Medical College of Wisconsin
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CURRICULUM VITAE

Pengyuan Liu PhD
Adjunct Professor
Department of Physiology

OFFICE ADDRESS:
Basic Science Building
8701 Watertown Plank Rd
Milwaukee, WI 53226

EDUCATION:
09/1992 - 08/1996 BS, Zhejiang University, Hangzhou, China
09/1996 - 01/2002 PhD, Zhejiang University, Hangzhou, China

POSTGRADUATE TRAINING AND FELLOWSHIP APPOINTMENTS:
04/2002 - 11/2004 Postdoctoral Fellow, Osteoporosis Research Center, Statistical Genetics, Creighton University, Omaha, NE
12/2004 - 12/2006 Postdoctoral Associate, Dept of Surgery and Siteman Cancer Center, Statistical Genetics, Washington University, St. Louis, MO

FACULTY APPOINTMENTS:
01/2007 - 08/2010 Research Assistant Professor, Department of Surgery, Washington University, St. Louis, MO
09/2010 - Present Associate Professor, Department of Physiology & Cancer Center, Medical College of Wisconsin, Milwaukee, WI

AWARDS AND HONORS:
07/1996 Outstanding Undergraduate , Zhejiang Province, China
09/1999 Guanghua Award, Zhejiang University, China
11/2010 The First Prize for Natural Science of Colleges and Universities, Ministry of Education of China

MEMBERSHIPS IN HONORARY AND PROFESSIONAL SOCIETIES:
American Association for Cancer Research (Member)
American Society of Human Genetics (Member)

EDITORSHIPS/EDITORIAL BOARDS/JOURNAL REVIEWS:
Editorial Board
2010 - Present Frontiers in Statistical Genetics and Methodology
Journal Review
2003 - Present Genetica
2005 - 2006 Genetics
2005 - 2006 Annals of Human Genetics
2007 Hormone and Metabolic Research
2009 Osteoporosis International
2010 - Present Statistics and Its Interface
2010 - Present PLoS One

RESEARCH GRANTS/AWARDS/CONTRACTS/PROJECTS:
Active
Peer Review
Title:
Molecular Genetics of Lung Tumor Promotion in Mice
Source:
NCI
Role:
Co-Principal Investigator
Dates:
07/01/2009 - 06/30/2014
Direct Funds:
$76,000
 
Title:
Genome-Wide Association Studies of Inherited Predisposition to Lung Cancer
Source:
NCI
Role:
Co-Principal Investigator
Dates:
07/01/2009 - 06/30/2014
Direct Funds:
$1,434,431
 
Title:
Environment & Genetics of Monoclonal Gammopathy of Uncertain Significance
Source:
NIH Aging
Role:
sub-PI
Dates:
07/01/2011 - 06/30/2013
Direct Funds:
$47,943
 

INVITED LECTURES/WORKSHOPS/PRESENTATIONS:
Regional
Genome-wide association studies of lung cancer, Department of Internal Medicine, University of Iowa, 11/03/2008
Genetic Susceptibility to Lung Cancer, Cancer Center, University of Kansas, 10/16/2009
 
National
Genetic Susceptibility to Lung Cancer, Department of Genetics, University of North Carolina at Chapel Hill, 06/10/2009
Genetic Susceptibility to Lung Cancer, Vanderbilt Epidemiology Center, Department of Medicine, Vanderbilt University, Nashville, TN, 02/22/2010
 

EXTRAMURAL TEACHING:
Medical Student Education
09/1999 - 12/1999 Zhejiang University, Hangzhou, China, Elementary Genetics
02/2001 - 06/2001 Zhejiang University, Hangzhou, China, Genetic Data Analysis
01/2003 - 04/2003 Creighton University, Omaha, NE, Population/Quantitative and Molecular Genetics
 


BIBLIOGRAPHY
Refereed Journal Publications/Original Papers
1. Deng HW, Li YM, Li MX, Liu PY. Robust indices of Hardy-Weinberg disequilibrium for QTL fine mapping. Hum Hered. 2003;56:160-5.
2. 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.
3. Long J, Liu P, Zhang Y, Shen H, Liu Y, Dvornyk V, et al. Interaction effects between estrogen receptor alpha gene, vitamin D receptor gene, age, and sex on bone mineral density in Chinese. J Hum Genet. 2003;48:514-9.
4. 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.
5. Zhang YY, Liu PY, Deng HW. The impact of reproductive and menstrual history on bone mineral density in Chinese women. J Clin Densitom. 2003;6:289-96.
6. Zhang YY, Long JR, Liu PY, Liu YJ, Shen H, Zhao LJ, et al. Estrogen receptor alpha and vitamin D receptor gene polymorphisms and bone mineral density: association study of healthy pre- and postmenopausal Chinese women. Biochem Biophys Res Commun. 2003;308:777-83.
7. Dvornyk V, Long JR, Xiong DH, Liu PY, Zhao LJ, Shen H, et al. Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. BMC Genet. 2004;5:4.
8. Li MX, Liu PY, Li YM, Qin YJ, Liu YZ, Deng HW. A major gene model of adult height is suggested in Chinese. J Hum Genet. 2004;49:148-53.
9. Liu P, Zhu J, Lu Y. Marker-assisted selection in segregating generations of self-fertilizing crops. Theor Appl Genet. 2004;109:370-6.
10. Liu PY, Li YM, Li MX, Malkin I, Qin YJ, Chen XD, et al. Lack of evidence for a major gene in the Mendelian transmission of BMI in Chinese. Obes Res. 2004;12:1967-73.
11. 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.
12. Liu PY, Qin YJ, Recker RR, Deng HW. Evidence for a major gene underlying bone size variation in the Chinese. Am J Hum Biol. 2004;16:68-77.
13. Liu PY, Qin YJ, Zhou Q, Recker RR, Deng HW. Complex segregation analyses of bone mineral density in Chinese. Ann Hum Genet. 2004;68:154-64.
14. 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.
15. 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.
16. 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.
17. Long JR, Zhang YY, Liu PY, Liu YJ, Shen H, Dvornyk V, et al. Association of estrogen receptor alpha and vitamin D receptor gene polymorphisms with bone mineral density in Chinese males. Calcif Tissue Int. 2004;74:270-6.
18. 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.
19. 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.
20. Shen H, Zhang YY, Long JR, Xu FH, Liu YZ, Xiao P, et al. A genome-wide linkage scan for bone mineral density in an extended sample: evidence for linkage on 11q23 and Xq27. J Med Genet. 2004;41:743-51.
21. 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.
22. Dvornyk V, Liu PY, Long JR, Zhang YY, Lei SF, Recker RR, et al. Contribution of genotype and ethnicity to bone mineral density variation in Caucasians and Chinese: a test for five candidate genes for bone mass. Chin Med J (Engl). 2005;118:1235-44.
23. 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.
24. 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.
25. 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.
26. Long JR, Xu H, Zhao LJ, Liu PY, Shen H, Liu YJ, et al. The oestrogen receptor alpha gene is linked and/or associated with age of menarche in different ethnic groups. J Med Genet. 2005;42:796-800.
27. Lu Y, Liu PY, Xiao P, Deng HW. Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. Bioinformatics. 2005;21:3105-13.
28. Lu Y, Zhu J, Liu P. A two-step strategy for detecting differential gene expression in cDNA microarray data. Curr Genet. 2005;47:121-31.
29. Shen H, Liu Y, Liu P, Recker RR, Deng HW. Nonreplication in genetic studies of complex diseases--lessons learned from studies of osteoporosis and tentative remedies. J Bone Miner Res. 2005;20:365-76.
30. Shen H, Long JR, Xiong DH, Liu YJ, Liu YZ, Xiao P, et al. Mapping quantitative trait loci for cross-sectional geometry at the femoral neck. J Bone Miner Res. 2005;20:1973-82.
31. 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.
32. Xiong DH, Liu YZ, Liu PY, Zhao LJ, Deng HW. Association analysis of estrogen receptor alpha gene polymorphisms with cross-sectional geometry of the femoral neck in Caucasian nuclear families. Osteoporos Int. 2005;16:2113-22.
33. Xiong DH, Xu FH, Liu PY, Shen H, Long JR, Elze L, et al. Vitamin D receptor gene polymorphisms are linked to and associated with adult height. J Med Genet. 2005;42:228-34.
34. 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.
35. Dvornyk V, Long JR, Liu PY, Shen H, Recker RR, Deng HW. Polymorphisms of the vitamin D receptor gene predict the onset of surgical menopause in Caucasian females. Gynecol Endocrinol. 2006;22:552-6.
36. Dvornyk V, Long JR, Liu PY, Zhao LJ, Shen H, Recker RR, et al. Predictive factors for age at menopause in Caucasian females. Maturitas. 2006;54:19-26.
37. 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.
38. Liu PY, Lu Y, Deng HW. Accurate haplotype inference for multiple linked single-nucleotide polymorphisms using sibship data. Genetics. 2006;174:499-509.
39. Lou XY, Ma JZ, Yang MC, Zhu J, Liu PY, Deng HW, et al. Improvement of mapping accuracy by unifying linkage and association analysis. Genetics. 2006;172:647-61.
40. 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.
41. Xiao P, Liu P, Weber JL, Papasian CJ, Recker RR, Deng HW. Paternal uniparental isodisomy of the entire chromosome 3 revealed in a person with no apparent phenotypic disorders. Hum Mutat. 2006;27:133-7.
42. 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.
43. Zhao LJ, Liu PY, Recker R, Deng HW. Correlation of transmenopausal bone mass in healthy white women: a long-term longitudinal study. Osteoporos Int. 2006;17:1501-5.
44. Liu PY, Zhu J, Lu Y. Impacts of QTL x environment interactions on genetic response to marker-assisted selection. Yi Chuan Xue Bao. 2006;33:63-71
45. Deng FY, Xiao P, Lei SF, Zhang L, Yang F, Tang ZH, et al. Bivariate whole genome linkage analysis for femoral neck geometric parameters and total body lean mass. J Bone Miner Res. 2007;22:808-16.
46. 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.
47. 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.
48. Zhao LJ, Liu YJ, Liu PY, Hamilton J, Recker RR, Deng HW. Relationship of obesity with osteoporosis. J Clin Endocrinol Metab. 2007;92:1640-6.
49. 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.
50. Tan LJ, Liu YZ, Xiao P, Yang F, Tang ZH, Liu PY, et al. Evidence for major pleiotropic effects on bone size variation from a principal component analysis of 451 Caucasian families. Acta Pharmacol Sin. 2008;29:745-51.
51. Chen Y, Shen H, Yang F, Liu PY, Tang N, Recker RR, et al. Choice of study phenotype in osteoporosis genetic research. J Bone Miner Metab. 2009;27:121-6.
52. 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.
53. Liu Y, Liu P, Wen W, James MA, Wang Y, Bailey-Wilson JE, et al. Haplotype and cell proliferation analyses of candidate lung cancer susceptibility genes on chromosome 15q24-25.1. Cancer Res. 2009;69:7844-50.
54. Wang JC, Cruchaga C, Saccone NL, Bertelsen S, Liu P, Budde JP, et al. Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5. Hum Mol Genet. 2009;18:3125-35.
55. 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.
56. Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Brant KA, et al. Functional genomics of chlorine-induced acute lung injury in mice. Proc Am Thorac Soc. 2010;7:294-6.
57. 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.
58. 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.
59. 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.
60. 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.
61. 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.
62. 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.
63. Modulation of Gene Expression and Cell Cycle Signaling Pathways in Iressa-treated Urinary Bladder Cancer in Rats. Lu Y, Liu P, Wen W, Grubbs CJ, Lubet RA, You M. Cancer Prev Res (Phila). Cancer Prev Res (Phila). 2012 Feb;5(2):248-59.
64. Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA Jr, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional genomic assessment of phosgene-induced acute lung injury in mice. Am J Respir Cell Mol Biol. 2013 Sep;49(3):368-83. PMCID: PMC3824050
65. Lu Y, Liu P, Wen W, Grubbs CJ, Townsend RR, Malone JP, Lubet RA, You M. Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models. Am J Transl Res. 2010 Sep 20;3(1):8-27. PMCID: PMC2981423
66. Zhang Q, Pan J, Zhang J, Liu P, Chen R, Chen DR, Lubet R, Wang Y, You M. Aerosolized bexarotene inhibits lung tumorigenesis without increasing plasma triglyceride and cholesterol levels in mice. Cancer Prev Res (Phila). 2011 Feb;4(2):270-6.
67. Leikauf GD, Concel VJ, Liu P, Bein K, Berndt A, Ganguly K, Jang AS, Brant KA, Dietsch M, Pope-Varsalona H, Dopico RA Jr, Di YP, Li Q, Vuga LJ, Medvedovic M, Kaminski N, You M, Prows DR. Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1. Am J Respir Crit Care Med. 2011 Jun 01;183(11):1499-509. PMCID: PMC3137140
68. Freedman ML, Monteiro AN, Gayther SA, Coetzee GA, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D, James M, Liu P, Tichelaar JW, Vikis HG, You M, Mills IG. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet. 2011 Jun;43(6):513-8. PMCID: PMC3325768
69. 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.
70. 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. PMCID: PMC3264655
71. Lu Y, Liu P, Van den Bergh F, Zellmer V, James M, Wen W, Grubbs CJ, Lubet RA, You M. Modulation of gene expression and cell-cycle signaling pathways by the EGFR inhibitor gefitinib (Iressa) in rat urinary bladder cancer. Cancer Prev Res (Phila). 2012 Feb;5(2):248-59.
72. Lu Y, Govindan R, Wang L, Liu PY, Goodgame B, Wen W, Sezhiyan A, Pfeifer J, Li YF, 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. PMCID: PMC3334512
73. Vikis HG, Gelman AE, Franklin A, Stein L, Rymaszewski A, Zhu J, Liu P, Tichelaar JW, Krupnick AS, You M. Neutrophils are required for 3-methylcholanthrene-initiated, butylated hydroxytoluene-promoted lung carcinogenesis. Mol Carcinog. 2012 Dec;51(12):993-1002. PMCID: PMC3389580
74. Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA Jr, Upadhyay S, Di YP, Li Q, Hu Z, Vuga LJ, Medvedovic M, Kaminski N, You M, Alexander DC, McDunn JE, Prows DR, Knoell DL, Fabisiak JP. Integrative assessment of chlorine-induced acute lung injury in mice. Am J Respir Cell Mol Biol. 2012 Aug;47(2):234-44. PMCID: PMC3423464
75. Liu P, Morrison C, Wang L, Xiong D, Vedell P, Cui P, Hua X, Ding F, Lu Y, James M, Ebben JD, Xu H, Adjei AA, Head K, Andrae JW, Tschannen MR, Jacob H, Pan J, Zhang Q, Van den Bergh F, Xiao H, Lo KC, Patel J, Richmond T, Watt MA, Albert T, Selzer R, Anderson M, Wang J, Wang Y, Starnes S, Yang P, You M. Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis. 2012 Jul;33(7):1270-6. PMCID: PMC3499051
76. Xiong D, Li G, Li K, Xu Q, Pan Z, Ding F, Vedell P, Liu P, Cui P, Hua X, Jiang H, Yin Y, Zhu Z, Li X, Zhang B, Ma D, Wang Y, You M. Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients. Carcinogenesis. 2012 Sep;33(9):1797-805. PMCID: PMC3514907
77. Li HH, Li Q, Liu P, Liu Y, Li J, Wasserloos K, Chao W, You M, Oury TD, Chhinder S, Hackam DJ, Billiar TR, Leikauf GD, Pitt BR, Zhang LM. WNT1-inducible signaling pathway protein 1 contributes to ventilator-induced lung injury. Am J Respir Cell Mol Biol. 2012 Oct;47(4):528-35. PMCID: PMC3488625
78. Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA Jr, Upadhyay S, Cario C, Di YP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional genomic assessment of phosgene-induced acute lung injury in mice. Am J Respir Cell Mol Biol. 2013 Sep;49(3):368-83. PMCID: PMC3824050
79. 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 Nov;6(11):1151-61. PMCID: PMC3874590
80. Wilson IM, Vucic EA, Enfield KS, Thu KL, Zhang YA, Chari R, Lockwood WW, Radulovich N, Starczynowski DT, Banáth JP, Zhang M, Pusic A, Fuller M, Lonergan KM, Rowbotham D, Yee J, English JC, Buys TP, Selamat SA, Laird-Offringa IA, Liu P, Anderson M, You M, Tsao MS, Brown CJ, Bennewith KL, MacAulay CE, Karsan A, Gazdar AF, Lam S, Lam WL. EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk. Oncogene. 2014 Sep 04;33(36):4464-73. PMCID: PMC4527534
81. 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 Sep 05;93(3):439-51. PMCID: PMC3769934
82. Liu Y, Liu P, Yang C, Cowley AW Jr, Liang M. Base-resolution maps of 5-methylcytosine and 5-hydroxymethylcytosine in Dahl S rats: effect of salt and genomic sequence. Hypertension. 2014 Apr;63(4):827-38. PMCID: PMC4315612
83. Kriegel AJ, Liu Y, Liu P, Baker MA, Hodges MR, Hua X, Liang M. Characteristics of microRNAs enriched in specific cell types and primary tissue types in solid organs. Physiol Genomics. 2013 Dec 01;45(23):1144-56. PMCID: PMC3882707
84. Kaczorowski CC, Stodola TJ, Hoffmann BR, Prisco AR, Liu PY, Didier DN, Karcher JR, Liang M, Jacob HJ, Greene AS. Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediate angiogenic efficacy in a rodent model of vascular disease. Physiol Genomics. 2013 Nov 01;45(21):999-1011. PMCID: PMC3841789
85. Yang C, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Skelton M, O'Connor P, Kurth T, Ryan RP, Moreno C, Tsaih SW, Patone G, Hummel O, Jacob HJ, Liang M, Cowley AW Jr. Increased proliferative cells in the medullary thick ascending limb of the loop of Henle in the Dahl salt-sensitive rat. Hypertension. 2013 Jan;61(1):208-15. PMCID: PMC3760736
86. Leeman-Neill RJ, Kelly LM, Liu P, Brenner AV, Little MP, Bogdanova TI, Evdokimova VN, Hatch M, Zurnadzy LY, Nikiforova MN, Yue NJ, Zhang M, Mabuchi K, Tronko MD, Nikiforov YE. ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer. Cancer. 2014 Mar 15;120(6):799-807. PMCID: PMC3947712
87. Morrison CD, Liu P, Woloszynska-Read A, Zhang J, Luo W, Qin M, Bshara W, Conroy JM, Sabatini L, Vedell P, Xiong D, Liu S, Wang J, Shen H, Li Y, Omilian AR, Hill A, Head K, Guru K, Kunnev D, Leach R, Eng KH, Darlak C, Hoeflich C, Veeranki S, Glenn S, You M, Pruitt SC, Johnson CS, Trump DL. Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer. Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):E672-81. PMCID: PMC3926024
88. Kelly LM, Barila G, Liu P, Evdokimova VN, Trivedi S, Panebianco F, Gandhi M, Carty SE, Hodak SP, Luo J, Dacic S, Yu YP, Nikiforova MN, Ferris RL, Altschuler DL, Nikiforov YE. Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer. Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4233-8. PMCID: PMC3964116
89. Liu P, Liu Y, Liu H, Pan X, Li Y, Usa K, Mishra MK, Nie J, Liang M. Role of DNA De Novo (De)Methylation in the Kidney in Salt-Induced Hypertension. Hypertension. 2018 11;72(5):1160-1171. PMCID: PMC6314686
90. Li Y, Pan X, Roberts ML, Liu P, Kotchen TA, Cowley AW Jr, Mattson DL, Liu Y, Liang M, Kidambi S. Stability of global methylation profiles of whole blood and extracted DNA under different storage durations and conditions. Epigenomics. 2018 06;10(6):797-811.
91. Evans LC, Dayton A, Yang C, Liu P, Kurth T, Ahn KW, Komas S, Stingo FC, Laud PW, Vannucci M, Liang M, Cowley AW Jr. Transcriptomic analysis reveals inflammatory and metabolic pathways that are regulated by renal perfusion pressure in the outer medulla of Dahl-S rats. Physiol Genomics. 2018 06 01;50(6):440-447. PMCID: PMC6032288
92. Gao F, Liu P, Narayanan J, Yang M, Fish BL, Liu Y, Liang M, Jacobs ER, Medhora M. Changes in miRNA in the lung and whole blood after whole thorax irradiation in rats. Sci Rep. 2017 03 17;7:44132. PMCID: PMC5355888
93. 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 04;26(4):642-650.
94. Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie SA, Palleschi A, Alloisio M, Pariscenti G, Jones K, Zhou W, Bouk AJ, Boland J, Hicks B, Risch A, Bennett H, Luke BT, Song L, Duan J, Liu P, Kohno T, Chen Q, Meerzaman D, Marconett C, Laird-Offringa I, Mills I, Caporaso NE, Gail MH, Pesatori AC, Consonni D, Bertazzi PA, Chanock SJ, Landi MT. Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study. PLoS Med. 2016 Dec;13(12):e1002162. PMCID: PMC5140047
95. Amend SR, Wilson WC, Chu L, Lu L, Liu P, Serie D, Su X, Xu Y, Wang D, Gramolini A, Wen XY, O'Neal J, Hurchla M, Vachon CM, Colditz G, Vij R, Weilbaecher KN, Tomasson MH. Whole Genome Sequence of Multiple Myeloma-Prone C57BL/KaLwRij Mouse Strain Suggests the Origin of Disease Involves Multiple Cell Types. PLoS One. 2015;10(5):e0127828. PMCID: PMC4447437
96. 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;10(5):e0125412. PMCID: PMC4418692
97. 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, Wang L. Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet. 2015 Jan 01;24(1):154-66. PMCID: PMC4262497
98. Wang LS, Burke CA, Hasson H, Kuo CT, Molmenti CL, Seguin C, Liu P, Huang TH, Frankel WL, Stoner GD. A phase Ib study of the effects of black raspberries on rectal polyps in patients with familial adenomatous polyposis. Cancer Prev Res (Phila). 2014 Jul;7(7):666-74.
99. Chen EG, Liu P, Lu Y. Cancer genomics: new software tools making sequencing more accessible. Per Med. 2014 Mar;11(2):127-130.
100. Sun X, Han Y, Zhou L, Chen E, Lu B, Liu Y, Pan X, Cowley AW Jr, Liang M, Wu Q, Lu Y, Liu P. A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data. Bioinformatics. 2018 08 15;34(16):2715-2723.
101. Cheng Y, Song H, Pan X, Xue H, Wan Y, Wang T, Tian Z, Hou E, Lanza IR, Liu P, Liu Y, Laud PW, Usa K, He Y, Liang M. Urinary Metabolites Associated with Blood Pressure on a Low- or High-Sodium Diet. Theranostics. 2018;8(6):1468-1480. PMCID: PMC5858161
102. Stodola TJ, Liu P, Liu Y, Vallejos AK, Geurts AM, Greene AS, Liang M. Genome-wide map of proximity linkage to renin proximal promoter in rat. Physiol Genomics. 2018 05 01;50(5):323-331. PMCID: PMC6008118
103. Widlansky ME, Jensen DM, Wang J, Liu Y, Geurts AM, Kriegel AJ, Liu P, Ying R, Zhang G, Casati M, Chu C, Malik M, Branum A, Tanner MJ, Tyagi S, Usa K, Liang M. miR-29 contributes to normal endothelial function and can restore it in cardiometabolic disorders. EMBO Mol Med. 2018 03;10(3). PMCID: PMC5840545
104. Williams AM, Liu Y, Regner KR, Jotterand F, Liu P, Liang M. Artificial intelligence, physiological genomics, and precision medicine. Physiol Genomics. 2018 04 01;50(4):237-243. PMCID: PMC5966805
105. Chuppa S, Liang M, Liu P, Liu Y, Casati MC, Cowley AW, Patullo L, Kriegel AJ. MicroRNA-21 regulates peroxisome proliferator-activated receptor alpha, a molecular mechanism of cardiac pathology in Cardiorenal Syndrome Type 4. Kidney Int. 2018 02;93(2):375-389. PMCID: PMC5787401
106. Baker MA, Davis SJ, Liu P, Pan X, Williams AM, Iczkowski KA, Gallagher ST, Bishop K, Regner KR, Liu Y, Liang M. Tissue-Specific MicroRNA Expression Patterns in Four Types of Kidney Disease. J Am Soc Nephrol. 2017 Oct;28(10):2985-2992. PMCID: PMC5619963
107. Puissant MM, Mouradian GC Jr, Liu P, Hodges MR. Identifying Candidate Genes that Underlie Cellular pH Sensitivity in Serotonin Neurons Using Transcriptomics: A Potential Role for Kir5.1 Channels. Front Cell Neurosci. 2017;11:34. PMCID: PMC5318415
108. Mouradian GC Jr, Liu P, Hodges MR. Raphe gene expression changes implicate immune-related functions in ventilatory plasticity following carotid body denervation in rats. Exp Neurol. 2017 Jan;287(Pt 2):102-112. PMCID: PMC5086315
109. Wei Q, Liu Y, Liu P, Hao J, Liang M, Mi QS, Chen JK, Dong Z. MicroRNA-489 Induction by Hypoxia-Inducible Factor-1 Protects against Ischemic Kidney Injury. J Am Soc Nephrol. 2016 09;27(9):2784-96. PMCID: PMC5004659
110. Cowley AW Jr, Yang C, Kumar V, Lazar J, Jacob H, Geurts AM, Liu P, Dayton A, Kurth T, Liang M. Pappa2 is linked to salt-sensitive hypertension in Dahl S rats. Physiol Genomics. 2016 Jan;48(1):62-72. PMCID: PMC4757026
111. Kriegel AJ, Baker MA, Liu Y, Liu P, Cowley AW Jr, Liang M. Endogenous microRNAs in human microvascular endothelial cells regulate mRNAs encoded by hypertension-related genes. Hypertension. 2015 Oct;66(4):793-9. PMCID: PMC4567475
112. Chu C, Fang Z, Hua X, Yang Y, Chen E, Cowley AW Jr, Liang M, Liu P, Lu Y. deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies. BMC Genomics. 2015 Jun 13;16:455. PMCID: PMC4465298
113. Karcher JR, Hoffmann BR, Liu P, Liu Y, Liang M, Greene AS. Genome-wide epigenetic and proteomic analysis reveals altered Notch signaling in EPC dysfunction. Physiol Rep. 2015 Apr;3(4). PMCID: PMC4425964
114. Puissant MM, Echert AE, Yang C, Mouradian GC Jr, Novotny T, Liu P, Liang M, Hodges MR. RNASeq-derived transcriptome comparisons reveal neuromodulatory deficiency in the CO₂ insensitive brown Norway rat. J Physiol. 2015 01 15;593(2):415-30. PMCID: PMC4303386
115. Geurts AM, Mattson DL, Liu P, Cabacungan E, Skelton MM, Kurth TM, Yang C, Endres BT, Klotz J, Liang M, Cowley AW Jr. Maternal diet during gestation and lactation modifies the severity of salt-induced hypertension and renal injury in Dahl salt-sensitive rats. Hypertension. 2015 Feb;65(2):447-55. PMCID: PMC4289102
116. Wang F, Li L, Xu H, Liu Y, Yang C, Cowley AW Jr, Wang N, Liu P, Liang M. Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat. Sci Rep. 2014 Nov 21;4:7146. PMCID: PMC4894415
117. 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 01;31(1):25-32. PMCID: PMC4296142
118. Cowley AW Jr, Moreno C, Jacob HJ, Peterson CB, Stingo FC, Ahn KW, Liu P, Vannucci M, Laud PW, Reddy P, Lazar J, Evans L, Yang C, Kurth T, Liang M. Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats. Physiol Genomics. 2014 Jun 01;46(11):398-410. PMCID: PMC4042181
119. Ilatovskaya DV, Levchenko V, Pavlov TS, Isaeva E, Klemens CA, Johnson J, Liu P, Kriegel AJ, Staruschenko A. Salt-deficient diet exacerbates cystogenesis in ARPKD via epithelial sodium channel (ENaC). EBioMedicine. 2019 Feb;40:663-674. PMCID: PMC6413684
120. Wei Q, Sun H, Song S, Liu Y, Liu P, Livingston MJ, Wang J, Liang M, Mi QS, Huo Y, Nahman NS, Mei C, Dong Z. MicroRNA-668 represses MTP18 to preserve mitochondrial dynamics in ischemic acute kidney injury. J Clin Invest. 2018 12 03;128(12):5448-5464. PMCID: PMC6264638
121. Kong Y, Lu Z, Liu P, Liu Y, Wang F, Liang EY, Hou FF, Liang M. Long Noncoding RNA: Genomics and Relevance to Physiology. Compr Physiol. 2019 06 12;9(3):933-946.
122. Zhang L, Zhou Q, Qiu Q, Hou L, Wu M, Li J, Li X, Lu B, Cheng X, Liu P, Lu W, Lu Y. CircPLEKHM3 acts as a tumor suppressor through regulation of the miR-9/BRCA1/DNAJB6/KLF4/AKT1 axis in ovarian cancer. Mol Cancer. 2019 10 17;18(1):144. PMCID: PMC6796346
123. Abais-Battad JM, Alsheikh AJ, Pan X, Fehrenbach DJ, Dasinger JH, Lund H, Roberts ML, Kriegel AJ, Cowley AW Jr, Kidambi S, Kotchen TA, Liu P, Liang M, Mattson DL. Dietary Effects on Dahl Salt-Sensitive Hypertension, Renal Damage, and the T Lymphocyte Transcriptome. Hypertension. 2019 10;74(4):854-863. PMCID: PMC6739138
124. Abais-Battad JM, Alsheikh AJ, Pan X, Fehrenbach DJ, Dasinger JH, Lund H, Roberts ML, Kriegel AJ, Cowley AW Jr, Kidambi S, Kotchen TA, Liu P, Liang M, Mattson DL. Dietary Effects on Dahl Salt-Sensitive Hypertension, Renal Damage, and the T Lymphocyte Transcriptome. Hypertension. 2019 10;74(4):854-863. PMCID: PMC6739138
125. Lai PY, Jing X, Michalkiewicz T, Entringer B, Ke X, Majnik A, Kriegel AJ, Liu P, Lane RH, Konduri GG. Adverse early-life environment impairs postnatal lung development in mice. Physiol Genomics. 2019 09 01;51(9):462-470. PMCID: PMC6766700
126. Han Y, Yang J, Qian X, Cheng WC, Liu SH, Hua X, Zhou L, Yang Y, Wu Q, Liu P, Lu Y. DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies. Nucleic Acids Res. 2019 05 07;47(8):e45. PMCID: PMC6486576
127. Han Y, Yang J, Qian X, Cheng WC, Liu SH, Hua X, Zhou L, Yang Y, Wu Q, Liu P, Lu Y. DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies. Nucleic Acids Res. 2019 05 07;47(8):e45. PMCID: PMC6486576
128. Li X, Li J, Wu P, Zhou L, Lu B, Ying K, Chen E, Lu Y, Liu P. Smoker and non-smoker lung adenocarcinoma is characterized by distinct tumor immune microenvironments OncoImmunology. 3 October 2018;7(10).
129. Yao D, Zhang L, Zheng M, Sun X, Lu Y, Liu P. Circ2Disease: a manually curated database of experimentally validated circRNAs in human disease. Sci Rep. 2018 07 20;8(1):11018. PMCID: PMC6054656
130. Efanov AA, Brenner AV, Bogdanova TI, Kelly LM, Liu P, Little MP, Wald AI, Hatch M, Zurnadzy LY, Nikiforova MN, Drozdovitch V, Leeman-Neill R, Mabuchi K, Tronko MD, Chanock SJ, Nikiforov YE. Investigation of the Relationship Between Radiation Dose and Gene Mutations and Fusions in Post-Chernobyl Thyroid Cancer. J Natl Cancer Inst. 2018 04 01;110(4):371-378. PMCID: PMC6059206
131. 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 07 06;36(27):3925-3933.
132. Panebianco F, Kelly LM, Liu P, Zhong S, Dacic S, Wang X, Singhi AD, Dhir R, Chiosea SI, Kuan SF, Bhargava R, Dabbs D, Trivedi S, Gandhi M, Diaz R, Wald AI, Carty SE, Ferris RL, Lee AV, Nikiforova MN, Nikiforov YE. <i>THADA</i> fusion is a mechanism of IGF2BP3 activation and IGF1R signaling in thyroid cancer. Proc Natl Acad Sci U S A. 2017 02 28;114(9):2307-2312. PMCID: PMC5338560
133. Xu J, Zhou W, Yang F, Chen G, Li H, Zhao Y, Liu P, Li H, Tan M, Xiong X, Sun Y. The β-TrCP-FBXW2-SKP2 axis regulates lung cancer cell growth with FBXW2 acting as a tumour suppressor. Nat Commun. 2017 01 16;8:14002. PMCID: PMC5241824
134. 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 associated with complete hydatidiform mole in Chinese Han women Oncotarget. 2017;8(43):75264-75271.
135. Lu Y, Liu PY, Deng HW. Multivariate Analysis of Microarray Data Using Hotelling's T <sup>2</sup> Test Medical Biostatistics for Complex Diseases. 19 July 2010:113-130.
 
Books, Chapters, and Reviews
1. Lu Y. Liu P, Deng H.W. Multivariate analysis of microarray data using Hotelling's T2 test. In Medical Biostatistics for Complex Diseases, edited by F. Emmert-Streib and M. Dehmer. Wiley-VCH; 2010. p. 113-30.
 
Abstracts
1. Lu Y, Liu PY, Deng HW, "Quantifying the relationship between gene expressions and clinical traits in general pedigrees". The American Society of Human Genetics 53rd Annual Meeting, Los Angeles, California, USA, November 4-8, 2003.
2. Zhao LJ, Long JR, Shen H, Liu PY, Zhang YY, Xiao P, Xiong DH, Elze L, Recker RR, Deng HW, "Testing Association and Linkage of 8 Candidate Genes with BMD in 405 Caucasian Families Using Multiple SNP Markers and Haplotypes" The American Society for Bone and Mineral Research 25th Annual Meeting, Minneapolis, Minnesota, USA, September 18-23, 2003.
3. Deng HW, Shen H, Liu YJ, Liu PY, Recker RR. "Non-replication in Genetic Studies of Complex Diseases-Lessons Learned from Osteoporosis". The American Society for Bone and Mineral Research 26th Annual Meeting, Seattle, Washington, USA, October 1-5, 2004.
4. Liu PY, Vikis H, Wang Y, You M, "In silico fine-mapping of genetic loci for mammary metastasis in mice". The American Society of Human Genetics 55th Annual Meeting, Salt Lake City, Utah, October 25-29, 2005.
5. Lou XY, Ma JZ, Yang MCK, Zhu J, Liu PY, Deng HW, Elston RC, Li MD. 2005. "Improvement of mapping accuracy by unifying linkage and association analyses". The American Society of Human Genetics 55th Annual Meeting, Salt Lake City, Utah, October 25-29, 2005.
6. Lu Y, 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.