1. Liu P, Zhu J, Lou X, Lu Y. A method for marker-assisted selection based on QTLs with epistatic effects. Genetica. 2003;119:75-86.
2. Long JR, Liu PY, Liu YJ, Lu Y, Xiong DH, Elze L, et al. APOE and TGF-beta1 genes are associated with obesity phenotypes. J Med Genet. 2003;40:918-24.
3. Liu P, Zhu J, Lu Y. Marker-assisted selection in segregating generations of self-fertilizing crops. TheorAppl Genet. 2004;109:370-6.
4. Liu PY, Lu Y, Long JR, Xu FH, Shen H, Recker RR, et al. Common variants at the PCOL2 and Sp1 binding sites of the COL1A1 gene and their interactive effect influence bone mineral density in Caucasians. J Med Genet. 2004;41:752-7.
5. Liu YJ, Rocha-Sanchez SM, Liu PY, Long JR, Lu Y, Elze L, et al. Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families. Physiol Genomics. 2004;17:101-6.
6. Long JR, Liu PY, Liu YJ, Lu Y, Shen H, Zhao LJ, et al. APOE haplotypes influence bone mineral density in Caucasian males but not females. Calcif Tissue Int. 2004;75:299-304.
7. Long JR, Liu PY, Lu Y, Xiong DH, Zhao LJ, Zhang YY, et al. Association between COL1A1 gene polymorphisms and bone size in Caucasians. Eur J Hum Genet. 2004;12:383-8.
8. Long JR, Zhao LJ, Liu PY, Lu Y, Dvornyk V, Shen H, et al. Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes. BMC Genet. 2004;5:11.
9. Lu Y, Liu PY, Liu YJ, Xu FH, Deng HW. Quantifying the relationship between gene expressions and trait values in general pedigrees. Genetics. 2004;168:2395-405.
10. Zhao LJ, Liu PY, Long JR, Lu Y, Xu FH, Zhang YY, et al. Test of linkage and/or association between the estrogen receptor alpha gene with bone mineral density in Caucasian nuclear families. Bone. 2004;35:395-402.
11. Liu PY, Zhang YY, Lu Y, Long JR, Shen H, Zhao LJ, et al. A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases. J Med Genet. 2005;42:221-7.
12. Liu YJ, Liu PY, Long J, Lu Y, Elze L, Recker RR, et al. Linkage and association analyses of the UCP3 gene with obesity phenotypes in Caucasian families. Physiol Genomics. 2005;22:197-203.
13. Liu YZ, Dvornyk V, Lu Y, Shen H, Lappe JM, Recker RR, et al. A novel pathophysiological mechanism for osteoporosis suggested by an in vivo gene expression study of circulating monocytes.J Biol Chem. 2005;280:29011-6.
14. Long JR, Liu PY, Lu Y, Dvornyk V, Xiong DH, Zhao LJ, et al. Tests of linkage and/or association of TGF-beta1 and COL1A1 genes with bone mass. Osteoporos Int. 2005;16:86-92.
15. Lu Y, Zhu J, Liu PY. A two-step strategy for detecting differential gene expression of cDNA microarray data.Curr Genet.2005;47:121-131.
16. Lu Y, Liu PY, Xiao P, Deng HW. Hotelling's T2 multivariate profiling for detecting differential expression in microarrays.Bioinformatics. 2005;21:3105-13.
17. Xiao P, Liu PY, Lu Y, Guo YF, Xiong DH, Li LH, et al. Association tests of interleukin-6 (IL-6) and type II tumor necrosis factor receptor (TNFR2) genes with bone mineral density in Caucasians using a re-sampling approach. Hum Genet. 2005;117:340-8.
18. Zhang YY, Liu PY, Lu Y, Davies KM, Dvornyk V, Recker RR, et al. Race and sex differences and contribution of height: a study on bone size in healthy Caucasians and Chinese. Am J Hum Biol. 2005;17:568-75.
19. Liu P, Wang Y, Vikis H, Maciag A, Wang D, Lu Y, et al. Candidate lung tumor susceptibility genes identified through whole-genome association analyses in inbred mice. Nat Genet. 2006;38:888-95.
20. Liu PY, Lu Y, Deng HW. Accurate haplotype inference for multiple linked single-nucleotide polymorphisms using sibship data.Genetics. 2006;174:499-509.
21. Liu PY, Zhu J, Lu Y. Impacts of QTL x environment interactions on genetic response to marker-assisted selection. Yi ChuanXueBao. 2006;33:63-71.
22. Lu Y, Lemon W, Liu PY, Yi Y, Morrison C, Yang P, et al. A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med. 2006;3:e467.
23. Lu Y, Yao R, Yan Y, Wang Y, Hara Y, Lubet RA, et al. A gene expression signature that can predict green tea exposure and chemopreventive efficacy of lung cancer in mice.Cancer Res. 2006;66:1956-63.
24. Yan Y, Lu Y, Wang M, Vikis H, Yao R, Wang Y, et al. Effect of an epidermal growth factor receptor inhibitor in mouse models of lung cancer. Mol Cancer Res. 2006;4:971-81.
25. Yao R, Wang Y, Lu Y, Lemon WJ, End DW, Grubbs CJ, et al. Efficacy of the farnesyltransferase inhibitor R115777 in a rat mammary tumor model: role of Ha-ras mutations and use of microarray analysis in identifying potential targets. Carcinogenesis. 2006;27:1420-31.
26. Zhang YY, Liu PY, Lu Y, Xiao P, Liu YJ, Long JR, et al. Tests of linkage and association of PTH/PTHrP receptor type 1 gene with bone mineral density and height in Caucasians. J Bone Miner Metab. 2006;24:36-41.
27. Liu P, Vikis H, Lu Y, Wang D, You M. Large-scale in silico mapping of complex quantitative traits in inbred mice. PLoS One. 2007;2:e651.
28. Lu Y, Yi Y, Liu P, Wen W, James M, Wang D, et al. Common human cancer genes discovered by integrated gene-expression analysis. PLoS One. 2007;2:e1149.
29. Liu P, Vikis HG, Wang D, Lu Y, Wang Y, Schwartz AG, et al. Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. J Natl Cancer Inst. 2008;100:1326-30.
30. James MA, Lu Y, Liu Y, Vikis HG, You M. RGS17, an overexpressed gene in human lung and prostate cancer, induces tumor cell proliferation through the cyclic AMP-PKA-CREB pathway. Cancer Res. 2009;69:2108-16.
31. Liu PY, Vikis H, James M, Lu Y, Wang DL, Liu HB, et al. Identification of Las2, a major modifier gene affecting the Pas1 mouse lung tumor susceptibility locus. Cancer Res. 2009;69:6290-8.
32. You M, Wang D, Liu P, Vikis H, James M, Lu Y, et al. Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene. Clin Cancer Res. 2009;15:2666-74.
33. Liu P, Lu Y, Recker RR, Deng HW, Dvornyk V. ALOX12 gene is associated with the onset of natural menopause in white women. Menopause. 2010;17:152-6.
34. Liu P, Lu Y, Recker RR, Deng HW, Dvornyk V. Association analyses suggest multiple interaction effects of the methylenetetrahydrofolate reductase polymorphisms on timing of menarche and natural menopause in white women. Menopause. 2010;17:185-90.
35. Liu P, Vikis HG, Lu Y, Wang Y, Schwartz AG, Pinney SM, et al. Cumulative effect of multiple loci on genetic susceptibility to familial lung cancer. Cancer Epidemiol Biomarkers Prev. 2010;19:517-24.
36. Liu P, Yang P, Wu X, Vikis HG, Lu Y, Wang Y, et al. A second genetic variant on chromosome 15q24-25.1 associates with lung cancer.Cancer Res. 2010;70:3128-35.
37. Lu Y, Liu P, James M, Vikis HG, Liu H, Wen W, et al. Genetic variants cis-regulating Xrn2 expression contribute to the risk of spontaneous lung tumor. Oncogene. 2010;29:1041-9.
38. Lu Y, Liu P, Recker RR, Deng HW, Dvornyk V. TNFRSF11A and TNFSF11 are associated with age at menarche and natural menopause in white women. Menopause. 2010;17:1048-54.
39. Wang Y, James M, Wen W, Lu Y, Szabo E, Lubet RA, et al. Chemopreventive effects of pioglitazone on chemically induced lung carcinogenesis in mice. Mol Cancer Ther. 2010;9:3074-82.
40. Lu Y, Liu P, Wen W, Grubbs CJ, Townsend RR, Malone JP, et al. Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models. Am J Translational Res. 2011;3:8-21.
41. Fu H, Zhang J, Pan J, Zhang Q, Lu Y, Wen W, Lubet RA, Szabo E, Chen R, Wang Y, Chen DR, You M. Chemoprevention of Lung Carcinogenesis bythe Combination of Aerosolized Budesonide andOral Pioglitazone in A/J Mice. MolCarcinog. 2011 Mar 3. doi: 10.1002/mc.20751.
42. Lubet RA, Lu Y, Bode AM, You M, Verney ZM, Steele VE, Townsend R, Juliana MM, Grubbs CJ.Efficacy of the EGFr inhibitor Iressa on development of chemically-induced urinary bladder cancers: dose dependency and modulation of biomarkers.Oncol Rep. 2011 25(5):1389-97.
43. Lu Y, Liu YZ, Liu PY, Dvornyk V, Deng HW. A bootstrap-based regression method for comprehensive discovery of differential gene expressions: An application to the osteoporosis study. Eur J Med Genet.2011 Jul 30.
44. LuY, Liu P, Van den BerghF, Zellmer V, James M, Wen W, Grubbs CJ, Lubet RA, and You M. Modulation of Gene Expression and Cell Cycle Signaling Pathways in Iressa-treated Urinary Bladder Cancer in Rats. Cancer Prevention Research.2012 Feb;5(2):248-59.
45. Liu P, Lu Y, Liu H, Wen W, Jia D, Wang Y, You M. Genome-wide association and fine mapping of genetic loci predisposing to colon carcinogenesis in mice.Mol Cancer Res. 2012 Jan;10(1):66-74. Epub 2011 Nov 29.
46. Lu Y, Govindan R, Wang L, Liu P, Goodgame B, Wen W, Sezhiyan A, Li Y, Hua X, Wang Y, Yang P, You M. MicroRNA profiling and prediction of recurrence/relapse-free survival in stage I lung cancer. Carcinogenesis. 2012 May;33(5):1046-54.
47. Lu Y, Wang L, Liu P, Yang P, You M.Gene-expression signature predicts postoperative recurrence in stage I non-small cell lung cancer patients. PLoS One. 2012;7(1):e30880..
48. Liu P, Morrison C, Wang L, Xiong D, Vedell P, Cui P, Hua X, Ding F, Lu Y, et al. Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing.Carcinogenesis.2012;33(7):1270-6
49. Vedell P, Lu Y, Grubbs C, Yin Y, Jiang H, Bland K, Muccio DD, Cvetkovic D, You M, Lubet R. Effects on Gene Expression in Rat Liver after Administration of RXR Agonists:
UAB30, 4-Methyl-UAB30, and Targretin (Bexarotene).MolPharmacol2013;83(3):698-708
50. Hua X, Xu H, Yang Y, Zhu J, Liu P*,Lu Y*.DrGaP: A Powerful Tool for Identifying Driver Genes and Pathways in Cancer Sequencing Studies.Am J Hum Genet. 2013;93(3):439-51 (co-corresponding author).
51. Lu Y, You M, Ghazoui Z, Liu P, Vedell PT, Wen W, Bode AM, Grubbs CJ, Lubet RA. Concordant Effects of Aromatase Inhibitors on Gene Expression in ER+ Rat and Human Mammary Cancers and Modulation of the Proteins Coded by these Genes.Cancer Prev Res (Phila).2013 Sep 25.[Epub ahead of print].
52. Nicastro HL, Grubbs CJ, Juliana MM, Bode AM, Kim MS, Lu Y, You M, Milne G, Boring D, Steele VE, Lubet RA.Preventive effects of NSAIDs, NO-NSAIDs, and NSAIDs plus difluoromethylornithine in a chemically induced urinary bladder cancer model.Cancer Prev Res (Phila).2013 Dec 17. [Epub ahead of print]
53. Chen E, Liu P, Lu Y*. Cancer genomics: new software tools making sequencing more accessible. Personalized Medicine.2014, 2.
54. Huang X, Yuan T, Liang M, Du M, Xia S, DittmarR, Wang D, See W, Costello BA, QuevedoF, Tan W,NandyD, Bevan GH, LongenbachS, Sun Z, Lu Y,Wang T, Thibodeaum SN, Boardman L, Kohli M, Wang L. Exosomal miR-1290 and miR-375 as Prognostic Markers in Castration-resistantProstate Cancer. Eur Urol (2014), http://dx.doi.org/10.1016/j.eururo.2014.07.035
55. Du M, Yuan T, Schilter KF, Dittmar RL, Mackinnon A, Huang X, Tschannen M, Worthey E, Jacob H, Xia S, Gao J, Tillmans L, Lu Y, Liu P, Thibodeau SN, Liang Wang. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome.Human Molecular Genetics (2014).p38γ MAPK is required for inflammation-associated colon tumorigenesis
56. Chu C, Fang Z, Hua X, Yang Y, Chen E, Cowley A, Liang M, Liu P*, Lu Y*. deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies. BMC Genomics. 2015 http://www.biomedcentral.com/1471-2164/16/455 (co-corresponding author)
57. Li L, Chen E, Yang C, Zhu J, Jayaraman P, De Pons J, Kaczorowski CC, Jacob HJ, Greene AS, Hodges MR, Cowley AW Jr, Liang M, Xu H, Liu P*, Lu Y*. Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. Bioinformatics. 2015 Jan 1;31(1):25-32. doi: 10.1093/bioinformatics/btu608. (co-corresponding author).
58. Olasz EB, Seline LN, Schock AM, Duncan NE, Lopez A, Lazar J, Flister MJ, Lu Y, Liu P, Sokumbi O, Harwood CA, Proby CM, Neuburg M, Lazarova Z. MicroRNA-135b Regulates Leucine Zipper Tumor Suppressor 1 in Cutaneous Squamous Cell Carcinoma. PLoS One. 2015 May 4;10(5):e0125412.
59. Xu H, Ma Y, Zhang Y, Pan Z, Lu Y, Liu P, Lu B. Identification of Cathepsin K in the Peritoneal Metastasis of Ovarian Carcinoma Using In-silico, Gene Expression Analysis. J Cancer. 2016 Mar 26;7(6):722-9.
60. Yin N, Qi X, Tsai S, Lu Y, Basir Z, Oshima K, Thomas JP, Myers CR, Stoner G, Chen G. p38γ MAPK is required for inflammation-associated colon tumorigenesis. Oncogene. 2016 Feb 25;35(8):1039-48.
61. Dong A, Lu Y, Lu B. Genomic/Epigenomic Alterations in Ovarian Carcinoma: Translational Insight into Clinical Practice. J Cancer. 2016 Jul 5;7(11):1441-51.
62. Ma Y, Lu Y, Lu B. MicroRNA and Long Non-Coding RNA in Ovarian Carcinoma: Translational Insights and Potential Clinical Applications. Cancer Invest. 2016 Oct 20;34(9):465-476.
63. Liu P, Iden M, Fye S, Huang YW, Hopp E, Chu C, Lu Y, Rader JS. Targeted, deep sequencing reveals full methylation profiles of multiple HPV types and potential biomarkers for cervical cancer progression. Cancer Epidemiol Biomarkers Prev. 2017 Apr;26(4):642-650.
64. Zhang H#, Lu Y#, Chen E#, Li X, Lv B , Vikis HG, Liu P*, XRN2 promotes EMT and metastasis through regulating maturation of miR-10a. Oncogene. 2017 Jul 6; 36(27):3925-3933.。
65. Yu Y, Lu B, Lu W, Li S, Li X, Wang X, Wan X, Chen Y, Feng S, Jia Y, Yang R, Tang F, Li X, Zhang S, Wang X, Wei H, Peng Z, Lu L, Zhong H, Zhao L, Huang Z, Lin L, Shen W, Lu Y, Cao Z, Zou J, Ma Y, Chen X, Tian Q, Lu S, Liu P*, Ma D*, Xie X*, Cheng X*. Whole-exome sequencing reveals genetic variants in ERC1 and KCNG4 in complete hydatidiform moles from Chinese Han women. Oncotarget. 2017 Sep 8;8(43):75264-75271.
66. Xiwei Sun#, Yi Han#, Liyuan Zhou, Enguo Chen, Bingjian Lv, Yong Liu, Xiaoqing Pan, Allen W. Cowley, Jr. , Mingyu Liang, Qingbiao Wu, Yan Lu*, Pengyuan Liu*. A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data. Bioinformatics. 2018 Mar 22. doi: 10.1093/bioinformatics/bty174.
BOOKS, CHAPTERS & REVIEWS
Lu Y. Liu P, Deng H.W. Multivariate analysis of microarray data using Hotelling's T2 test. InMedical Biostatistics for Complex Diseases, edited by F. Emmert-Streib and M. Dehmer.Wiley-VCH; 2010. p. 113-30.
CONFERENCE ABSTRACTS
1. Lu Y, Liu PY, Deng HW, “Quantifying the relationship between gene expressionsand clinical traits in general pedigrees”. The American Society of Human Genetics 53rdAnnual Meeting, Los Angeles, California, USA, November 4-8, 2003.
2. Lu Y, Yao R, Yang P, Sun ZF, Watson M, Govindan R, You M, “Gene-expression profiles predict survival of patients with stage I non-small cell lung cancer: Results of a meta-analysis of four microarray studies”. The American Society of Human Genetics 55th AnnualMeeting, Salt Lake City, Utah, October 25-29, 2005.
3. Liu P, Vikis H, Lu Y, Wang D, You M, “Large-scale in silico mapping of complex quantitative traits in inbred mice”.The American Society of Human Genetics 57th AnnualMeeting, San Diego, California, October 23-27, 2007.
4. Lu Y, Yi Y, Liu PY, James M, Wang D, You M, “Common human cancer genes discovered by integrated gene-expression analysis”.The American Society of Human Genetics 57th AnnualMeeting, San Diego, California, October 23-27, 2007.
5. Lu Y, Liu PY, Wang Y, Grubbs CJ, Lubet RA, You M,“A gene expression signature predicts chemopreventive response of a EGFR inhibitor in a rat mammary tumor model”, The31st Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, December 10-14, 2008.
6. LuY, Liu P, Wen W, Grubbs CJ, Lubet RA, and You M. “Modulation of gene expression and cell cycle signaling pathways in Iressa-treated urinary bladder cancer in rats”,American Association for Cancer Research 102rd Annual Meeting, Orlando, Florida, April 2-6, 2011.
7. Liu PY, Yang C, Tschannen M, Lu Y, Jacob H, Liang MY, Cowley A., “RNA-seq Reveals Numerous Novel Transcripts, Transcript Isoforms, and Sequence Variations in the Dahl Salt-Sensitive Rat”, American Heart Association's Council for High Blood Pressure Research 2011 Scientific Sessions, Orlando, Florida, September 20-24, 2011.
8. Yang C, Lu Y, Liang MY, Cowley A, “ The Dahl Salt-sensitive and the Injury-resistant Hypertensive Consomic SS.2BN Rat Exhibit Distinct Renal Molecular Responses to High Salt”, American Heart Association's Council for High Blood Pressure Research 2011 Scientific Sessions, Orlando, Florida, September 20-24, 2011.
9. Liu PY, Hua X, Xu HM, Park S, Lu Y, “A General Statistical Approach to Somatic Mutation Discovery in Cancer Genome Sequence”, the 12th International Congress of Human Genetics/American Society of Human Genetics 61st Annual Meeting, Montreal, Canada, October 11-15, 2011.
10. Lu Y, Hua X, Xu HM, Liu PY, “DrGaP: A powerful tool for identifying driver genes and pathways in cancer sequencing studies”,American Association for Cancer Research 103rd Annual Meeting, Chicago, Illinois, March 31-April 4, 2012.
11. OlaszEB, NeuburgM, LazarJ, DuncanNE, Schock AM,Seline L, Lopez A, Lu Y, Liu P, Lazarova Z, “MicroRNAs signatures in cutaneous squamous cell carcinomas of immunocompetent and organ transplant patients”. 2012 SID Annual Meeting, Raleigh, North Carolina, May 9–12, 2012.
12. Liu P, Chu C, Hua X, Lu Y, Liang M. A New Statistical Method for Identifying Differentially Methylated Regions in Complex Diseases. American Society of Human Genetics 63rd Annual Meeting, Boston, Massachusett, October 22-26, 2013.
13. Lu Y, Vikis H, Liu P. The allelic variants of Dock9 contribute to urethane-induced lung tumor susceptibility. American Association for Cancer Research 105rd Annual Meeting, San Diego, California, April 5-9, 2014.
