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1. M Hayes and J Li. Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next generation sequencing data. BMC Bioinformatics, accepted, 2013. Also presented at RECOMB Seq conference.
2. W Wang, S Yang and J Li. Drug Target Predictions Based on Heterogeneous Graph Inference, Pacific Symposium on Biocomputing, 18:53-64, 2013.
3. 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.
4. R Azad and J Li. Interpreting Biological Data via Entropic Dissection. Nucleic Acids Research doi: 10.1093/nar/gks917, 2012.
5. 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.
6. Y Chen and J Li. Generation of synthetic data and experimental designs in evaluating interactions for association studies. J Bioinform Comput Biol 10(1): (1240005), 2012.
7. 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.
8. A Assareh, LG Volkert and J Li. Interaction Trees: Optimizing Ensembles of Decision Trees for Gene-Gene Interaction Detections. Proc of 11th International Conference on Machine Learning and Applications (ICMLA), 616-621, Boca Raton, FL, 2012.
9. A Assareh, LG Volkert and J Li. Feature Selections Using AdaBoost: Application in Gene-Gene Interaction Detection. Proc IEEE International Conference on Bioinformatics & Biomedicine Workshops (BIBMW), 831 - 837, 2012.
10. M Wu, CK Kwoh, TM Przytycka, J Li and J Zheng. Integration of Genomic and Epigenomic Features to Predict Meiotic Recombination Hotspots in Human and Mouse. Proc ACM Conference on Bioinformatics and Computational Biology, 297-304, Orlando, FL, 2012.
11. W Cheng, X Zhang, W Wang, Y Wu, X Yin, J Li and D Heckerman. Inferring novel associations between SNP sets and gene sets in eQTL study using sparse graphical model. PProc ACM Conference on Bioinformatics and Computational Biology, 466-473, Orlando, FL, 2012.
12. 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).
13. 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.
14. Y-S Pyon, X Li and J Li. Cancer Progression Analysis based on Ordinal Relationship of Cancer Stages and co-Expression Network Modularity. International Journal of Data Mining and Bioinformatics. 5 (3):233-251, 2011. (Journal version of the BIBM09 paper).
15. 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).
16. M Wu, CK Kwoh, T Przytycka, J Li, and J Zheng. Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome. Proc IEEE International Conference on Bioinformatics & Biomedicine (BIBM), 57 - 62, 2011.
17. X Li and J Li. Haplotype Reconstruction in Large Pedigrees with Many Untyped Individuals. In Proc. 15th Annual Conference on Research in Computational Molecular Biology (RECOMB11), Lecture Notes in Computer Science, 6577:189-203, 2011.
18. Y Chen and J Li. Generating Samples Involving Genetic and Non-genetic Interactions for Association Studies. Proc ACM Conference on Bioinformatics and Computational Biology, 325-329, Chicago, IL, 2011.
19. Y S Pyon, M Hayes and J Li. Model Based Clustering Approach for Identifying Structural Variation Using Next Generation Sequencing Data. In Proc. 1st International Conference on Computational Advances in Bio and medical Sciences (IEEE ICCABS' 11), 153-158, 2011.
20. C Gao and J Li. Machine Learning Approaches for the Investigation of Features beyond Seed Matches Affecting miRNA Binding. Proc IEEE International Conference on Bioinformatics & Biomedicine (BIBM), 209-213, 2010.
21. M Xie, J Li and T Jiang. Accurate HLA Type Inference Using a Weighted Similarity Graph. BMC Bioinformatics 2010, 11(Suppl 11):S10. 21st international Conference on Genome Informatics (GIW) special issue.
22. 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).
23. X-L Yin and J Li, Conditional random field model for detecting copy number variation. Volume: 8, Issue: 2(2010) pp. 295-314, Journal of Bioinformatics and Computational Biology.
24. K Narayanan and J Li, MAVEN: a Visualization and Functional Analysis Tool for Genome-Wide Association Results. Bioinformatics 2010 26(2):270-272.
25. X Li, Y Chen and J Li. Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Population Local Structure. Pacific Symposium on Biocomputing 15:348-358(2010).
26. Y Chen, X Li and J Li. A New Approach for Family-based Haplotype Association Testing and Fine Mapping. BMC Bioinformatics 2010, 11(Suppl 1):S45. Presented at APBC'10.
27. Y-S Pyon and J Li. Identifying Gene Signatures from Cancer Progression Data Using Ordinal Analysis. Proc of BIBM, 136-141, 2009.
28. S Erten, X Li, G Bebek, J Li and M Koyuturk. Phylogenetic analysis of modularity in protein interaction networks. BMC Bioinformatics, 10:333, 2009.
29. X-L Yin and J Li, A general graphical framework for detecting copy number variation. Proc of Comput Syst Bioinformatics Conf (CSB), 47-58, 2009.
30. 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.
31. M. Hayes and J Li. A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation, International Symposium on Bioinformatics Research and Applications (ISBRA), Lecture Notes in Bioinformatics (5542) 248-259, May 2009.
32. K Narayanan and J Li, Visualization and Functional Analysis of Genome-Wide Association Results, Proceedings of Ohio Collaborative Conference in Bioinformatics (OCCBIO'09), 9-13, June 2009.
33. X Li, S Erten, G Bebek, M Koyuturk and J Li, Comparative Analysis of Modularity in Biological Systems. Proceedings of Ohio Collaborative Conference in Bioinformatics (OCCBIO'09), 104-109, June 2009.
34. Igo, R.P., Jr., Li, J. & Goddard, K.A. Association Mapping by Generalized Linear Regression with Density-based Haplotype Clustering. Genetic Epidemiology 33, 16-26 (2009).
35. X Li and Li, J. Efficient Haplotype Inference from Pedigrees with Missing Data using Linear Systems with Disjoint-Set Data Structures. CSB 2008.
36. Li, J. Prioritize and Select SNPs for Association Studies with Multi-stage Designs. Journal of Computational Biology 15:241-57, 2008.
37. Li, J and Y Chen. Generating samples for association studies based on HapMap data. BMC Bioinformatics 9:44, 2008.
38. Li, J. and T. Jiang. A survey on haplotyping algorithms for tightly linked markers. Journal of Bioinformatics and Computational Biology (JBCB), 6: 241-259. 2008.
39. Li, J A Novel Strategy for Detecting Multiple Loci in Genome-Wide Association Studies of Complex Diseases. Int. J. Bioinformatics Research and Applications, 4:150-63, 2008.
40. Li, J. Marker selection for whole genome association studies with two-stage designs using dense SNPs. BMC Proceedings 1:S136.
41. X. Li and J Li. Comparisons of haplotype inference from pedigree data and population data. BMC Proceedings 1:S55.
42. Wu, S. and J. Li. Comparative Analysis of Gene-Coexpression Networks Across Four Plant Species. International Symposium on Bioinformatics Research and Applications (ISBRA), May 2007, Lecture Notes in Bioinformatics (4463) 615-626.
43. She, GQ, GQ Shen, L Li, D Girelli, C Fan, JE Park, Q Xi, S Rao, J Li, Y Hu, O Olivieri, K Marchant, J Barnard, R Corrocher, R Elston, J Cassano, S Henderson, SL Hazen, EF Plow, EJ Topol & QK Wan. Variants in the LRP8 gene encoding the LDL receptor-related protein 8 confer risk of coronary artery disease and myocardial infarction. Am J Human Genet. 81:780-791, 2007.
44. RP Igo, D Londono, K Miller, AR Parrado, SRE Quade, M Sinha, S Kim, S Won, J Li and KAB Goddard, Density-based Clustering in Haplotype Analysis for Association Mapping. BMC Proceedings 1:S27.
45. Liu, Z, S.F. Yan, J. Walker, T. Zwingman, T. Jiang, J. Li and Y. Zhou. Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas. BMC Systems Biology, 1:19 2007.
46. Jing Li, Yingyao Zhou and Robert C. Elston. Haplotype-based Quantitative Trait Mapping Using a Clustering Algorithm. BMC Bioinformatics 2006, 7:258..
47. Jing Li and Tao Jiang. Haplotype-based linkage disequilibrium mapping via direct data mining. Bioinformatics, 2005 21(24):4384-4393.
48. Jing Li and Tao Jiang. Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming. Journal of Computational Biology, 12:719-739, 2005.
49. 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.
51. 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.
53. Li, J. et al. Statistical Validation of Compound Structure-Selectivity Relationship using NCI Cancer Database . The International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS 03), 146-151..
54. Koichiro Doi, Jing Li and Tao Jiang. Minimum Recombinant Haplotype Configuration on Tree Pedigrees. In Proc. 3rd Annual Workshop on Algorithms in Bioinformatics (WABI'03), 339-353.
55. Bonizzoni, P., G. D. Vedova, R. Dondi and J. Li. The Haplotyping Problem: An Overview of Computational Models and Solutions. Journal of Computer Science and Technology (JCST) 18(6):675-688, 2003.
56. Jing Li and Tao Jiang. PedPhase: Haplotype Inference for Pedigree Data. Submitted.
58. Deng, H.-W. and J. Li. The effect of selective sampling on transmission disequilibrium test of a QTL. Genet Res 79(2):161-174, 2002
59. Deng HW, Mahaney MC, Williams J, Li J, Conway T, Davies KM, Li JL, Deng HY, Lai DB, and Recker RR. Relevance of the genes for Bone Mass Variation to Susceptibility to Osteoporotic Fractures and its implications to gene search for complex human diseases. Genet Epidemiology, 22:12-25, 2002
60. Deng, H.-W., J. Li and R. R. Recker. Effect of polygenes on Xiong's transmission disequilibrium test of a QTL in nuclear families with multiple children. Genet Epidemiology. 2001 Nov; 21(3): 243-65. PMID: 11668580.
61. Deng, H.-W., J. Li and R. R. Recker. LOD score exclusion analyses for candidate genes using random population samples. Annals of Human Genetics, 2001 May; 65(3): 313-29. PMID: 11427187.
62. Deng, HW, Lai DB, Conway T, Jing Li, Xu FH, Davies KM, Recker RR 2001 Characterization of genetic and life-style factors for determining variation of BMI, fat mass, percentage fat mass, and lean mass. J Clinical Densitometry 4: 353-362
63. Deng HW, Li J, Conway T, Lappe M, Deng XT, Davies KM, Li JL, Lai DB, Chen WM, M Johnson, FH Xu, HY Deng, and Recker RR. No evidence of linkage to BMD variation for the marker d11s987 on chromosome 11q12-13. J Bone and Miner Res 15: S214, 2000.
64. Deng HW, Mahaney MC, Williams J, Li J, Conway T, Davies KM, Li JL, Deng HY, Lai DB, and Recker RR "Are genes important for bone mass variation relevant to risk of osteoporotic fractures?" J Bone and Miner Res 15: S162, 2000.
65. P Bonizzoni, G D Vedova, R Dondi and J Li. "The Haplotyping Problem: An Overview of Computational Models and Solutions" in Genome Sequencing Technology and Algorithms Editors: Kim, Tang and Mardis. Artech House Publishers. 2007.
66. J Li. "A Survey on Haplotyping Algorithms For Tightly Linked Markers" in Current Topics in Human Genetics Editors: Deng, She, Liu & Hu. World Scientific Publishing, Singapore. 2007.
67. J Li and GQ Zhang (Eds.) Proceedings of 2009 Ohio Collaborative Conferences on Bioinformatics. IEEE Computer Society.
68. J Li and W-B Wang. "Tag SNP Selection" in Analysis of Complex Disease Association Studies. Editors: ZEGGINI & MORRIS. Elsevier. 2011.
69. X Li and J Li. "Haplotype Inference, a Practical Guide" in Statistical Human Genetics. Editors: , Elston, Satagopan and Sun. Humana Press. 2012.
70. X Yin and J Li. "Detection of copy number variations from array CGH data using linear-chain conditional random field models" in Probabilistic graphical models dedicated to applications in genetics/genomics/ postgenomics.
71. S Sun, R Shields, X Li and and J Li. Joint analysis of sequence data and SNP data using pedigree information for imputation and recombination inference
1. X-L Yin and J Li, A general graphical framework for detecting copy number variation. RECOMB'09, Tucson, AZ. Also presented at Case Research Showcase, April, 2009.
2. X Li and J Li. Zero recombinant haplotype inference with missing, RECOMB'08 Singapore.
3. S. Wu and J. Li. Comparative Analysis of Gene-coexpression Networks across Species. RECOMB Satellite Meeting on Systems Biology. Dec 2006. San Diego, CA.
4. Li, J. Prioritize and select SNPs for whole genome association studies with two-stage designs. HapMap conference, May 2006. Cambridge, MI.
5. Li, J. Association mapping of quantitative traits using haplotypes (Poster) ISMB'05
6. Li, J. and T. Jiang Efficient Haplotyping Algorithms for Pedigree Data. SIGCSE, Feb 2003 Reno, NV
7. Li, J. and T. Jiang Experimental Study on Phylogenetic Reconstruction Algorithms. 3rd Annual Industry Day of College of Engineering of Univ. of California, Riverside 2001(Poster).
8. Li, J. et al. Transmission disequilibrium mapping of QTL with polygenes background, The 31st MidWest Student BioMedical Research Forum 2000 (Poster)
9. Li, J. et al. The effect of selected sampling on TDT of QTL. 1st Annual Great Plains States Society for Molecular Biology and Genetics 2000 (Poster)
10. Jin-Long Li, Dong-Bing Lai, J. Li,Wei-Min Chen, Jian Li, Xu-Tao Deng, R. Recker and Hong-Wen Deng 2000 GENOTYPING DBMS-A database for managing the genotyping data. (1st Annual Great Plains States Society for Molecular Biology and Genetics; May19-20,2000 Poster)