Faculty

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Kimberly Siegmund, PhD
Professor of Preventive Medicine
Preventive Medicine
SSB 202W 2001 N. Soto Street Health Sciences Campus Los Angeles
+1 323 442 1310

Overview

Dr. Siegmund is a biostatistician with expertise in cancer modeling and the statistical analysis of epigenetic data in human disease. She has published numerous papers studying DNA methylation, and teaches a course on the statistical analysis of high-dimensional data. Her current research focuses on developing mathematical models to understand the growth and spread of cancer. These models address fundamental questions about aging through modeling cell division processes from a molecular phylogenetic approach.

Dr. Siegmund is interested the analysis of DNA methylation and gene expression data. She is developing mathematical models that will allow the identification of disease sub-types based on DNA methylation profiles. Other interests and skills relate to the design and analysis of family studies for gene characterization.

Publications

Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund KD, Charlet J, Weisenberger DJ, Jones PA, Liang G. Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma. Cancer Res. 2016 Apr 1; 76(7):1954-64. View in: PubMed

Siegmund K, Shibata D. At least two well-spaced samples are needed to genotype a solid tumor. BMC Cancer. 2016; 16(1):250. View in: PubMed

Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016; 17(1):469. View in: PubMed

Kang H, Salomon MP, Sottoriva A, Zhao J, Toy M, Press MF, Curtis C, Marjoram P, Siegmund K, Shibata D. Many private mutations originate from the first few divisions of a human colorectal adenoma. J Pathol. 2015 Nov; 237(3):355-62. View in: PubMed

Weisenberger DJ, Levine AJ, Long TI, Buchanan DD, Walters R, Clendenning M, Rosty C, Joshi AD, Stern MC, Le Marchand 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. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history. Cancer Epidemiol Biomarkers Prev. 2015 Mar; 24(3):512-9. View in: PubMed

Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, Marjoram P, Siegmund K, Press MF, Shibata D, Curtis C. A Big Bang model of human colorectal tumor growth. Nat Genet. 2015 Mar; 47(3):209-16. View in: PubMed

Wu DY, Bittencourt D, Stallcup MR, Siegmund KD. Identifying differential transcription factor binding in ChIP-seq. Front Genet. 2015; 6:169. View in: PubMed

Marconett CN, Zhou B, Siegmund KD, Borok Z, Laird-Offringa IA. Transcriptomic Profiling of Primary Alveolar Epithelial Cell Differentiation in Human and Rat. Genom Data. 2014 Dec 1; 2:105-109. View in: PubMed

Zhao J, Siegmund KD, Shibata D, Marjoram P. Ancestral inference in tumors: How much can we know? J Theor Biol. 2014 Oct 21; 359:136-45. View in: PubMed

Su SF, de Castro Abreu AL, Chihara Y, Tsai Y, Andreu-Vieyra C, Daneshmand S, Skinner EC, Jones PA, Siegmund KD, Liang G. A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence. Clin Cancer Res. 2014 Apr 1; 20(7):1978-89. View in: PubMed

Breton CV, Park C, Siegmund K, Gauderman WJ, Whitfield-Maxwell L, Hodis HN, Avol E, Gilliland FD. NOS1 Methylation and Carotid Artery Intima-Media Thickness in Children. Circ Cardiovasc Genet. 2014 Apr 1; 7(2):116-22. View in: PubMed

Wu DY, Ou CY, Chodankar R, Siegmund KD, Stallcup MR. Distinct, genome-wide, gene-specific selectivity patterns of four glucocorticoid receptor coregulators. Nucl Recept Signal. 2014; 12:e002. View in: PubMed

Wang X, Laird PW, Hinoue T, Groshen S, Siegmund KD. Non-specific filtering of beta-distributed data. BMC Bioinformatics. 2014; 15(1):199. View in: PubMed

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. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun. 2014; 5:3365. View in: PubMed

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. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One. 2014; 9(6):e99716. View in: PubMed

Thomas JP, Davis-Dao C, Lewinger JP, Siegmund KD, Hamilton AS, Daneshmand S, Skinner EC, Thomas DC, Cortessis VK. Null association between histology of first and second primary malignancies in men with bilateral testicular germ cell tumors. Am J Epidemiol. 2013 Oct 15; 178(8):1240-5. View in: PubMed

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. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. View in: PubMed

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. Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23. Hum Mol Genet. 2013 Jul 1; 22(13):2748-53. View in: PubMed

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. Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. PLoS Genet. 2013 Jun; 9(6):e1003513. View in: PubMed

Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD. Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res. 2013 Apr; 41(7):e90. View in: PubMed

Bittencourt D, Wu DY, Jeong KW, Gerke DS, Herviou L, Ianculescu I, Chodankar R, Siegmund KD, Stallcup MR. G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of glucocorticoid receptor target genes. Proc Natl Acad Sci U S A. 2012 Nov 27; 109(48):19673-8. View in: PubMed

Cortessis VK, Thomas DC, Levine AJ, Breton CV, Mack TM, Siegmund KD, Haile RW, Laird PW. Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet. 2012 Oct; 131(10):1565-89. View in: PubMed

Breton CV, Salam MT, Wang X, Byun HM, Siegmund KD, Gilliland FD. Particulate matter, DNA methylation in nitric oxide synthase, and childhood respiratory disease. Environ Health Perspect. 2012 Sep; 120(9):1320-6. View in: PubMed

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-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res. 2012 Jul; 22(7):1197-211. View in: PubMed

Wang J, Joshi AD, Corral R, Siegmund KD, Marchand LL, Martinez ME, Haile RW, Ahnen DJ, Sandler RS, Lance P, Stern MC. Carcinogen metabolism genes, red meat and poultry intake, and colorectal cancer risk. Int J Cancer. 2012 Apr 15; 130(8):1898-907. View in: PubMed

Davis-Dao C, Koh CJ, Hardy BE, Chang A, Kim SS, De Filippo R, Hwang A, Pike MC, Carroll JD, Coetzee GA, Vandenberg D, Siegmund K, Cortessis VK. Shorter Androgen Receptor CAG Repeat Lengths Associated with Cryptorchidism Risk among Hispanic White Boys. J Clin Endocrinol Metab. 2012 Mar; 97(3):E393-9. View in: PubMed

Ianculescu I, Wu DY, Siegmund KD, Stallcup MR. 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. J Biol Chem. 2012 Feb 3; 287(6):4000-13. View in: PubMed

Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012; 13(7):R61. View in: PubMed

Cortessis VK, Siegmund K, Houshdaran S, Laird PW, Sokol RZ. Repeated assessment by high-throughput assay demonstrates that sperm DNA methylation levels are highly reproducible. Fertil Steril. 2011 Dec; 96(6):1325-30. View in: PubMed

Wang J, Siegmund K, Tseng CC, Lee AS, Wu AH. Soy food supplementation, dietary fat reduction and peripheral blood gene expression in postmenopausal women--a randomized, controlled trial. Mol Nutr Food Res. 2011 Sep; 55 Suppl 2:S264-77. View in: PubMed

Davis-Dao CA, Siegmund KD, Vandenberg DJ, Skinner EC, Coetzee GA, Thomas DC, Pike MC, Cortessis VK. Heterogenous effect of androgen receptor CAG tract length on testicular germ cell tumor risk: shorter repeats associated with seminoma but not other histologic types. Carcinogenesis. 2011 Aug; 32(8):1238-43. View in: PubMed

Breton CV, Byun HM, Wang X, Salam MT, Siegmund K, Gilliland FD. DNA methylation in the arginase-nitric oxide synthase pathway is associated with exhaled nitric oxide in children with asthma. Am J Respir Crit Care Med. 2011 Jul 15; 184(2):191-7. View in: PubMed

Siegmund KD. Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet. 2011 Jun; 129(6):585-95. View in: PubMed

Wang X, Kang GH, Campan M, Weisenberger DJ, Long TI, Cozen W, Bernstein L, Wu AH, Siegmund KD, Shibata D, Laird PW. Epigenetic subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors. PLoS One. 2011; 6(10):e25985. View in: PubMed

Selamat SA, Galler JS, Joshi AD, Fyfe MN, Campan M, Siegmund KD, Kerr KM, Laird-Offringa IA. DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One. 2011; 6(6):e21443. View in: PubMed

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. Genome-scale screen for DNA methylation-based detection markers for ovarian cancer. PLoS One. 2011; 6(12):e28141. View in: PubMed

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. The PREMM(1,2,6) model predicts risk of MLH1, MSH2, and MSH6 germline mutations based on cancer history. Gastroenterology. 2011 Jan; 140(1):73-81. View in: PubMed

Moser AB, Steinberg SJ, Watkins PA, Moser HW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG. Human and great ape red blood cells differ in plasmalogen levels and composition. Lipids Health Dis. 2011; 10:101. View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers. PLoS One. 2011; 6(6):e21657. View in: PubMed

Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD. Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011; 12:284. View in: PubMed

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. Polymorphisms in base excision repair genes as colorectal cancer risk factors and modifiers of the effect of diets high in red meat. Cancer Epidemiol Biomarkers Prev. 2010 Dec; 19(12):3167-73. View in: PubMed

Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund KD, Sugano K, Kawashima K, Laird PW, Jones PA, Liang G. Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res. 2010 Oct 15; 70(20):8169-78. View in: PubMed

Wu AH, Siegmund KD, Long TI, Cozen W, Wan P, Tseng CC, Shibata D, Laird PW. Hormone therapy, DNA methylation and colon cancer. Carcinogenesis. 2010 Jun; 31(6):1060-7. View in: PubMed

Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet. 2010 Apr; 6(4):e1000917. View in: PubMed

Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund KD, Sinha UK, Müschen M, Jaeger EB, Weisenburger DD, Chan WC, Shibata D, Fan JB, Hacia JG. Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations. J Cell Biochem. 2010 Mar 1; 109(4):818-27. View in: PubMed

Hong YJ, Marjoram P, Shibata D, Siegmund KD. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010; 5(8):e12002. View in: PubMed

Watkins PA, Moser AB, Toomer CB, Steinberg SJ, Moser HW, Karaman MW, Ramaswamy K, Siegmund KD, Lee DR, Ely JJ, Ryder OA, Hacia JG. Identification of differences in human and great ape phytanic acid metabolism that could influence gene expression profiles and physiological functions. BMC Physiol. 2010; 10:19. View in: PubMed

Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, Yang AS. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet. 2009 Dec 15; 18(24):4808-17. View in: PubMed

Poynter JN, Haile RW, Siegmund KD, Campbell PT, Figueiredo JC, Limburg P, Young J, Le Marchand L, Potter JD, Cotterchio M, Casey G, Hopper JL, Jenkins MA, Thibodeau SN, Newcomb PA, Baron JA. Associations between smoking, alcohol consumption, and colorectal cancer, overall and by tumor microsatellite instability status. Cancer Epidemiol Biomarkers Prev. 2009 Oct; 18(10):2745-50. View in: PubMed

Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. View in: PubMed

Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D. Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A. 2009 Mar 24; 106(12):4828-33. View in: PubMed

Joshi AD, Corral R, Siegmund KD, Haile RW, Le Marchand L, Martínez ME, Ahnen DJ, Sandler RS, Lance P, Stern MC. Red meat and poultry intake, polymorphisms in the nucleotide excision repair and mismatch repair pathways and colorectal cancer risk. Carcinogenesis. 2009 Mar; 30(3):472-9. View in: PubMed

Woo YJ, Siegmund KD, Tavaré S, Shibata D. Older individuals appear to acquire mitotically older colorectal cancers. J Pathol. 2009 Mar; 217(4):483-8. View in: PubMed

Bapat B, Lindor NM, Baron J, Siegmund K, Li L, Zheng Y, Haile R, Gallinger S, Jass JR, Young JP, Cotterchio M, Jenkins M, Grove J, Casey G, Thibodeau SN, Bishop DT, Hopper JL, Ahnen D, Newcomb PA, Le Marchand L, Potter JD, Seminara D. The association of tumor microsatellite instability phenotype with family history of colorectal cancer. Cancer Epidemiol Biomarkers Prev. 2009 Mar; 18(3):967-75. View in: PubMed

Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. BMC Proc. 2009; 3 Suppl 7:S133. View in: PubMed

Toleno DM, Renaud G, Wolfsberg TG, Islam M, Wildman DE, Siegmund KD, Hacia JG. Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics. 2009; 10:77. View in: PubMed

Poynter JN, Siegmund KD, Weisenberger DJ, Long TI, Thibodeau SN, Lindor N, Young J, Jenkins MA, Hopper JL, Baron JA, Buchanan D, Casey G, Levine AJ, Le Marchand L, Gallinger S, Bapat B, Potter JD, Newcomb PA, Haile RW, Laird PW. Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening. Cancer Epidemiol Biomarkers Prev. 2008 Nov; 17(11):3208-15. View in: PubMed

Chu M, Siegmund KD, Hao QL, Crooks GM, Tavaré S, Shibata D. Inferring relative numbers of human leucocyte genome replications. Br J Haematol. 2008 Jun; 141(6):862-71. View in: PubMed

Anglim PP, Galler JS, Koss MN, Hagen JA, Turla S, Campan M, Weisenberger DJ, Laird PW, Siegmund KD, Laird-Offringa IA. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer. 2008; 7:62. View in: PubMed

Magda D, Lecane P, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund KD, Hacia JG. mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft. BMC Genomics. 2008; 9:521. View in: PubMed

Siegmund KD, Marjoram P, Shibata D. Modeling DNA methylation in a population of cancer cells. Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. View in: PubMed

Wasserberg N, Haney M, Petrone P, Ritter M, Emami C, Rosca J, Siegmund K, Kaufman HS. Morbid obesity adversely impacts pelvic floor function in females seeking attention for weight loss surgery. Dis Colon Rectum. 2007 Dec; 50(12):2096-103. View in: PubMed

Poynter JN, Figueiredo JC, Conti DV, Kennedy K, Gallinger S, Siegmund KD, Casey G, Thibodeau SN, Jenkins MA, Hopper JL, Byrnes GB, Baron JA, Goode EL, Tiirikainen M, Lindor N, Grove J, Newcomb P, Jass J, Young J, Potter JD, Haile RW, Duggan DJ, Le Marchand L. Variants on 9p24 and 8q24 are associated with risk of colorectal cancer: results from the Colon Cancer Family Registry. Cancer Res. 2007 Dec 1; 67(23):11128-32. View in: PubMed

Tsou JA, Galler JS, Wali A, Ye W, Siegmund KD, Groshen S, Laird PW, Turla S, Koss MN, Pass HI, Laird-Offringa IA. DNA methylation profile of 28 potential marker loci in malignant mesothelioma. Lung Cancer. 2007 Nov; 58(2):220-30. View in: PubMed

Stern MC, Conti DV, Siegmund KD, Corral R, Yuan JM, Koh WP, Yu MC. DNA repair single-nucleotide polymorphisms in colorectal cancer and their role as modifiers of the effect of cigarette smoking and alcohol in the Singapore Chinese Health Study. Cancer Epidemiol Biomarkers Prev. 2007 Nov; 16(11):2363-72. View in: PubMed

Chu MW, Siegmund KD, Eckstam CL, Kim JY, Yang AS, Kanel GC, Tavaré S, Shibata D. Lack of increases in methylation at three CpG-rich genomic loci in non-mitotic adult tissues during aging. BMC Med Genet. 2007; 8:50. View in: PubMed

Houshdaran S, Cortessis VK, Siegmund K, Yang A, Laird PW, Sokol RZ. Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One. 2007; 2(12):e1289. View in: PubMed

Alonzo TA, Siegmund KD. Statistical methods for evaluating DNA methylation as a marker for early detection or prognosis. Dis Markers. 2007; 23(1-2):113-20. View in: PubMed

Tsou JA, Galler JS, Siegmund KD, Laird PW, Turla S, Cozen W, Hagen JA, Koss MN, Laird-Offringa IA. Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer. 2007; 6:70. View in: PubMed

Siegmund KD, Connor CM, Campan M, Long TI, Weisenberger DJ, Biniszkiewicz D, Jaenisch R, Laird PW, Akbarian S. DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS One. 2007; 2(9):e895. View in: PubMed

Stern MC, Siegmund KD, Conti DV, Corral R, Haile RW. XRCC1, XRCC3, and XPD polymorphisms as modifiers of the effect of smoking and alcohol on colorectal adenoma risk. Cancer Epidemiol Biomarkers Prev. 2006 Dec; 15(12):2384-90. View in: PubMed

Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, Kang GH, Widschwendter M, Weener D, Buchanan D, Koh H, Simms L, Barker M, Leggett B, Levine J, Kim M, French AJ, Thibodeau SN, Jass J, Haile R, Laird PW. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet. 2006 Jul; 38(7):787-93. View in: PubMed

Siegmund KD, Levine AJ, Chang J, Laird PW. Modeling exposures for DNA methylation profiles. Cancer Epidemiol Biomarkers Prev. 2006 Mar; 15(3):567-72. View in: PubMed

Marjoram P, Chang J, Laird PW, Siegmund KD. Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006; 7:361. View in: PubMed

Friedrich MG, Chandrasoma S, Siegmund KD, Weisenberger DJ, Cheng JC, Toma MI, Huland H, Jones PA, Liang G. Prognostic relevance of methylation markers in patients with non-muscle invasive bladder carcinoma. Eur J Cancer. 2005 Nov; 41(17):2769-78. View in: PubMed

Millstein J, Siegmund KD, Conti DV, Gauderman WJ. Testing association and linkage using affected-sib-parent study designs. Genet Epidemiol. 2005 Nov; 29(3):225-33. View in: PubMed

Lindor NM, Rabe K, Petersen GM, Haile R, Casey G, Baron J, Gallinger S, Bapat B, Aronson M, Hopper J, Jass J, LeMarchand L, Grove J, Potter J, Newcomb P, Terdiman JP, Conrad P, Moslein G, Goldberg R, Ziogas A, Anton-Culver H, de Andrade M, Siegmund K, Thibodeau SN, Boardman LA, Seminara D. Lower cancer incidence in Amsterdam-I criteria families without mismatch repair deficiency: familial colorectal cancer type X. JAMA. 2005 Apr 27; 293(16):1979-85. View in: PubMed

Stern MC, Siegmund KD, Corral R, Haile RW. XRCC1 and XRCC3 polymorphisms and their role as effect modifiers of unsaturated fatty acids and antioxidant intake on colorectal adenomas risk. Cancer Epidemiol Biomarkers Prev. 2005 Mar; 14(3):609-15. View in: PubMed

Tsou JA, Shen LY, Siegmund KD, Long TI, Laird PW, Seneviratne CK, Koss MN, Pass HI, Hagen JA, Laird-Offringa IA. Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung. Lung Cancer. 2005 Feb; 47(2):193-204. View in: PubMed

Millstein J, Siegmund KD, Conti DV, Gauderman WJ. Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis. BMC Genet. 2005; 6 Suppl 1:S147. View in: PubMed

Kim JY, Siegmund KD, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med. 2005; 3:10. View in: PubMed

Friedrich MG, Weisenberger DJ, Cheng JC, Chandrasoma S, Siegmund KD, Gonzalgo ML, Toma MI, Huland H, Yoo C, Tsai YC, Nichols PW, Bochner BH, Jones PA, Liang G. Detection of methylated apoptosis-associated genes in urine sediments of bladder cancer patients. Clin Cancer Res. 2004 Nov 15; 10(22):7457-65. View in: PubMed

Siegmund KD, Laird PW, Laird-Offringa IA. A comparison of cluster analysis methods using DNA methylation data. Bioinformatics. 2004 Aug 12; 20(12):1896-904. View in: PubMed

Widschwendter M, Siegmund KD, Müller HM, Fiegl H, Marth C, Müller-Holzner E, Jones PA, Laird PW. Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res. 2004 Jun 1; 64(11):3807-13. View in: PubMed

Cortessis VK, Siegmund K, Xue S, Ross RK, Yu MC. A case-control study of cyclin D1 CCND1 870A-->G polymorphism and bladder cancer. Carcinogenesis. 2003 Oct; 24(10):1645-50. View in: PubMed

Tsao JL, Dudley S, Kwok B, Nickel AE, Laird PW, Siegmund KD, Liskay RM, Shibata D. Diet, cancer and aging in DNA mismatch repair deficient mice. Carcinogenesis. 2002 Nov; 23(11):1807-10. View in: PubMed

Siegmund KD, Laird PW. Analysis of complex methylation data. Methods. 2002 Jun; 27(2):170-8. View in: PubMed

Siegmund KD, Langholz B. Ascertainment bias in family-based case-control studies. Am J Epidemiol. 2002 May 1; 155(9):875-80. View in: PubMed

Virmani AK, Tsou JA, Siegmund KD, Shen LY, Long TI, Laird PW, Gazdar AF, Laird-Offringa IA. Hierarchical clustering of lung cancer cell lines using DNA methylation markers. Cancer Epidemiol Biomarkers Prev. 2002 Mar; 11(3):291-7. View in: PubMed

Siegmund KD, Langholz B. Stratified case sampling and the use of family controls. Genet Epidemiol. 2001 Apr; 20(3):316-27. View in: PubMed

Siegmund KD, Gauderman WJ. Association tests in nuclear families. Hum Hered. 2001; 52(2):66-76. View in: PubMed

Siegmund KD, Langholz B, Kraft P, Thomas DC. Testing linkage disequilibrium in sibships. Am J Hum Genet. 2000 Jul; 67(1):244-8. View in: PubMed

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