Medical College of Wisconsin
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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 PMCID: PMC3964116 03/13/2014
  • 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 PMCID: PMC3926024 01/29/2014
  • 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 PMCID: PMC4315612 01/15/2014
  • 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 PMCID: PMC3947712 12/12/2013
  • 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 04;33(36):4464-73 PMID: 24096489 PMCID: PMC4527534 10/08/2013
  • 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 01;45(23):1144-56 PMID: 24085797 PMCID: PMC3882707 10/03/2013
  • 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 PMCID: PMC3874590 09/27/2013
  • 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 01;45(21):999-1011 PMID: 24022221 PMCID: PMC3841789 09/12/2013
  • 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 05;93(3):439-51 PMID: 23954162 PMCID: PMC3769934 08/21/2013
  • 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 PMCID: PMC3824050 04/18/2013
  • 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 PMCID: PMC3760736 11/28/2012
  • 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 PMCID: PMC3488625 06/16/2012
  • 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 PMCID: PMC3514907 06/15/2012
  • 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 PMCID: PMC3499051 04/19/2012
  • 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 PMCID: PMC3423464 03/27/2012
  • 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 PMCID: PMC3334512 02/15/2012
  • 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 PMCID: PMC3264655 02/01/2012
  • 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 12/01/2011
  • 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 PMCID: PMC3389580 10/19/2011
  • 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 10/11/2011
  • 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 PMCID: PMC3325768 05/27/2011
  • 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 01;183(11):1499-509 PMID: 21297076 PMCID: PMC3137140 02/08/2011
  • 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 12/18/2010
  • 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 Sep 20;3(1):8-27 PMID: 21139803 PMCID: PMC2981423 12/09/2010
  • 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 PMCID: PMC3136967 07/06/2010
  • 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 PMCID: PMC3378320 04/17/2010
  • 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 PMCID: PMC2846747 02/10/2010
  • 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 11/17/2009
  • 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 01;69(19):7844-50 PMID: 19789337 PMCID: PMC2846106 10/01/2009
  • 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 01;69(15):6290-8 PMID: 19622765 07/23/2009
  • 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 PMCID: PMC2714722 05/16/2009
  • 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 PMCID: PMC2746091 04/09/2009
  • 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 PMCID: PMC2538550 09/11/2008
  • 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 Nov 07;2(11):e1149 PMID: 17989776 PMCID: PMC2065803 11/09/2007
  • 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 Jul 25;2(7):e651 PMID: 17653278 PMCID: PMC1920557 07/27/2007
  • 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 PMCID: PMC1716187 12/30/2006
  • 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 07/25/2006
  • 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 PMCID: PMC1569787 06/20/2006
  • 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 02/03/2006
  • 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 PMCID: PMC1456190 09/21/2005
  • 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 05/21/2005
  • 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 PMCID: PMC1736011 03/04/2005
  • 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 02/03/2005
  • 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 PMCID: PMC1735608 10/07/2004
  • 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 PMCID: PMC1448709 09/17/2004
  • 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 04/08/2004
  • 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 03/20/2004
  • 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 03/11/2004
  • 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 08/09/2003
  • Last update: 04/28/2014
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