Loading...

Kimberly Siegmund, PhD

Title(s)Professor of Preventive Medicine
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 Research 
    Collapse Research Activities and Funding
    LA?s Biostatistics Education Summer Training Program (LA?s BEST @USC)
    NIH/NHLBI R25HL147236Mar 15, 2019 - Feb 28, 2022
    Role: Co-Principal Investigator
    Statistical Analysis of Epigenomics Data
    NIH/NHGRI R01HG006705Mar 26, 2013 - Feb 29, 2016
    Role: Principal Investigator
    Applying Molecular Phylogeny to Predict Clinical Outcomes in Cancer
    NIH/NCI R21CA151139Sep 1, 2010 - Aug 31, 2013
    Role: Principal Investigator
    Statistical Models in Epigenomics
    NIH/NCI R01CA097346Jul 1, 2002 - Jun 30, 2014
    Role: Principal Investigator
    Statistical Models in Epigenomics
    NIH/NCI R56CA097346Jul 1, 2002 - Jun 30, 2009
    Role: Principal Investigator

    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.
    List All   |   Timeline
    1. Yang Z, Pandey P, Shibata D, Conti DV, Marjoram P, Siegmund KD. HiLDA: a statistical approach to investigate differences in mutational signatures. PeerJ. 2019; 7:e7557. PMID: 31523512.
      View in: PubMed
    2. Hom M, Sriprasert I, Ihenacho U, Castelao JE, Siegmund K, Bernstein L, Cortessis VK. Systematic Review and Meta-analysis of Testicular Germ Cell Tumors Following In Utero Exposure to Diethylstilbestrol. JNCI Cancer Spectr. 2019 Sep; 3(3):pkz045. PMID: 31555759.
      View in: PubMed
    3. Tommasi S, Caliri AW, Caceres A, Moreno DE, Li M, Chen Y, Siegmund KD, Besaratinia A. Deregulation of Biologically Significant Genes and Associated Molecular Pathways in the Oral Epithelium of Electronic Cigarette Users. Int J Mol Sci. 2019 Feb 10; 20(3). PMID: 30744164.
      View in: PubMed
    4. Wang J, Van Den Berg D, Hwang AE, Weisenberger D, Triche T, Nathwani BN, Conti DV, Siegmund K, Mack TM, Horvath S, Cozen W. DNA methylation patterns of adult survivors of adolescent/young adult Hodgkin lymphoma compared to their unaffected monozygotic twin. Leuk Lymphoma. 2019 Jun; 60(6):1429-1437. PMID: 30668190.
      View in: PubMed
    5. Ryser MD, Yu M, Grady W, Siegmund K, Shibata D. Epigenetic Heterogeneity in Human Colorectal Tumors Reveals Preferential Conservation And Evidence of Immune Surveillance. Sci Rep. 2018 11 23; 8(1):17292. PMID: 30470817.
      View in: PubMed
    6. Gao L, Urman R, Millstein J, Siegmund KD, Dubeau L, Breton CV. Association between AXL promoter methylation and lung function growth during adolescence. Epigenetics. 2018; 13(10-11):1027-1038. PMID: 30277126.
      View in: PubMed
    7. Liu J, Liang G, Siegmund KD, Lewinger JP. Data integration by multi-tuning parameter elastic net regression. BMC Bioinformatics. 2018 Oct 10; 19(1):369. PMID: 30305021.
      View in: PubMed
    8. Park SL, Patel YM, Loo LWM, Mullen DJ, Offringa IA, Maunakea A, Stram DO, Siegmund K, Murphy SE, Tiirikainen M, Le Marchand L. Association of internal smoking dose with blood DNA methylation in three racial/ethnic populations. Clin Epigenetics. 2018 08 23; 10(1):110. PMID: 30139389.
      View in: PubMed
    9. 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. Self-reported prenatal tobacco smoke exposure, AXL gene-body methylation, and childhood asthma phenotypes. Clin Epigenetics. 2018 07 20; 10(1):98. PMID: 30029617.
      View in: PubMed
    10. Ryser MD, Min BH, Siegmund KD, Shibata D. Spatial mutation patterns as markers of early colorectal tumor cell mobility. Proc Natl Acad Sci U S A. 2018 05 29; 115(22):5774-5779. PMID: 29760052.
      View in: PubMed
    11. Cortessis VK, Azadian M, Buxbaum J, Sanogo F, Song AY, Sriprasert I, Wei PC, Yu J, Chung K, Siegmund KD. Comprehensive meta-analysis reveals association between multiple imprinting disorders and conception by assisted reproductive technology. J Assist Reprod Genet. 2018 Jun; 35(6):943-952. PMID: 29696471.
      View in: PubMed
    12. Gao L, Millstein J, Siegmund KD, Dubeau L, Maguire R, Gilliland FD, Murphy SK, Hoyo C, Breton CV. Epigenetic regulation of AXL and risk of childhood asthma symptoms. Clin Epigenetics. 2017; 9:121. PMID: 29177020.
      View in: PubMed
    13. 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
    14. 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
    15. 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. Cross-Species Transcriptome Profiling Identifies New Alveolar Epithelial Type I Cell-Specific Genes. Am J Respir Cell Mol Biol. 2017 03; 56(3):310-321. PMID: 27749084.
      View in: PubMed
    16. 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. 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
    17. 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. Identifying aggressive prostate cancer foci using a DNA methylation classifier. Genome Biol. 2017 01 12; 18(1):3. PMID: 28081708.
      View in: PubMed
    18. 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
    19. Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016 06 22; 17:469. PMID: 27334613.
      View in: PubMed
    20. Breton CV, Gao L, Yao J, Siegmund KD, Lurmann F, Gilliland F. Particulate matter, the newborn methylome, and cardio-respiratory health outcomes in childhood. Environ Epigenet. 2016 Apr; 2(2):dvw005. PMID: 29492287.
      View in: PubMed
    21. Breton CV, Yao J, Millstein J, Gao L, Siegmund KD, 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 12; 124(12):1905-1912. PMID: 27219456.
      View in: PubMed
    22. 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.
      View in: PubMed
    23. 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 04 01; 76(7):1954-64. PMID: 26759245.
      View in: PubMed
    24. 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.
      View in: PubMed
    25. Wu DY, Bittencourt D, Stallcup MR, Siegmund KD. Identifying differential transcription factor binding in ChIP-seq. Front Genet. 2015; 6:169. PMID: 25972895.
      View in: PubMed
    26. 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.
      View in: PubMed
    27. 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. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history. Cancer Epidemiol Biomarkers Prev. 2015 Mar; 24(3):512-519. PMID: 25587051.
      View in: PubMed
    28. 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 01; 2:105-109. PMID: 25343132.
      View in: PubMed
    29. 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. PMID: 25422592.
      View in: PubMed
    30. 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. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One. 2014; 9(6):e99716. PMID: 24964093.
      View in: PubMed
    31. Wang X, Laird PW, Hinoue T, Groshen S, Siegmund KD. Non-specific filtering of beta-distributed data. BMC Bioinformatics. 2014 Jun 19; 15:199. PMID: 24943962.
      View in: PubMed
    32. 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. PMID: 24907673.
      View in: PubMed
    33. 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 01; 20(7):1978-89. PMID: 24691641.
      View in: PubMed
    34. 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.
      View in: PubMed
    35. 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 Feb 27; 5:3365. PMID: 24572595.
      View in: PubMed
    36. 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. PMID: 24076989.
      View in: PubMed
    37. 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. PMID: 23928263.
      View in: PubMed
    38. 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. PMID: 23818859.
      View in: PubMed
    39. 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. PMID: 23476028.
      View in: PubMed
    40. 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 01; 22(13):2748-53. PMID: 23462292.
      View in: PubMed
    41. 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. PMID: 23151507.
      View in: PubMed
    42. Liu Y, Siegmund KD, 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.
      View in: PubMed
    43. 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. PMID: 22740325.
      View in: PubMed
    44. 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. PMID: 22613842.
      View in: PubMed
    45. 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. PMID: 22591701.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. 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 03; 287(6):4000-13. PMID: 22174411.
      View in: PubMed
    48. 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. PMID: 22163280.
      View in: PubMed
    49. 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.
      View in: PubMed
    50. 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. PMID: 22028801.
      View in: PubMed
    51. 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.
      View in: PubMed
    52. 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. PMID: 21618522.
      View in: PubMed
    53. Rakovski C, Weisenberger DJ, Marjoram P, Laird PW, Siegmund KD. Modeling measurement error in tumor characterization studies. BMC Bioinformatics. 2011 Jul 13; 12:284. PMID: 21752297.
      View in: PubMed
    54. 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. PMID: 21738754.
      View in: PubMed
    55. 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. PMID: 21731750.
      View in: PubMed
    56. 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 Jun 17; 10:101. PMID: 21679470.
      View in: PubMed
    57. 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. PMID: 21642359.
      View in: PubMed
    58. Siegmund KD. Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet. 2011 Jun; 129(6):585-95. PMID: 21519831.
      View in: PubMed
    59. 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.
      View in: PubMed
    60. 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. PMID: 21037106.
      View in: PubMed
    61. 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 Oct 08; 10:19. PMID: 20932325.
      View in: PubMed
    62. 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. PMID: 20841482.
      View in: PubMed
    63. 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. PMID: 20727894.
      View in: PubMed
    64. Hong YJ, Marjoram P, Shibata D, Siegmund KD. Using DNA methylation patterns to infer tumor ancestry. PLoS One. 2010 Aug 09; 5(8):e12002. PMID: 20711251.
      View in: PubMed
    65. 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 22; 6(4):e1000917. PMID: 20421991.
      View in: PubMed
    66. 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 01; 109(4):818-27. PMID: 20069569.
      View in: PubMed
    67. 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. PMID: 20064828.
      View in: PubMed
    68. 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.
      View in: PubMed
    69. 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. PMID: 19776032.
      View in: PubMed
    70. 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. PMID: 19755657.
      View in: PubMed
    71. Siegmund KD, Marjoram P, Tavaré S, Shibata D. Many colorectal cancers are "flat" clonal expansions. Cell Cycle. 2009 Jul 15; 8(14):2187-93. PMID: 19556889.
      View in: PubMed
    72. 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 Mar 05; 10:77. PMID: 19265541.
      View in: PubMed
    73. 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. PMID: 19261858.
      View in: PubMed
    74. 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.
      View in: PubMed
    75. 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. PMID: 19165870.
      View in: PubMed
    76. 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. PMID: 19029193.
      View in: PubMed
    77. 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 Nov 03; 9:521. PMID: 18980691.
      View in: PubMed
    78. 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. PMID: 18990764.
      View in: PubMed
    79. 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 Jul 10; 7:62. PMID: 18616821.
      View in: PubMed
    80. 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. PMID: 18597664.
      View in: PubMed
    81. 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. PMID: 18410448.
      View in: PubMed
    82. Pike BL, Greiner TC, Wang X, Weisenburger DD, Hsu YH, Renaud G, Wolfsberg TG, Kim M, Weisenberger DJ, Siegmund KD, Ye W, Groshen S, Mehrian-Shai R, Delabie J, Chan WC, Laird PW, Hacia JG. DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia. 2008 May; 22(5):1035-43. PMID: 18288132.
      View in: PubMed
    83. 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.
      View in: PubMed
    84. 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 01; 67(23):11128-32. PMID: 18056436.
      View in: PubMed
    85. 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. PMID: 18006925.
      View in: PubMed
    86. 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 Oct 29; 6:70. PMID: 17967182.
      View in: PubMed
    87. 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.
      View in: PubMed
    88. 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 Sep 19; 2(9):e895. PMID: 17878930.
      View in: PubMed
    89. 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 Jul 31; 8:50. PMID: 17672908.
      View in: PubMed
    90. 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. PMID: 17659810.
      View in: PubMed
    91. 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. PMID: 17325431.
      View in: PubMed
    92. 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. PMID: 17164360.
      View in: PubMed
    93. Marjoram P, Chang J, Laird PW, Siegmund KD. Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics. 2006 Jul 26; 7:361. PMID: 16872497.
      View in: PubMed
    94. 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. PMID: 16804544.
      View in: PubMed
    95. Siegmund KD, Levine AJ, Chang J, Laird PW. Modeling exposures for DNA methylation profiles. Cancer Epidemiol Biomarkers Prev. 2006 Mar; 15(3):567-72. PMID: 16537717.
      View in: PubMed
    96. 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 Dec 30; 6 Suppl 1:S147. PMID: 16451607.
      View in: PubMed
    97. 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. PMID: 16121357.
      View in: PubMed
    98. 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. PMID: 16242928.
      View in: PubMed
    99. Kim JY, Siegmund KD, Tavaré S, Shibata D. Age-related human small intestine methylation: evidence for stem cell niches. BMC Med. 2005 Jun 23; 3:10. PMID: 15975143.
      View in: PubMed
    100. 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.
      View in: PubMed
    101. 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. PMID: 15767338.
      View in: PubMed
    102. 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. PMID: 15639718.
      View in: PubMed
    103. 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. PMID: 15569975.
      View in: PubMed
    104. 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 01; 64(11):3807-13. PMID: 15172987.
      View in: PubMed
    105. 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. PMID: 15044245.
      View in: PubMed
    106. 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.
      View in: PubMed
    107. 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. PMID: 12419828.
      View in: PubMed
    108. Siegmund KD, Laird PW. Analysis of complex methylation data. Methods. 2002 Jun; 27(2):170-8. PMID: 12095277.
      View in: PubMed
    109. Siegmund KD, Langholz B. Ascertainment bias in family-based case-control studies. Am J Epidemiol. 2002 May 01; 155(9):875-80. PMID: 11978593.
      View in: PubMed
    110. 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. PMID: 11895880.
      View in: PubMed
    111. Siegmund KD, Langholz B. Stratified case sampling and the use of family controls. Genet Epidemiol. 2001 Apr; 20(3):316-27. PMID: 11255241.
      View in: PubMed
    112. Cortessis V, Siegmund K, Chen Q, Zhou N, Diep A, Frankl H, Lee E, Zhu QS, Haile R, Levy D. A case-control study of microsomal epoxide hydrolase, smoking, meat consumption, glutathione S-transferase M3, and risk of colorectal adenomas. Cancer Res. 2001 Mar 15; 61(6):2381-5. PMID: 11289100.
      View in: PubMed
    113. Gauderman WJ, Morrison JL, Siegmund KD. Should we consider gene x environment interaction in the hunt for quantitative trait loci? Genet Epidemiol. 2001; 21 Suppl 1:S831-6. PMID: 11793788.
      View in: PubMed
    114. Gauderman WJ, Siegmund KD. Gene-environment interaction and affected sib pair linkage analysis. Hum Hered. 2001; 52(1):34-46. PMID: 11359066.
      View in: PubMed
    115. Siegmund KD, Vora H, Gauderman WJ. Combined linkage and association analysis in pedigrees. Genet Epidemiol. 2001; 21 Suppl 1:S358-63. PMID: 11793698.
      View in: PubMed
    116. Siegmund KD, Gauderman WJ. Association tests in nuclear families. Hum Hered. 2001; 52(2):66-76. PMID: 11474207.
      View in: PubMed
    117. Knox SS, Adelman A, Ellison RC, Arnett DK, Siegmund K, Weidner G, Province MA. Hostility, social support, and carotid artery atherosclerosis in the National Heart, Lung, and Blood Institute Family Heart Study. Am J Cardiol. 2000 Nov 15; 86(10):1086-9. PMID: 11074204.
      View in: PubMed
    118. Levine AJ, Siegmund KD, Ervin CM, Diep A, Lee ER, Frankl HD, Haile RW. The methylenetetrahydrofolate reductase 677C-->T polymorphism and distal colorectal adenoma risk. Cancer Epidemiol Biomarkers Prev. 2000 Jul; 9(7):657-63. PMID: 10919734.
      View in: PubMed
    119. Siegmund KD, Langholz B, Kraft P, Thomas DC. Testing linkage disequilibrium in sibships. Am J Hum Genet. 2000 Jul; 67(1):244-8. PMID: 10831398.
      View in: PubMed
    120. Siegmund KD, Todorov AA. Linkage analysis for diseases with variable age of onset. Hum Hered. 2000 May-Jun; 50(3):205-10. PMID: 10686502.
      View in: PubMed
    121. Siegmund KD, Todorov AA, Province MA. A frailty approach for modelling diseases with variable age of onset in families: the NHLBI Family Heart Study. Stat Med. 1999 Jun 30; 18(12):1517-28. PMID: 10398289.
      View in: PubMed
    122. Siegmund KD, Gauderman WJ, Thomas DC. Association tests using unaffected-sibling versus pseudo-sibling controls. Genet Epidemiol. 1999; 17 Suppl 1:S731-6. PMID: 10597522.
      View in: PubMed
    123. Thomas DC, Qian D, Gauderman WJ, Siegmund K, Morrison JL. A generalized estimating equations approach to linkage analysis in sibships in relation to multiple markers and exposure factors. Genet Epidemiol. 1999; 17 Suppl 1:S737-42. PMID: 10597523.
      View in: PubMed
    124. Haile RW, Siegmund KD, Gauderman WJ, Thomas DC. Study-design issues in the development of the University of Southern California Consortium's Colorectal Cancer Family Registry. J Natl Cancer Inst Monogr. 1999; (26):89-93. PMID: 10854491.
      View in: PubMed
    125. Siegmund KD, Whittemore AS, Thomas DC. Multistage sampling for disease family registries. J Natl Cancer Inst Monogr. 1999; (26):43-8. PMID: 10854485.
      View in: PubMed
    126. Gauderman WJ, Morrison JL, Siegmund KD, Thomas DC. A joint test of linkage and gene x environment interaction, with affected sib pairs. Genet Epidemiol. 1999; 17 Suppl 1:S563-8. PMID: 10597493.
      View in: PubMed
    127. Hopkins PN, Hunt SC, Schreiner PJ, Eckfeldt JH, Borecki IB, Ellison CR, Williams RR, Siegmund KD. Lipoprotein(a) interactions with lipid and non-lipid risk factors in patients with early onset coronary artery disease: results from the NHLBI Family Heart Study. Atherosclerosis. 1998 Dec; 141(2):333-45. PMID: 9862182.
      View in: PubMed
    128. Siegmund KD, Province MA, Higgins M, Williams RR, Keller J, Todorov AA. Modeling disease incidence rates in families. Epidemiology. 1998 Sep; 9(5):557-62. PMID: 9730037.
      View in: PubMed
    129. Siegmund K, McKnight B. Modeling hazard functions in families. Genet Epidemiol. 1998; 15(2):147-71. PMID: 9554553.
      View in: PubMed
    130. Gordon W, Siegmund K, Stanisic TH, McKnight B, Harris IT, Carroll PR, Paradelo JC, Meyers FJ, Chapman RA, Meyskens FL. A study of reproductive function in patients with seminoma treated with radiotherapy and orchidectomy: (SWOG-8711). Southwest Oncology Group. Int J Radiat Oncol Biol Phys. 1997 Apr 01; 38(1):83-94. PMID: 9212008.
      View in: PubMed
    131. Siegmund KD, Todorov AA, Rao DC, Borecki IB. The role of smoothing techniques in the interpretation of results from genomic scans using sib-pair data. Genet Epidemiol. 1997; 14(6):1047-52. PMID: 9433622.
      View in: PubMed
    132. Todorov AA, Siegmund KD, Gu C, Borecki IB, Elston RC. Probabilities of identity-by-descent patterns in sibships when the parents are not genotyped. Genet Epidemiol. 1997; 14(6):909-13. PMID: 9433599.
      View in: PubMed
    133. Goddard KA, Jarvik GP, Graham J, McNeney B, Hsu L, Siegmund K, Grosser S, Olson J, Wijsman EM. Analysis of quantitative risk factors for a common oligogenic disease. Genet Epidemiol. 1995; 12(6):759-64. PMID: 8788005.
      View in: PubMed