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    Kimberly Siegmund, PhD

    TitleProfessor of Preventive Medicine
    SchoolKeck School of Medicine of USC
    DepartmentPreventive Medicine
    AddressSSB 202W 2001 N. Soto Street
    Health Sciences Campus
    Los Angeles California 90033
    Phone+1 323 442 1310
    vCardDownload vCard

      Collapse Overview 
      Collapse 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.


      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Byun HM, Eshaghian S, Douer D, Trent J, Garcia-Manero G, Bhatia R, Siegmund K, Yang AS. Impact of Chromosomal Rearrangement upon DNA Methylation Patterns in Leukemia. Open Med (Wars). 2017; 12:76-85. PMID: 28730166.
        View in: PubMed
      2. Zhao J, Salomon MP, Shibata D, Curtis C, Siegmund K, Marjoram P. Early mutation bursts in colorectal tumors. PLoS One. 2017; 12(3):e0172516. PMID: 28257429.
        View in: PubMed
      3. Marconett CN, Zhou B, Sunohara M, Pouldar TM, Wang H, Liu Y, Rieger ME, Tran E, Flodby P, Siegmund K, Crandall ED, Laird-Offringa IA, Borok Z. Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol. 2017 Mar; 56(3):310-321. PMID: 27749084.
        View in: PubMed
      4. 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 K. Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers. Oncotarget. 2017 Jan 17; 8(3):5439-5448. PMID: 27690297.
        View in: PubMed
      5. Mundbjerg K, Chopra S, Alemozaffar M, Duymich C, Lakshminarasimhan R, Nichols PW, Aron M, Siegmund K, Ukimura O, Aron M, Stern M, Gill P, Carpten JD, Ørntoft TF, Sørensen KD, Weisenberger DJ, Jones PA, Duddalwar V, Gill I, Liang G. Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol. 2017 Jan 12; 18(1):3. PMID: 28081708.
        View in: PubMed
      6. Cantor RM, Pan C, Siegmund K. Genetic complexity at expression quantitative trait loci. BMC Proc. 2016; 10(Suppl 7):85-89. PMID: 27980616.
        View in: PubMed
      7. Liu J, Siegmund K. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016 Jun 22; 17:469. PMID: 27334613; PMCID: PMC4918139.
      8. Breton CV, Yao J, Millstein J, Gao L, Siegmund K, Mack W, Whitfield-Maxwell L, Lurmann F, Hodis H, Avol E, Gilliland FD. 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. Environ Health Perspect. 2016 Dec; 124(12):1905-1912. PMID: 27219456.
        View in: PubMed
      9. Siegmund K, Shibata D. At least two well-spaced samples are needed to genotype a solid tumor. BMC Cancer. 2016 Mar 25; 16:250. PMID: 27015839; PMCID: PMC4807557.
      10. Becket E, Chopra S, Duymich CE, Lin JJ, You JS, Pandiyan K, Nichols PW, Siegmund K, Charlet J, Weisenberger DJ, Jones PA, Liang G. Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma. Cancer Res. 2016 04 01; 76(7):1954-64. PMID: 26759245; PMCID: PMC4873378 [Available on 04/01/17].
      11. 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. PMID: 26119426; PMCID: PMC4607608 [Available on 11/01/16].
      12. Wu DY, Bittencourt D, Stallcup MR, Siegmund K. Identifying differential transcription factor binding in ChIP-seq. Front Genet. 2015; 6:169. PMID: 25972895; PMCID: PMC4413818.
      13. 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. PMID: 25665006; PMCID: PMC4575589.
      14. Marconett CN, Zhou B, Siegmund K, Borok Z, Laird-Offringa IA. Transcriptomic Profiling of Primary Alveolar Epithelial Cell Differentiation in Human and Rat. Genom Data. 2014 Dec 01; 2:105-109. PMID: 25343132.
        View in: PubMed
      15. Wu DY, Ou CY, Chodankar R, Siegmund K, Stallcup MR. Distinct, genome-wide, gene-specific selectivity patterns of four glucocorticoid receptor coregulators. Nucl Recept Signal. 2014; 12:e002. PMID: 25422592; PMCID: PMC4242289.
      16. Breton CV, Siegmund K, 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. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One. 2014; 9(6):e99716. PMID: 24964093; PMCID: PMC4070909.
      17. Wang X, Laird PW, Hinoue T, Groshen S, Siegmund K. Non-specific filtering of beta-distributed data. BMC Bioinformatics. 2014 Jun 19; 15:199. PMID: 24943962; PMCID: PMC4230495.
      18. Zhao J, Siegmund K, Shibata D, Marjoram P. Ancestral inference in tumors: how much can we know? J Theor Biol. 2014 Oct 21; 359:136-45. PMID: 24907673; PMCID: PMC4138290.
      19. Su SF, de Castro Abreu AL, Chihara Y, Tsai Y, Andreu-Vieyra C, Daneshmand S, Skinner EC, Jones PA, Siegmund K, Liang G. A panel of three markers hyper- and hypomethylated in urine sediments accurately predicts bladder cancer recurrence. Clin Cancer Res. 2014 Apr 01; 20(7):1978-89. PMID: 24691641.
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      20. 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; 7(2):116-22. PMID: 24622112; PMCID: PMC4008829.
      21. 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 K, 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 Feb 27; 5:3365. PMID: 24572595; PMCID: PMC3982882.
      22. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund K, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. PMID: 24076989.
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      23. Thomas JP, Davis-Dao C, Lewinger JP, Siegmund K, 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. PMID: 23928263; PMCID: PMC3792726.
      24. Marconett CN, Zhou B, Rieger ME, Selamat SA, Dubourd M, Fang X, Lynch SK, Stueve TR, Siegmund K, 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. PMID: 23818859; PMCID: PMC3688557.
      25. Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund K. Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res. 2013 Apr; 41(7):e90. PMID: 23476028; PMCID: PMC3627582.
      26. 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 K, 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 01; 22(13):2748-53. PMID: 23462292; PMCID: PMC3674801.
      27. Bittencourt D, Wu DY, Jeong KW, Gerke DS, Herviou L, Ianculescu I, Chodankar R, Siegmund K, 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. PMID: 23151507; PMCID: PMC3511704.
      28. Liu Y, Siegmund K, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012 Jul 11; 13(7):R61. PMID: 22784381; PMCID: PMC3491382.
      29. Selamat SA, Chung BS, Girard L, Zhang W, Zhang Y, Campan M, Siegmund K, 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. PMID: 22613842; PMCID: PMC3396362.
      30. Breton CV, Salam MT, Wang X, Byun HM, Siegmund K, Gilliland FD. Particulate matter, DNA methylation in nitric oxide synthase, and childhood respiratory disease. Environ Health Perspect. 2012 Sep; 120(9):1320-6. PMID: 22591701; PMCID: PMC3440108.
      31. 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. PMID: 22188741.
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      32. Ianculescu I, Wu DY, Siegmund K, 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 03; 287(6):4000-13. PMID: 22174411; PMCID: PMC3281703.
      33. Campan M, Moffitt M, Houshdaran S, Shen H, Widschwendter M, Daxenbichler G, Long T, Marth C, Laird-Offringa IA, Press MF, Dubeau L, Siegmund K, 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. PMID: 22163280; PMCID: PMC3233546.
      34. 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. PMID: 22035967; PMCID: PMC3448450.
      35. Wang X, Kang GH, Campan M, Weisenberger DJ, Long TI, Cozen W, Bernstein L, Wu AH, Siegmund K, 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. PMID: 22028801; PMCID: PMC3197593.
      36. Wang J, Joshi AD, Corral R, Siegmund K, 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. PMID: 21618522; PMCID: PMC3883510.
      37. 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. PMID: 21823222; PMCID: PMC3819223.
      38. Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund K. Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011 Jul 13; 12:284. PMID: 21752297; PMCID: PMC3213130.
      39. Siegmund K, 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. PMID: 21738754; PMCID: PMC3125304.
      40. Selamat SA, Galler JS, Joshi AD, Fyfe MN, Campan M, Siegmund K, Kerr KM, Laird-Offringa IA. DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One. 2011; 6(6):e21443. PMID: 21731750; PMCID: PMC3121768.
      41. Moser AB, Steinberg SJ, Watkins PA, Moser HW, Ramaswamy K, Siegmund K, 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 Jun 17; 10:101. PMID: 21679470; PMCID: PMC3129581.
      42. Davis-Dao CA, Siegmund K, 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. PMID: 21642359; PMCID: PMC3202310.
      43. Siegmund K. Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet. 2011 Jun; 129(6):585-95. PMID: 21519831; PMCID: PMC3166559.
      44. 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. PMID: 21512169; PMCID: PMC3172885.
      45. Brevik A, Joshi AD, Corral R, Onland-Moret NC, Siegmund K, 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. PMID: 21037106; PMCID: PMC3058341.
      46. Watkins PA, Moser AB, Toomer CB, Steinberg SJ, Moser HW, Karaman MW, Ramaswamy K, Siegmund K, 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 Oct 08; 10:19. PMID: 20932325; PMCID: PMC2964658.
      47. Wolff EM, Chihara Y, Pan F, Weisenberger DJ, Siegmund K, 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. PMID: 20841482; PMCID: PMC2955801.
      48. Kastrinos F, Steyerberg EW, Mercado R, Balmaña J, Holter S, Gallinger S, Siegmund K, 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. PMID: 20727894; PMCID: PMC3125673.
      49. Hong YJ, Marjoram P, Shibata D, Siegmund K. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010 Aug 09; 5(8):e12002. PMID: 20711251; PMCID: PMC2918495.
      50. Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund K, 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 22; 6(4):e1000917. PMID: 20421991; PMCID: PMC2858672.
      51. Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund K, 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 01; 109(4):818-27. PMID: 20069569; PMCID: PMC3122883.
      52. Wu AH, Siegmund K, 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. PMID: 20064828; PMCID: PMC2878358.
      53. Shtir C, Pique-Regi R, Siegmund K, Morrison J, Schumacher F, Marjoram P. Copy number variation in the Framingham Heart Study. BMC Proc. 2009 Dec 15; 3 Suppl 7:S133. PMID: 20018000; PMCID: PMC2795907.
      54. Byun HM, Siegmund K, 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. PMID: 19776032; PMCID: PMC4481584.
      55. Poynter JN, Haile RW, Siegmund K, 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. PMID: 19755657; PMCID: PMC2759847.
      56. Siegmund K, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. PMID: 19556889; PMCID: PMC4145878.
      57. Toleno DM, Renaud G, Wolfsberg TG, Islam M, Wildman DE, Siegmund K, Hacia JG. Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. BMC Bioinformatics. 2009 Mar 05; 10:77. PMID: 19265541; PMCID: PMC2660304.
      58. Siegmund K, 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. PMID: 19261858; PMCID: PMC2651202.
      59. 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. PMID: 19258475; PMCID: PMC2763617.
      60. Woo YJ, Siegmund K, Tavaré S, Shibata D. Older individuals appear to acquire mitotically older colorectal cancers. J Pathol. 2009 Mar; 217(4):483-8. PMID: 19165870; PMCID: PMC4418435.
      61. Joshi AD, Corral R, Siegmund K, 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. PMID: 19029193; PMCID: PMC2722151.
      62. Magda D, Lecane P, Prescott J, Thiemann P, Ma X, Dranchak PK, Toleno DM, Ramaswamy K, Siegmund K, Hacia JG. mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft. BMC Genomics. 2008 Nov 03; 9:521. PMID: 18980691; PMCID: PMC2612029.
      63. Poynter JN, Siegmund K, 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. PMID: 18990764; PMCID: PMC2628332.
      64. Anglim PP, Galler JS, Koss MN, Hagen JA, Turla S, Campan M, Weisenberger DJ, Laird PW, Siegmund K, Laird-Offringa IA. Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer. 2008 Jul 10; 7:62. PMID: 18616821; PMCID: PMC2483990.
      65. Siegmund K, Marjoram P, Shibata D. Modeling DNA methylation in a population of cancer cells. Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. PMID: 18597664.
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      66. Chu M, Siegmund K, 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. PMID: 18410448.
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      67. 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 Dec 12; 2(12):e1289. PMID: 18074014; PMCID: PMC2100168.
      68. Poynter JN, Figueiredo JC, Conti DV, Kennedy K, Gallinger S, Siegmund K, 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 01; 67(23):11128-32. PMID: 18056436.
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      69. Stern MC, Conti DV, Siegmund K, 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. PMID: 18006925.
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      70. Tsou JA, Galler JS, Siegmund K, 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 Oct 29; 6:70. PMID: 17967182; PMCID: PMC2206053.
      71. 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. PMID: 17899277.
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      72. Siegmund K, 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 Sep 19; 2(9):e895. PMID: 17878930; PMCID: PMC1964879.
      73. Chu MW, Siegmund K, 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 Jul 31; 8:50. PMID: 17672908; PMCID: PMC1950491.
      74. Tsou JA, Galler JS, Wali A, Ye W, Siegmund K, 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. PMID: 17659810; PMCID: PMC2752414.
      75. Alonzo TA, Siegmund K. Statistical methods for evaluating DNA methylation as a marker for early detection or prognosis. Dis Markers. 2007; 23(1-2):113-20. PMID: 17325431; PMCID: PMC3850861.
      76. Stern MC, Siegmund K, 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. PMID: 17164360.
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      77. Marjoram P, Chang J, Laird PW, Siegmund K. Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006 Jul 26; 7:361. PMID: 16872497; PMCID: PMC1555616.
      78. Weisenberger DJ, Siegmund K, 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. PMID: 16804544.
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      79. Siegmund K, Levine AJ, Chang J, Laird PW. Modeling exposures for DNA methylation profiles. Cancer Epidemiol Biomarkers Prev. 2006 Mar; 15(3):567-72. PMID: 16537717.
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      80. Millstein J, Siegmund K, Conti DV, Gauderman WJ. Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis. BMC Genet. 2005 Dec 30; 6 Suppl 1:S147. PMID: 16451607; PMCID: PMC1866788.
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      82. Friedrich MG, Chandrasoma S, Siegmund K, 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. PMID: 16242928.
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      83. Kim JY, Siegmund K, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med. 2005 Jun 23; 3:10. PMID: 15975143; PMCID: PMC1168897.
      84. 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. PMID: 15855431; PMCID: PMC2933042.
      85. Stern MC, Siegmund K, 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. PMID: 15767338.
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      86. Tsou JA, Shen LY, Siegmund K, 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. PMID: 15639718.
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      87. Friedrich MG, Weisenberger DJ, Cheng JC, Chandrasoma S, Siegmund K, 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. PMID: 15569975.
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      88. Widschwendter M, Siegmund K, 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 01; 64(11):3807-13. PMID: 15172987.
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      89. Siegmund K, Laird PW, Laird-Offringa IA. A comparison of cluster analysis methods using DNA methylation data. Bioinformatics. 2004 Aug 12; 20(12):1896-904. PMID: 15044245.
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      90. 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. PMID: 12896908.
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      91. Tsao JL, Dudley S, Kwok B, Nickel AE, Laird PW, Siegmund K, Liskay RM, Shibata D. Diet, cancer and aging in DNA mismatch repair deficient mice. Carcinogenesis. 2002 Nov; 23(11):1807-10. PMID: 12419828.
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      92. Siegmund K, Laird PW. Analysis of complex methylation data. Methods. 2002 Jun; 27(2):170-8. PMID: 12095277.
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      93. Siegmund K, Langholz B. Ascertainment bias in family-based case-control studies. Am J Epidemiol. 2002 May 01; 155(9):875-80. PMID: 11978593.
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      94. Virmani AK, Tsou JA, Siegmund K, 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. PMID: 11895880.
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      95. Siegmund K, Langholz B. Stratified case sampling and the use of family controls. Genet Epidemiol. 2001 Apr; 20(3):316-27. PMID: 11255241.
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      96. Siegmund K, Gauderman WJ. Association tests in nuclear families. Hum Hered. 2001; 52(2):66-76. PMID: 11474207.
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      97. Siegmund K, Langholz B, Kraft P, Thomas DC. Testing linkage disequilibrium in sibships. Am J Hum Genet. 2000 Jul; 67(1):244-8. PMID: 10831398; PMCID: PMC1287084.