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Copyright
Notice: The papers presented here are to ensure timely dissemination of
scholarly and technical work and only for personal or classroom use.
Copyright and all rights therein are retained by authors and/or by other
copyright holders. Extended versions of some conference publications have
been accepted by bioinformatics/computational biology journals. |
2013
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.
2012
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.
2011
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 (RECOMB’11),
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.
2010
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.
2009
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).
2008
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.
2007
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.
2006
46. Jing
Li, Yingyao Zhou and Robert C. Elston. Haplotype-based
Quantitative Trait Mapping Using a Clustering Algorithm. BMC Bioinformatics
2006, 7:258..
2005
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.
2004
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.
50. Jing
Li and Tao Jiang. Haplotype Association Mapping
by Density-Based Clustering in Case-Control Studies. Second RECOMB Satellite
Workshop on Computational Methods for SNPs and Haplotypes, 47-57.
2003
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.
52. Jing
Li and Tao Jiang. Efficient Inference
of Haplotypes from Genotype on a Pedigree. Journal of
Bioinformatics and Computational Biology(JBCB) 1(1):41-69.
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.
2002
57. Vedova,
G. D,, T. Jiang, J. Li and J. Wen. Approximating
Minimum Quartet Inconsistency. 14th
Annual proceedings of ACM-SIAM SODA 2002
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
2001
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
1999-2000
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.
Book Chapters
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.
Submitted
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
Posters
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)
Updated 03/15/2013.