Medical College of Wisconsin
CTSICores SearchResearch InformaticsREDCap

Pengyuan Liu PhD

Associate Professor

Institution: Medical College of Wisconsin
Department: Physiology
Program: Cancer Center

Member of the Cancer Center


Research Experience

  • Genome sequence analysis, Cancer genetics, Statistical genetics, Bioinformatics
  • Publications

  • Identification of the transforming STRN-ALK fusion as a potential therapeutic target in the aggressive forms of thyroid cancer. (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) Proc Natl Acad Sci U S A 2014 Mar 18;111(11):4233-8 PMID 24613930
  • Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer. (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) Proc Natl Acad Sci U S A 2014 Feb 11;111(6):E672-81 PMID 24469795
  • Base-resolution maps of 5-methylcytosine and 5-hydroxymethylcytosine in Dahl S rats: effect of salt and genomic sequence. (Liu Y, Liu P, Yang C, Cowley AW Jr, Liang M) Hypertension 2014 Apr;63(4):827-38 PMID 24420542
  • ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer. (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) Cancer 2014 Mar 15;120(6):799-807 PMID 24327398
  • EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk. (Wilson IM, Vucic EA, Enfield KS, Thu KL, Zhang YA, Chari R, Lockwood WW, Radulovich N, Starczynowski DT, BanĂ¡th 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) Oncogene 2014 Sep 4;33(36):4464-73 PMID 24096489
  • Characteristics of microRNAs enriched in specific cell types and primary tissue types in solid organs. (Kriegel AJ, Liu Y, Liu P, Baker MA, Hodges MR, Hua X, Liang M) Physiol Genomics 2013 Dec 1;45(23):1144-56 PMID 24085797
  • Concordant effects of aromatase inhibitors on gene expression in ER+ Rat and human mammary cancers and modulation of the proteins coded by these genes. (Lu Y, You M, Ghazoui Z, Liu P, Vedell PT, Wen W, Bode AM, Grubbs CJ, Lubet RA) Cancer Prev Res (Phila) 2013 Nov;6(11):1151-61 PMID 24067424
  • Targeting the endothelial progenitor cell surface proteome to identify novel mechanisms that mediate angiogenic efficacy in a rodent model of vascular disease. (Kaczorowski CC, Stodola TJ, Hoffmann BR, Prisco AR, Liu PY, Didier DN, Karcher JR, Liang M, Jacob HJ, Greene AS) Physiol Genomics 2013 Nov 1;45(21):999-1011 PMID 24022221
  • DrGaP: a powerful tool for identifying driver genes and pathways in cancer sequencing studies. (Hua X, Xu H, Yang Y, Zhu J, Liu P, Lu Y) Am J Hum Genet 2013 Sep 5;93(3):439-51 PMID 23954162
  • Functional genomic assessment of phosgene-induced acute lung injury in mice. (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) Am J Respir Cell Mol Biol 2013 Sep;49(3):368-83 PMID 23590305
  • Increased proliferative cells in the medullary thick ascending limb of the loop of Henle in the Dahl salt-sensitive rat. (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) Hypertension 2013 Jan;61(1):208-15 PMID 23184381
  • WNT1-inducible signaling pathway protein 1 contributes to ventilator-induced lung injury. (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) Am J Respir Cell Mol Biol 2012 Oct;47(4):528-35 PMID 22700866
  • Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients. (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) Carcinogenesis 2012 Sep;33(9):1797-805 PMID 22696596
  • Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. (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) Carcinogenesis 2012 Jul;33(7):1270-6 PMID 22510280
  • Integrative assessment of chlorine-induced acute lung injury in mice. (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) Am J Respir Cell Mol Biol 2012 Aug;47(2):234-44 PMID 22447970
  • MicroRNA profiling and prediction of recurrence/relapse-free survival in stage I lung cancer. (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) Carcinogenesis 2012 May;33(5):1046-54 PMID 22331473
  • Gene-expression signature predicts postoperative recurrence in stage I non-small cell lung cancer patients. (Lu Y, Wang L, Liu P, Yang P, You M) PLoS One 2012;7(1):e30880 PMID 22292069
  • Genome-wide association and fine mapping of genetic loci predisposing to colon carcinogenesis in mice. (Liu P, Lu Y, Liu H, Wen W, Jia D, Wang Y, You M) Mol Cancer Res 2012 Jan;10(1):66-74 PMID 22127497
  • Neutrophils are required for 3-methylcholanthrene-initiated, butylated hydroxytoluene-promoted lung carcinogenesis. (Vikis HG, Gelman AE, Franklin A, Stein L, Rymaszewski A, Zhu J, Liu P, Tichelaar JW, Krupnick AS, You M) Mol Carcinog 2012 Dec;51(12):993-1002 PMID 22006501
  • Modulation of gene expression and cell-cycle signaling pathways by the EGFR inhibitor gefitinib (Iressa) in rat urinary bladder cancer. (Lu Y, Liu P, Van den Bergh F, Zellmer V, James M, Wen W, Grubbs CJ, Lubet RA, You M) Cancer Prev Res (Phila) 2012 Feb;5(2):248-59 PMID 21982874
  • Principles for the post-GWAS functional characterization of cancer risk loci. (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) Nat Genet 2011 Jun;43(6):513-8 PMID 21614091
  • Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1. (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) Am J Respir Crit Care Med 2011 Jun 1;183(11):1499-509 PMID 21297076
  • Aerosolized bexarotene inhibits lung tumorigenesis without increasing plasma triglyceride and cholesterol levels in mice. (Zhang Q, Pan J, Zhang J, Liu P, Chen R, Chen DR, Lubet R, Wang Y, You M) Cancer Prev Res (Phila) 2011 Feb;4(2):270-6 PMID 21163938
  • Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models. (Lu Y, Liu P, Wen W, Grubbs CJ, Townsend RR, Malone JP, Lubet RA, You M) Am J Transl Res 2010;3(1):8-27 PMID 21139803
  • Functional genomics of chlorine-induced acute lung injury in mice. (Leikauf GD, Pope-Varsalona H, Concel VJ, Liu P, Bein K, Brant KA, Dopico RA, Di YP, Jang AS, Dietsch M, Medvedovic M, Li Q, Vuga LJ, Kaminski N, You M, Prows DR) Proc Am Thorac Soc 2010 Jul;7(4):294-6 PMID 20601635
  • A second genetic variant on chromosome 15q24-25.1 associates with lung cancer. (Liu P, Yang P, Wu X, Vikis HG, Lu Y, Wang Y, Schwartz AG, Pinney SM, de Andrade M, Gazdar A, Gaba C, Mandal D, Lee J, Kupert E, Seminara D, Minna J, Bailey-Wilson JE, Spitz M, Amos CI, Anderson MW, You M) Cancer Res 2010 Apr 15;70(8):3128-35 PMID 20395203
  • Cumulative effect of multiple loci on genetic susceptibility to familial lung cancer. (Liu P, Vikis HG, Lu Y, Wang Y, Schwartz AG, Pinney SM, Yang P, de Andrade M, Gazdar A, Gaba C, Mandal D, Lee J, Kupert E, Seminara D, Minna J, Bailey-Wilson JE, Amos CI, Anderson MW, You M) Cancer Epidemiol Biomarkers Prev 2010 Feb;19(2):517-24 PMID 20142248
  • Genetic variants cis-regulating Xrn2 expression contribute to the risk of spontaneous lung tumor. (Lu Y, Liu P, James M, Vikis HG, Liu H, Wen W, Franklin A, You M) Oncogene 2010 Feb 18;29(7):1041-9 PMID 19915612
  • Haplotype and cell proliferation analyses of candidate lung cancer susceptibility genes on chromosome 15q24-25.1. (Liu Y, Liu P, Wen W, James MA, Wang Y, Bailey-Wilson JE, Amos CI, Pinney SM, Yang P, de Andrade M, Petersen GM, Wiest JS, Fain PR, Schwartz AG, Gazdar A, Gaba C, Rothschild H, Mandal D, Kupert E, Lee J, Seminara D, Minna J, Anderson MW, You M) Cancer Res 2009 Oct 1;69(19):7844-50 PMID 19789337
  • Identification of Las2, a major modifier gene affecting the Pas1 mouse lung tumor susceptibility locus. (Liu PY, Vikis H, James M, Lu Y, Wang DL, Liu HB, Wen WD, Wang Y, You M) Cancer Res 2009 Aug 1;69(15):6290-8 PMID 19622765
  • Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5. (Wang JC, Cruchaga C, Saccone NL, Bertelsen S, Liu P, Budde JP, Duan W, Fox L, Grucza RA, Kern J, Mayo K, Reyes O, Rice J, Saccone SF, Spiegel N, Steinbach JH, Stitzel JA, Anderson MW, You M, Stevens VL, Bierut LJ, Goate AM, COGEND collaborators and GELCC collaborators) Hum Mol Genet 2009 Aug 15;18(16):3125-35 PMID 19443489
  • Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene. (You M, Wang D, Liu P, Vikis H, James M, Lu Y, Wang Y, Wang M, Chen Q, Jia D, Liu Y, Wen W, Yang P, Sun Z, Pinney SM, Zheng W, Shu XO, Long J, Gao YT, Xiang YB, Chow WH, Rothman N, Petersen GM, de Andrade M, Wu Y, Cunningham JM, Wiest JS, Fain PR, Schwartz AG, Girard L, Gazdar A, Gaba C, Rothschild H, Mandal D, Coons T, Lee J, Kupert E, Seminara D, Minna J, Bailey-Wilson JE, Amos CI, Anderson MW) Clin Cancer Res 2009 Apr 15;15(8):2666-74 PMID 19351763
  • Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. (Liu P, Vikis HG, Wang D, Lu Y, Wang Y, Schwartz AG, Pinney SM, Yang P, de Andrade M, Petersen GM, Wiest JS, Fain PR, Gazdar A, Gaba C, Rothschild H, Mandal D, Coons T, Lee J, Kupert E, Seminara D, Minna J, Bailey-Wilson JE, Wu X, Spitz MR, Eisen T, Houlston RS, Amos CI, Anderson MW, You M) J Natl Cancer Inst 2008 Sep 17;100(18):1326-30 PMID 18780872
  • Common human cancer genes discovered by integrated gene-expression analysis. (Lu Y, Yi Y, Liu P, Wen W, James M, Wang D, You M) PLoS One 2007;2(11):e1149 PMID 17989776
  • Large-scale in silico mapping of complex quantitative traits in inbred mice. (Liu P, Vikis H, Lu Y, Wang D, You M) PLoS One 2007;2(7):e651 PMID 17653278
  • A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. (Lu Y, Lemon W, Liu PY, Yi Y, Morrison C, Yang P, Sun Z, Szoke J, Gerald WL, Watson M, Govindan R, You M) PLoS Med 2006 Dec;3(12):e467 PMID 17194181
  • Candidate lung tumor susceptibility genes identified through whole-genome association analyses in inbred mice. (Liu P, Wang Y, Vikis H, Maciag A, Wang D, Lu Y, Liu Y, You M) Nat Genet 2006 Aug;38(8):888-95 PMID 16862160
  • Accurate haplotype inference for multiple linked single-nucleotide polymorphisms using sibship data. (Liu PY, Lu Y, Deng HW) Genetics 2006 Sep;174(1):499-509 PMID 16783022
  • Impacts of QTL x environment interactions on genetic response to marker-assisted selection. (Liu PY, Zhu J, Yan L) Yi Chuan Xue Bao 2006 Jan;33(1):63-71 PMID 16450589
  • Improvement of mapping accuracy by unifying linkage and association analysis. (Lou XY, Ma JZ, Yang MC, Zhu J, Liu PY, Deng HW, Elston RC, Li MD) Genetics 2006 Jan;172(1):647-61 PMID 16172505
  • Hotelling's T2 multivariate profiling for detecting differential expression in microarrays. (Lu Y, Liu PY, Xiao P, Deng HW) Bioinformatics 2005 Jul 15;21(14):3105-13 PMID 15905280
  • A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases. (Liu PY, Zhang YY, Lu Y, Long JR, Shen H, Zhao LJ, Xu FH, Xiao P, Xiong DH, Liu YJ, Recker RR, Deng HW) J Med Genet 2005 Mar;42(3):221-7 PMID 15744035
  • A two-step strategy for detecting differential gene expression in cDNA microarray data. (Lu Y, Zhu J, Liu P) Curr Genet 2005 Feb;47(2):121-31 PMID 15688252
  • Common variants at the PCOL2 and Sp1 binding sites of the COL1A1 gene and their interactive effect influence bone mineral density in Caucasians. (Liu PY, Lu Y, Long JR, Xu FH, Shen H, Recker RR, Deng HW) J Med Genet 2004 Oct;41(10):752-7 PMID 15466008
  • Quantifying the relationship between gene expressions and trait values in general pedigrees. (Lu Y, Liu PY, Liu YJ, Xu FH, Deng HW) Genetics 2004 Dec;168(4):2395-405 PMID 15371358
  • Marker-assisted selection in segregating generations of self-fertilizing crops. (Liu P, Zhu J, Lu Y) Theor Appl Genet 2004 Jul;109(2):370-6 PMID 15069599
  • Robust indices of Hardy-Weinberg disequilibrium for QTL fine mapping. (Deng HW, Li YM, Li MX, Liu PY) Hum Hered 2003;56(4):160-5 PMID 15031618
  • Complex segregation analyses of bone mineral density in Chinese. (Liu PY, Qin YJ, Zhou Q, Recker RR, Deng HW) Ann Hum Genet 2004 Mar;68(Pt 2):154-64 PMID 15008794
  • A method for marker-assisted selection based on QTLs with epistatic effects. (Liu P, Zhu J, Lou X, Lu Y) Genetica 2003 Sep;119(1):75-86 PMID 12903749