David Threadgill and Wei Wang. Proceedings of the the 14th Pacific Symposium on Biocomputing (PSB’ 09) .

Inferring Genome-Wide Mosaic Structure, by Qi Zhang, Wei Wang, Leonard McMillan, Fernando Pardo-Manuel de Villena, and David Threadgill. Proceedings of the the 14th Pacific Symposium on Biocomputing (PSB’ 09) .

FastChi: an efficient algorithm for analyzing gene-gene interactions, by Xiang Zhang, Fei Zou, and Wei Wang. Proceedings of the the 14th Pacific Symposium on Biocomputing (PSB’ 09) .

COE: a general approach for efficient genome-wide two-locus epistasis test in disease association study, by Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, and Wei Wang. Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 253-269, 2009.

Structure-based function inference using protein family-specific fingerprints, by Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, and Alexander Tropsha, Protein Science, v.15, 2006, p. 1537

Benchmarking the effectiveness of sequential pattern mining methods, by Hye-Chung Kum, J. H. Chang, and Wei Wang, Data and Knowledge Engineering, v.60, 2007, p. 30.

Sequential pattern mining in multi-databases via multiple alignment, by Hye-Chung Kum, Joong-Hyuk Chang, and Wei Wang, Data Mining and Knowledge Discovery (DMKD), v.12, 2006, p. 151

CRD: fast co-clustering on large datasets utilizing sample-based matrix decomposition, by Feng Pan, Xiang Zhang, and Wei Wang, Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD), 2008, p. 173.

Accelerating Profile Queries in Elevation Maps, by Pan Feng, Wei Wang, and Leonard McMillan, International Conference on Data Engineering (ICDE 2007), 2007.

Mining approximate order preserving clusters in the presence of noise, by Mengsheng Zhang, Wei Wang, and Jinze Liu, Proceedings of the 24th IEEE International Conference on Data Engineering (ICDE), 2008, p. 160

Split-order distance for clustering and classification hierarchies, by Zhang, Q., Liu, E. Y., Sarkar, A., and Wang, W., Proceedings of the 21st International Conference on Scientific and Statistical Database Management (SSDBM), 2009, p. 517.