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Items: 1 to 50 of 115

1.

HiLDA: a statistical approach to investigate differences in mutational signatures.

Yang Z, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD.

PeerJ. 2019 Aug 28;7:e7557. doi: 10.7717/peerj.7557. eCollection 2019.

2.

Deregulation of Biologically Significant Genes and Associated Molecular Pathways in the Oral Epithelium of Electronic Cigarette Users.

Tommasi S, Caliri AW, Caceres A, Moreno DE, Li M, Chen Y, Siegmund KD, Besaratinia A.

Int J Mol Sci. 2019 Feb 10;20(3). pii: E738. doi: 10.3390/ijms20030738.

3.

Data integration by multi-tuning parameter elastic net regression.

Liu J, Liang G, Siegmund KD, Lewinger JP.

BMC Bioinformatics. 2018 Oct 10;19(1):369. doi: 10.1186/s12859-018-2401-1.

4.

Association between AXL promoter methylation and lung function growth during adolescence.

Gao L, Urman R, Millstein J, Siegmund KD, Dubeau L, Breton CV.

Epigenetics. 2018;13(10-11):1027-1038. doi: 10.1080/15592294.2018.1529517. Epub 2018 Oct 19.

5.

Self-reported prenatal tobacco smoke exposure, AXL gene-body methylation, and childhood asthma phenotypes.

Gao L, Liu X, Millstein J, Siegmund KD, Dubeau L, Maguire RL, Jim Zhang J, Fuemmeler BF, Kollins SH, Hoyo C, Murphy SK, Breton CV.

Clin Epigenetics. 2018 Jul 20;10(1):98. doi: 10.1186/s13148-018-0532-x.

6.

Spatial mutation patterns as markers of early colorectal tumor cell mobility.

Ryser MD, Min BH, Siegmund KD, Shibata D.

Proc Natl Acad Sci U S A. 2018 May 29;115(22):5774-5779. doi: 10.1073/pnas.1716552115. Epub 2018 May 14.

7.

Comprehensive meta-analysis reveals association between multiple imprinting disorders and conception by assisted reproductive technology.

Cortessis VK, Azadian M, Buxbaum J, Sanogo F, Song AY, Sriprasert I, Wei PC, Yu J, Chung K, Siegmund KD.

J Assist Reprod Genet. 2018 Jun;35(6):943-952. doi: 10.1007/s10815-018-1173-x. Epub 2018 Apr 25. Review.

8.

Epigenetic regulation of AXL and risk of childhood asthma symptoms.

Gao L, Millstein J, Siegmund KD, Dubeau L, Maguire R, Gilliland FD, Murphy SK, Hoyo C, Breton CV.

Clin Epigenetics. 2017 Nov 7;9:121. doi: 10.1186/s13148-017-0421-8. eCollection 2017.

9.

Identifying aggressive prostate cancer foci using a DNA methylation classifier.

Mundbjerg K, Chopra S, Alemozaffar M, Duymich C, Lakshminarasimhan R, Nichols PW, Aron M, Siegmund KD, Ukimura O, Aron M, Stern M, Gill P, Carpten JD, Ørntoft TF, Sørensen KD, Weisenberger DJ, Jones PA, Duddalwar V, Gill I, Liang G.

Genome Biol. 2017 Jan 12;18(1):3. doi: 10.1186/s13059-016-1129-3.

10.

Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes.

Marconett CN, Zhou B, Sunohara M, Pouldar TM, Wang H, Liu Y, Rieger ME, Tran E, Flodby P, Siegmund KD, Crandall ED, Laird-Offringa IA, Borok Z.

Am J Respir Cell Mol Biol. 2017 Mar;56(3):310-321. doi: 10.1165/rcmb.2016-0071OC.

11.

Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers.

Chopra S, Liu J, Alemozaffar M, Nichols PW, Aron M, Weisenberger DJ, Collings CK, Syan S, Hu B, Desai M, Aron M, Duddalwar V, Gill I, Liang G, Siegmund KD.

Oncotarget. 2017 Jan 17;8(3):5439-5448. doi: 10.18632/oncotarget.12276.

12.

An evaluation of processing methods for HumanMethylation450 BeadChip data.

Liu J, Siegmund KD.

BMC Genomics. 2016 Jun 22;17:469. doi: 10.1186/s12864-016-2819-7.

13.

Particulate matter, the newborn methylome, and cardio-respiratory health outcomes in childhood.

Breton CV, Gao L, Yao J, Siegmund KD, Lurmann F, Gilliland F.

Environ Epigenet. 2016 Jun 12;2(2):dvw005. doi: 10.1093/eep/dvw005. eCollection 2016 Apr.

14.

Prenatal Air Pollution Exposures, DNA Methyl Transferase Genotypes, and Associations with Newborn LINE1 and Alu Methylation and Childhood Blood Pressure and Carotid Intima-Media Thickness in the Children's Health Study.

Breton CV, Yao J, Millstein J, Gao L, Siegmund KD, Mack W, Whitfield-Maxwell L, Lurmann F, Hodis H, Avol E, Gilliland FD.

Environ Health Perspect. 2016 Dec;124(12):1905-1912. Epub 2016 May 24.

15.

Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma.

Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund KD, Charlet J, Weisenberger DJ, Jones PA, Liang G.

Cancer Res. 2016 Apr 1;76(7):1954-64. doi: 10.1158/0008-5472.CAN-15-2622. Epub 2016 Jan 12.

16.

Identifying differential transcription factor binding in ChIP-seq.

Wu DY, Bittencourt D, Stallcup MR, Siegmund KD.

Front Genet. 2015 Apr 29;6:169. doi: 10.3389/fgene.2015.00169. eCollection 2015.

17.

Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history.

Weisenberger DJ, Levine AJ, Long TI, Buchanan DD, Walters R, Clendenning M, Rosty C, Joshi AD, Stern MC, LeMarchand L, Lindor NM, Daftary D, Gallinger S, Selander T, Bapat B, Newcomb PA, Campbell PT, Casey G, Ahnen DJ, Baron JA, Haile RW, Hopper JL, Young JP, Laird PW, Siegmund KD; Colon Cancer Family Registry.

Cancer Epidemiol Biomarkers Prev. 2015 Mar;24(3):512-519. doi: 10.1158/1055-9965.EPI-14-1161. Epub 2015 Jan 13.

18.

Distinct, genome-wide, gene-specific selectivity patterns of four glucocorticoid receptor coregulators.

Wu DY, Ou CY, Chodankar R, Siegmund KD, Stallcup MR.

Nucl Recept Signal. 2014 Nov 4;12:e002. doi: 10.1621/nrs.12002. eCollection 2014.

19.

Transcriptomic Profiling of Primary Alveolar Epithelial Cell Differentiation in Human and Rat.

Marconett CN, Zhou B, Siegmund KD, Borok Z, Laird-Offringa IA.

Genom Data. 2014 Dec 1;2:105-109.

20.

Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation.

Breton CV, Siegmund KD, Joubert BR, Wang X, Qui W, Carey V, Nystad W, Håberg SE, Ober C, Nicolae D, Barnes KC, Martinez F, Liu A, Lemanske R, Strunk R, Weiss S, London S, Gilliland F, Raby B; Asthma BRIDGE consortium.

PLoS One. 2014 Jun 25;9(6):e99716. doi: 10.1371/journal.pone.0099716. eCollection 2014. Erratum in: PLoS One. 2014;9(10):e112422.

21.

Non-specific filtering of beta-distributed data.

Wang X, Laird PW, Hinoue T, Groshen S, Siegmund KD.

BMC Bioinformatics. 2014 Jun 19;15:199. doi: 10.1186/1471-2105-15-199.

22.

Ancestral inference in tumors: how much can we know?

Zhao J, Siegmund KD, Shibata D, Marjoram P.

J Theor Biol. 2014 Oct 21;359:136-45. doi: 10.1016/j.jtbi.2014.05.027. Epub 2014 Jun 5.

23.

A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence.

Su SF, de Castro Abreu AL, Chihara Y, Tsai Y, Andreu-Vieyra C, Daneshmand S, Skinner EC, Jones PA, Siegmund KD, Liang G.

Clin Cancer Res. 2014 Apr 1;20(7):1978-89. doi: 10.1158/1078-0432.CCR-13-2637.

24.

Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue.

Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, Hutchinson A, Chen PH, Chung BS, Pesatori AC, Consonni D, Bertazzi PA, Bergen AW, Freedman M, Siegmund KD, Berman BP, Borok Z, Chatterjee N, Tucker MA, Caporaso NE, Chanock SJ, Laird-Offringa IA, Landi MT.

Nat Commun. 2014 Feb 27;5:3365. doi: 10.1038/ncomms4365.

25.

Recommendations for the design and analysis of epigenome-wide association studies.

Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA.

Nat Methods. 2013 Oct;10(10):949-55. doi: 10.1038/nmeth.2632. Review.

PMID:
24076989
26.

Null association between histology of first and second primary malignancies in men with bilateral testicular germ cell tumors.

Thomas JP, Davis-Dao C, Lewinger JP, Siegmund KD, Hamilton AS, Daneshmand S, Skinner EC, Thomas DC, Cortessis VK.

Am J Epidemiol. 2013 Oct 15;178(8):1240-5. doi: 10.1093/aje/kwt100. Epub 2013 Aug 8.

27.

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.

Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, Lynch SK, Stueve TR, Siegmund KD, Berman BP, Borok Z, Laird-Offringa IA.

PLoS Genet. 2013 Jun;9(6):e1003513. doi: 10.1371/journal.pgen.1003513. Epub 2013 Jun 20.

28.

Low-level processing of Illumina Infinium DNA Methylation BeadArrays.

Triche TJ Jr, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD.

Nucleic Acids Res. 2013 Apr;41(7):e90. doi: 10.1093/nar/gkt090. Epub 2013 Mar 9.

29.

Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23.

Schumacher FR, Wang Z, Skotheim RI, Koster R, Chung CC, Hildebrandt MA, Kratz CP, Bakken AC, Bishop DT, Cook MB, Erickson RL, Fosså SD, Greene MH, Jacobs KB, Kanetsky PA, Kolonel LN, Loud JT, Korde LA, Le Marchand L, Lewinger JP, Lothe RA, Pike MC, Rahman N, Rubertone MV, Schwartz SM, Siegmund KD, Skinner EC, Turnbull C, Van Den Berg DJ, Wu X, Yeager M, Nathanson KL, Chanock SJ, Cortessis VK, McGlynn KA.

Hum Mol Genet. 2013 Jul 1;22(13):2748-53. doi: 10.1093/hmg/ddt109. Epub 2013 Mar 5.

30.

G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of glucocorticoid receptor target genes.

Bittencourt D, Wu DY, Jeong KW, Gerke DS, Herviou L, Ianculescu I, Chodankar R, Siegmund KD, Stallcup MR.

Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):19673-8. doi: 10.1073/pnas.1211803109. Epub 2012 Nov 14.

31.

Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data.

Liu Y, Siegmund KD, Laird PW, Berman BP.

Genome Biol. 2012 Jul 11;13(7):R61. doi: 10.1186/gb-2012-13-7-r61.

32.

Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships.

Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, Laird PW.

Hum Genet. 2012 Oct;131(10):1565-89. doi: 10.1007/s00439-012-1189-8. Epub 2012 Jun 28. Review.

33.

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression.

Selamat SA, Chung BS, Girard L, Zhang W, Zhang Y, Campan M, Siegmund KD, Koss MN, Hagen JA, Lam WL, Lam S, Gazdar AF, Laird-Offringa IA.

Genome Res. 2012 Jul;22(7):1197-211. doi: 10.1101/gr.132662.111. Epub 2012 May 21.

34.

Particulate matter, DNA methylation in nitric oxide synthase, and childhood respiratory disease.

Breton CV, Salam MT, Wang X, Byun HM, Siegmund KD, Gilliland FD.

Environ Health Perspect. 2012 Sep;120(9):1320-6. doi: 10.1289/ehp.1104439. Epub 2012 May 16.

35.

Selective roles for cAMP response element-binding protein binding protein and p300 protein as coregulators for androgen-regulated gene expression in advanced prostate cancer cells.

Ianculescu I, Wu DY, Siegmund KD, Stallcup MR.

J Biol Chem. 2012 Feb 3;287(6):4000-13. doi: 10.1074/jbc.M111.300194. Epub 2011 Dec 15. Erratum in: J Biol Chem. 2012 Oct 19;287(43):35985.

36.

Genome-scale screen for DNA methylation-based detection markers for ovarian cancer.

Campan M, Moffitt M, Houshdaran S, Shen H, Widschwendter M, Daxenbichler G, Long T, Marth C, Laird-Offringa IA, Press MF, Dubeau L, Siegmund KD, Wu AH, Groshen S, Chandavarkar U, Roman LD, Berchuck A, Pearce CL, Laird PW.

PLoS One. 2011;6(12):e28141. doi: 10.1371/journal.pone.0028141. Epub 2011 Dec 7.

37.

Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors.

Wang X, Kang GH, Campan M, Weisenberger DJ, Long TI, Cozen W, Bernstein L, Wu AH, Siegmund KD, Shibata D, Laird PW.

PLoS One. 2011;6(10):e25985. doi: 10.1371/journal.pone.0025985. Epub 2011 Oct 20.

38.

Modeling measurement error in tumor characterization studies.

Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD.

BMC Bioinformatics. 2011 Jul 13;12:284. doi: 10.1186/1471-2105-12-284.

39.

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

Siegmund KD, Marjoram P, Tavaré S, Shibata D.

PLoS One. 2011;6(6):e21657. doi: 10.1371/journal.pone.0021657. Epub 2011 Jun 28.

40.

DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma.

Selamat SA, Galler JS, Joshi AD, Fyfe MN, Campan M, Siegmund KD, Kerr KM, Laird-Offringa IA.

PLoS One. 2011;6(6):e21443. doi: 10.1371/journal.pone.0021443. Epub 2011 Jun 23.

41.

Human and great ape red blood cells differ in plasmalogen levels and composition.

Moser AB, Steinberg SJ, Watkins PA, Moser HW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG.

Lipids Health Dis. 2011 Jun 17;10:101. doi: 10.1186/1476-511X-10-101.

42.

Heterogenous effect of androgen receptor CAG tract length on testicular germ cell tumor risk: shorter repeats associated with seminoma but not other histologic types.

Davis-Dao CA, Siegmund KD, Vandenberg DJ, Skinner EC, Coetzee GA, Thomas DC, Pike MC, Cortessis VK.

Carcinogenesis. 2011 Aug;32(8):1238-43. doi: 10.1093/carcin/bgr104. Epub 2011 Jun 3.

43.

Carcinogen metabolism genes, red meat and poultry intake, and colorectal cancer risk.

Wang J, Joshi AD, Corral R, Siegmund KD, Marchand LL, Martinez ME, Haile RW, Ahnen DJ, Sandler RS, Lance P, Stern MC.

Int J Cancer. 2012 Apr 15;130(8):1898-907. doi: 10.1002/ijc.26199. Epub 2011 Aug 8.

44.

Statistical approaches for the analysis of DNA methylation microarray data.

Siegmund KD.

Hum Genet. 2011 Jun;129(6):585-95. doi: 10.1007/s00439-011-0993-x. Epub 2011 Apr 26. Review.

45.

Polymorphisms in base excision repair genes as colorectal cancer risk factors and modifiers of the effect of diets high in red meat.

Brevik A, Joshi AD, Corral R, Onland-Moret NC, Siegmund KD, Le Marchand L, Baron JA, Martinez ME, Haile RW, Ahnen DJ, Sandler RS, Lance P, Stern MC.

Cancer Epidemiol Biomarkers Prev. 2010 Dec;19(12):3167-73. doi: 10.1158/1055-9965.EPI-10-0606. Epub 2010 Oct 29.

46.

Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions.

Watkins PA, Moser AB, Toomer CB, Steinberg SJ, Moser HW, Karaman MW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG.

BMC Physiol. 2010 Oct 8;10:19. doi: 10.1186/1472-6793-10-19.

47.

Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue.

Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund KD, Sugano K, Kawashima K, Laird PW, Jones PA, Liang G.

Cancer Res. 2010 Oct 15;70(20):8169-78. doi: 10.1158/0008-5472.CAN-10-1335. Epub 2010 Sep 14.

48.

The PREMM(1,2,6) model predicts risk of MLH1, MSH2, and MSH6 germline mutations based on cancer history.

Kastrinos F, Steyerberg EW, Mercado R, Balmaña J, Holter S, Gallinger S, Siegmund KD, Church JM, Jenkins MA, Lindor NM, Thibodeau SN, Burbidge LA, Wenstrup RJ, Syngal S.

Gastroenterology. 2011 Jan;140(1):73-81. doi: 10.1053/j.gastro.2010.08.021. Epub 2010 Aug 19. Erratum in: Gastroenterology. 2012 Nov;143(5):1399. Gastroenterology. 2012 Nov;143(5):1399.

49.

Using DNA methylation patterns to infer tumor ancestry.

Hong YJ, Marjoram P, Shibata D, Siegmund KD.

PLoS One. 2010 Aug 9;5(8):e12002. doi: 10.1371/journal.pone.0012002.

50.

Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer.

Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G.

PLoS Genet. 2010 Apr 22;6(4):e1000917. doi: 10.1371/journal.pgen.1000917.

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