Haplotype inference

• X Li and J Li. Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through IBD Inference. Journal of Computational Biology, 18(11):1411-21, 2011. PMID: 21923410. (journal version of RECOMB11 paper).
  
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  X Li, X-L Yin and J Li, Efficient identification of identical-by-descent status in pedigrees with many untyped individuals. Bioinformatics 2010 26(12):i191-i198 (ISMB'10 special issue).
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  Li, X. & Li, J. An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. Journal of Bioinformatics and Computational Biology (JBCB), 7(3): 521-545, 2009.
  
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  Jing Li and Tao Jiang. An Exact Solution for Finding Minimum Recombinant Haplotype Configurations on Pedigrees with Missing Data by Integer Linear Programming. RECOMB04, 101-110.
  
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  Jing Li and Tao Jiang. Efficient Rule-Based Haplotyping Algorithm for Pedigree Data. In Proc. 7th Annual Conference on Research in Computational Molecular Biology (RECOMB03), 197-206.

Association mapping

• M Xie, J Li and T Jiang. Detecting genome-wide epistases based on the clustering of relatively frequent items. Bioinformatics 28(1):5-12, 2012.

• J Li, B Horstman and Y Chen. Detecting Epistasis Effects in Genome-Wide Association Studies Based on Ensemble Approaches. Bioinformatics, 27(13):i230-i238, 2011 (ISMB'11 special issue).

• Jing Li and Tao Jiang. Haplotype-based linkage disequilibrium mapping via direct data mining. Bioinformatics, 2005 21(24):4384-4393. 
  

Structure variation & rare variants

• W Wang, X Yin, Y-S Pyon, M Hayes and J Li. Rare variant discovery and calling by sequencing pooled samples with overlaps. Bioinformatics 29 (1): 29-38. doi: 10.1093/bioinformatics/bts645, 2012.
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  M Hayes, YS Pyon and J Li. A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data. PLoS One 7(12): e52881. doi:10.1371/journal.pone.0052881, 2012.
  
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  R Azad and J Li. Interpreting Biological Data via Entropic Dissection. Nucleic Acids Research doi: 10.1093/nar/gks917, 2012.

Integration for disease gene ranking & target prediction

• W Wang, S Yang and J Li. Drug Target Predictions Based on Heterogeneous Graph Inference, Pacific Symposium on Biocomputing, 18:53-64, 2013.
  
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  Y Chen, W Wang, Y Zhou, R Shields, SK Chanda, RC Elston, and J Li. In Silico Gene Prioritization by Integrating Multiple Data Sources. Plos One 6(6): e21137, 2011.