Faculty
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.
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. . View in PubMed
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). . View in PubMed
HiLDA: a statistical approach to investigate differences in mutational signatures PeerJ. 2019; 7:e7557. . View in PubMed
Data integration by multi-tuning parameter elastic net regression BMC Bioinformatics. 2018 Oct 10; 19(1):369. . View in PubMed
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. . View in PubMed
Association of internal smoking dose with blood DNA methylation in three racial/ethnic populations Clin Epigenetics. 2018 08 23; 10(1):110. . View in PubMed
Epigenetic Heterogeneity in Human Colorectal Tumors Reveals Preferential Conservation And Evidence of Immune Surveillance Sci Rep. 2018 11 23; 8(1):17292. . View in PubMed
Association between AXL promoter methylation and lung function growth during adolescence Epigenetics. 2018; 13(10-11):1027-1038. . View in PubMed
Improving needle biopsy accuracy in small renal mass using tumor-specific DNA methylation markers Oncotarget. 2017 Jan 17; 8(3):5439-5448. . View in PubMed
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. . View in PubMed
Early mutation bursts in colorectal tumors PLoS One. 2017; 12(3):e0172516. . View in PubMed
Impact of Chromosomal Rearrangement upon DNA Methylation Patterns in Leukemia Open Med (Wars). 2017; 12:76-85. . View in PubMed
Epigenetic regulation of AXL and risk of childhood asthma symptoms Clin Epigenetics. 2017; 9:121. . View in PubMed
Identifying aggressive prostate cancer foci using a DNA methylation classifier Genome Biol. 2017 01 12; 18(1):3. . View in PubMed
Particulate matter, the newborn methylome, and cardio-respiratory health outcomes in childhood Environ Epigenet. 2016 Apr; 2(2):dvw005. . View in PubMed
At least two well-spaced samples are needed to genotype a solid tumor BMC Cancer. 2016 Mar 25; 16:250. . View in PubMed
Genetic complexity at expression quantitative trait loci BMC Proc. 2016; 10(Suppl 7):85-89. . View in PubMed
Identification of DNA Methylation-Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma Cancer Res. 2016 04 01; 76(7):1954-64. . View in PubMed
An evaluation of processing methods for HumanMethylation450 BeadChip data BMC Genomics. 2016 06 22; 17:469. . View in PubMed
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
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. . View in PubMed
A Big Bang model of human colorectal tumor growth Nat Genet. 2015 Mar; 47(3):209-16. . View in PubMed
Identifying differential transcription factor binding in ChIP-seq Front Genet. 2015; 6:169. . View in PubMed
Ancestral inference in tumors: how much can we know? J Theor Biol. 2014 Oct 21; 359:136-45.. View in PubMed
Non-specific filtering of beta-distributed data BMC Bioinformatics. 2014 Jun 19; 15:199. . View in PubMed
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. . View in PubMed
NOS1 methylation and carotid artery intima-media thickness in children Circ Cardiovasc Genet. 2014 Apr; 7(2):116-22. . View in PubMed
Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Nat Commun. 2014 Feb 27; 5:3365. . View in PubMed
Distinct, genome-wide, gene-specific selectivity patterns of four glucocorticoid receptor coregulators Nucl Recept Signal. 2014; 12:e002. . View in PubMed
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
Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation PLoS Genet. 2013 Jun; 9(6):e1003513. . View in PubMed
Low-level processing of Illumina Infinium DNA Methylation BeadArrays Nucleic Acids Res. 2013 Apr; 41(7):e90. . View in PubMed
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
Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships Hum Genet. 2012 Oct; 131(10):1565-89. . View in PubMed
Particulate matter, DNA methylation in nitric oxide synthase, and childhood respiratory disease Environ Health Perspect. 2012 Sep; 120(9):1320-6. . View in PubMed
Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data Genome Biol. 2012 Jul 11; 13(7):R61. . View in PubMed
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
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
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
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
Modeling measurement error in tumor characterization studies BMC Bioinformatics. 2011 Jul 13; 12:284. . View in PubMed
Human and great ape red blood cells differ in plasmalogen levels and composition Lipids Health Dis. 2011 Jun 17; 10:101. . View in PubMed
High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers PLoS One. 2011; 6(6):e21657. . View in PubMed
Genome-scale screen for DNA methylation-based detection markers for ovarian cancer PLoS One. 2011; 6(12):e28141. . View in PubMed
DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma PLoS One. 2011; 6(6):e21443. . View in PubMed
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
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. . View in PubMed
Hormone therapy, DNA methylation and colon cancer Carcinogenesis. 2010 Jun; 31(6):1060-7. . View in PubMed
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. . View in PubMed
Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations J Cell Biochem. 2010 Mar 01; 109(4):818-27. . View in PubMed
Copy number variation in the Framingham Heart Study BMC Proc. 2009 Dec 15; 3 Suppl 7:S133. . View in PubMed
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
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
Many colorectal cancers are "flat" clonal expansions Cell Cycle. 2009 Jul 15; 8(14):2187-93. . View in PubMed
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
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees BMC Bioinformatics. 2009 Mar 05; 10:77. . View in PubMed
Older individuals appear to acquire mitotically older colorectal cancers J Pathol. 2009 Mar; 217(4):483-8. . View in PubMed
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft BMC Genomics. 2008 Nov 03; 9:521. . View in PubMed
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
Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer Mol Cancer. 2008 Jul 10; 7:62. . View in PubMed
Inferring relative numbers of human leucocyte genome replications Br J Haematol. 2008 Jun; 141(6):862-71. . View in PubMed
DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status Leukemia. 2008 May; 22(5):1035-43. . View in PubMed
Modeling DNA methylation in a population of cancer cells Stat Appl Genet Mol Biol. 2008; 7(1):Article 18. . View in PubMed
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
DNA methylation profile of 28 potential marker loci in malignant mesothelioma Lung Cancer. 2007 Nov; 58(2):220-30. . View in PubMed
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
Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma Mol Cancer. 2007 Oct 29; 6:70. . View in PubMed
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. . View in PubMed
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. . View in PubMed
Cluster analysis for DNA methylation profiles having a detection threshold BMC Bioinformatics. 2006 Jul 26; 7:361. . View in PubMed
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
Modeling exposures for DNA methylation profiles Cancer Epidemiol Biomarkers Prev. 2006 Mar; 15(3):567-72. . View in PubMed
Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis BMC Genet. 2005 Dec 30; 6 Suppl 1:S147. . View in PubMed
Age-related human small intestine methylation: evidence for stem cell niches BMC Med. 2005 Jun 23; 3:10. . View in PubMed
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
Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung Lung Cancer. 2005 Feb; 47(2):193-204. . View in PubMed
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
A comparison of cluster analysis methods using DNA methylation data Bioinformatics. 2004 Aug 12; 20(12):1896-904. . View in PubMed
Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen Cancer Res. 2004 Jun 01; 64(11):3807-13. . View in PubMed
A case-control study of cyclin D1 CCND1 870A-->G polymorphism and bladder cancer Carcinogenesis. 2003 Oct; 24(10):1645-50. . View in PubMed
Diet, cancer and aging in DNA mismatch repair deficient mice Carcinogenesis. 2002 Nov; 23(11):1807-10. . View in PubMed
Analysis of complex methylation data Methods. 2002 Jun; 27(2):170-8. . View in PubMed
Ascertainment bias in family-based case-control studies Am J Epidemiol. 2002 May 01; 155(9):875-80. . View in PubMed
Hierarchical clustering of lung cancer cell lines using DNA methylation markers Cancer Epidemiol Biomarkers Prev. 2002 Mar; 11(3):291-7. . View in PubMed
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. . View in PubMed
Gene-environment interaction and affected sib pair linkage analysis Hum Hered. 2001; 52(1):34-46. . View in PubMed
Combined linkage and association analysis in pedigrees Genet Epidemiol. 2001; 21 Suppl 1:S358-63. . View in PubMed
Association tests in nuclear families Hum Hered. 2001; 52(2):66-76. . View in PubMed
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. . View in PubMed
Linkage analysis for diseases with variable age of onset Hum Hered. 2000 May-Jun; 50(3):205-10. . View in PubMed
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. . View in PubMed
Association tests using unaffected-sibling versus pseudo-sibling controls Genet Epidemiol. 1999; 17 Suppl 1:S731-6. . View in PubMed
A joint test of linkage and gene x environment interaction, with affected sib pairs Genet Epidemiol. 1999; 17 Suppl 1:S563-8. . View in PubMed
Multistage sampling for disease family registries J Natl Cancer Inst Monogr. 1999; (26):43-8. . View in PubMed
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. . View in PubMed
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. . View in PubMed
Modeling disease incidence rates in families Epidemiology. 1998 Sep; 9(5):557-62. . View in PubMed
Modeling hazard functions in families Genet Epidemiol. 1998; 15(2):147-71. . View in PubMed
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. . View in PubMed
Analysis of quantitative risk factors for a common oligogenic disease Genet Epidemiol. 1995; 12(6):759-64. . View in PubMed