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Research Paper

DNA Methylation Analysis as a Tool for Cell Typing

Pages 56-61 | Published online: 10 Mar 2006

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Iolanda Agliata, Nora Fernandez-Jimenez, Chloe Goldsmith, Julien C. Marie, Jose R. Bilbao, Robert Dante & Hector Hernandez-Vargas. (2020) The DNA methylome of inflammatory bowel disease (IBD) reflects intrinsic and extrinsic factors in intestinal mucosal cells. Epigenetics 15:10, pages 1068-1082.
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Devin C Koestler, Brock C Christensen, Margaret R Karagas, Carmen J Marsit, Scott M Langevin, Karl T Kelsey, John K Wiencke & E Andres Houseman. (2013) Blood-based profiles of DNA methylation predict the underlying distribution of cell types. Epigenetics 8:8, pages 816-826.
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Jalid Sehouli, Christoph Loddenkemper, Tatjana Cornu, Tim Schwachula, Ulrich Hoffmüller, Andreas Grützkau, Philipp Lohneis, Thorsten Dickhaus, Jörn Gröne, Martin Kruschewski, Alexander Mustea, Ivana Turbachova, Udo Baron & Sven Olek. (2011) Epigenetic quantification of tumor-infiltrating T-lymphocytes. Epigenetics 6:2, pages 236-246.
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Ji-Qing Chen, Lucas A. Salas, John K. Wiencke, Devin C. Koestler, Annette M. Molinaro, Angeline S. Andrew, John D. Seigne, Margaret R. Karagas, Karl T. Kelsey & Brock C. Christensen. (2022) Immune profiles and DNA methylation alterations related with non-muscle-invasive bladder cancer outcomes. Clinical Epigenetics 14:1.
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Dingqin He, Ming Chen, Wenjuan Wang, Chunhui Song & Yufang Qin. (2022) Deconvolution of tumor composition using partially available DNA methylation data. BMC Bioinformatics 23:1.
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Verena A. Katzke, Charlotte Le Cornet, Rayaan Mahfouz, Bianca Brauer, Theron Johnson, Federico Canzian, Vinciane Rebours, Marie-Christine Boutron-Ruault, Gianluca Severi, Matthias B. Schulze, Anja Olsen, Anne Tjønneland, Kim Overvad, Marta Crous-Bou, Esther Molina-Montes, Pilar Amiano, José María Huerta, Eva Ardanaz, Aurora Perez-Cornago, Giovanna Masala, Valeria Pala, Rosario Tumino, Carlotta Sacerdote, Salvatore Panico, Bas Bueno-de-Mesquita, Roel Vermeulen, Malin Sund, Oskar Franklin, Sofia Christakoudi, Laure Dossus, Elisabete Weiderpass, Sven Olek & Rudolf Kaaks. (2021) Are Circulating Immune Cells a Determinant of Pancreatic Cancer Risk? A Prospective Study Using Epigenetic Cell Count Measures. Cancer Epidemiology, Biomarkers & Prevention 30:12, pages 2179-2187.
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Yijin Xiang, Zeyuan Wang, Qin Hui, Marta Gwinn, Viola Vaccarino & Yan V. Sun. (2021) DNA Methylation of TXNIP Independently Associated with Inflammation and Diabetes Mellitus in Twins. Twin Research and Human Genetics 24:5, pages 273-280.
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Xīn Gào, Yan Zhang, Xiangwei Li, Lina Jansen, Elizabeth Alwers, Melanie Bewerunge-Hudler, Matthias Schick, Jenny Chang-Claude, Michael Hoffmeister & Hermann Brenner. (2021) DNA Methylation-Based Estimates of Circulating Leukocyte Composition for Predicting Colorectal Cancer Survival: A Prospective Cohort Study. Cancers 13:12, pages 2948.
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Dorota Iwaszkiewicz-Grzes, Magdalena Piotrowska, Mateusz Gliwinski, Zuzanna Urban-Wójciuk & Piotr Trzonkowski. (2021) Antigenic Challenge Influences Epigenetic Changes in Antigen-Specific T Regulatory Cells. Frontiers in Immunology 12.
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Liqiong Zhu, Meilan Liu, Suning Zhang, Yuhua Ou, Ying Chen, Jing Wei, Fang Su, Hui Chen & Jianping Zhang. (2020) Foxp3 TSDR Hypermethylation Is Correlated with Decreased Tregs in Patients with Unexplained Recurrent Spontaneous Abortion. Reproductive Sciences 28:2, pages 470-478.
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Alexis Zukowski, Satyanarayan Rao & Srinivas Ramachandran. (2020) Phenotypes from cell-free DNA. Open Biology 10:9.
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Douglas Arneson, Xia Yang & Kai Wang. (2020) MethylResolver—a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents. Communications Biology 3:1.
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Wenhui Li, Ziyi Chen, Aiping Wu, F. Xiao-Feng Qin & Lianjun Zhang. 2020. Epigenetics of the Immune System. Epigenetics of the Immune System 239 252 .
Rose Du, Vince Carey & Scott T Weiss. (2019) deconvSeq: deconvolution of cell mixture distribution in sequencing data. Bioinformatics 35:24, pages 5095-5102.
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Alexia Cardona, Felix R. DayJohn R.B. PerryMarie Loh, Audrey Y. Chu, Benjamin LehneDirk S. PaulLuca A. Lotta, Isobel D. StewartNicola D. KerrisonRobert A. ScottKay-Tee Khaw, Nita G. Forouhi, Claudia LangenbergChunyu Liu, Michael M. Mendelson, Daniel Levy, Stephan BeckR. David Leslie, Josée Dupuis, James B. Meigs, Jaspal S. KoonerJussi Pihlajamäki, Allan Vaag, Alexander Perfilyev, Charlotte Ling, Marie-France Hivert, John C. Chambers, Nicholas J. WarehamKen K. Ong. (2019) Epigenome-Wide Association Study of Incident Type 2 Diabetes in a British Population: EPIC-Norfolk Study. Diabetes 68:12, pages 2315-2326.
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Benjamin Goeppert, Reka Toth, Stephan Singer, Thomas Albrecht, Daniel B. Lipka, Pavlo Lutsik, David Brocks, Marion Baehr, Oliver Muecke, Yassen Assenov, Lei Gu, Volker Endris, Albrecht Stenzinger, Arianeb Mehrabi, Peter Schirmacher, Christoph Plass, Dieter Weichenhan & Stephanie Roessler. (2019) Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma. Hepatology 69:5, pages 2091-2106.
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A. Senst, J. Dressler, J. Edelmann & M. Kohl. (2019) Entwicklung eines qPCR-Assays zum Nachweis der SekretartDevelopment of a qPCR assay for detection of secretion types. Rechtsmedizin 29:2, pages 94-100.
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Athina Vidaki & Manfred Kayser. (2018) Recent progress, methods and perspectives in forensic epigenetics. Forensic Science International: Genetics 37, pages 180-195.
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Athina Vidaki, Vivian Kalamara, Elena Carnero-Montoro, Timothy Spector, Jordana Bell & Manfred Kayser. (2018) Investigating the Epigenetic Discrimination of Identical Twins Using Buccal Swabs, Saliva, and Cigarette Butts in the Forensic Setting. Genes 9:5, pages 252.
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Ehren R. V. Moler, Abdulkadir Abakir, Maria Eleftheriou, Jeremy S. Johnson, Konstantin V. Krutovsky, Lara C. Lewis, Alexey Ruzov, Amy V. Whipple & Om P. Rajora. 2019. Population Genomics. Population Genomics 179 260 .
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Athina Vidaki, Cecilia Johansson & Federica Giangasparo. (2017) Differentially methylated embryonal Fyn-associated substrate (EFS) gene as a blood-specific epigenetic marker and its potential application in forensic casework. Forensic Science International: Genetics 29, pages 165-173.
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Lorella Paparo, Rita Nocerino, Linda Cosenza, Rosita Aitoro, Valeria D’Argenio, Valentina Del Monaco, Carmen Di Scala, Antonio Amoroso, Margherita Di Costanzo, Francesco Salvatore & Roberto Berni Canani. (2016) Epigenetic features of FoxP3 in children with cow’s milk allergy. Clinical Epigenetics 8:1.
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Michelle L. Wright, Mikhail G. Dozmorov, Aaron R. Wolen, Colleen Jackson-Cook, Angela R. Starkweather, Debra E. Lyon & Timothy P. York. (2016) Establishing an analytic pipeline for genome-wide DNA methylation. Clinical Epigenetics 8:1.
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Yanhua Wen, Yanjun Wei, Shumei Zhang, Song Li, Hongbo Liu, Fang Wang, Yue Zhao, Dongwei Zhang & Yan Zhang. (2016) Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature. Briefings in Bioinformatics, pages bbw028.
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Sophia Forat, Bruno Huettel, Richard Reinhardt, Rolf Fimmers, Gerhard Haidl, Dominik Denschlag & Klaus Olek. (2016) Methylation Markers for the Identification of Body Fluids and Tissues from Forensic Trace Evidence. PLOS ONE 11:2, pages e0147973.
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Na Zhang, Shumin Zhao, Su-Hua Zhang, Jinzhong Chen, Daru Lu, Min Shen & Chengtao Li. (2015) Intra-Monozygotic Twin Pair Discordance and Longitudinal Variation of Whole-Genome Scale DNA Methylation in Adults. PLOS ONE 10:8, pages e0135022.
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Carlos M. Rodríguez López & Mike J. Wilkinson. (2015) Epi-fingerprinting and epi-interventions for improved crop production and food quality. Frontiers in Plant Science 6.
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Konstantin Schildknecht, Sven Olek & Thorsten Dickhaus. (2015) Simultaneous Statistical Inference for Epigenetic Data. PLOS ONE 10:5, pages e0125587.
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Jana Jeschke, Evelyne Collignon & François Fuks. (2015) DNA methylome profiling beyond promoters - taking an epigenetic snapshot of the breast tumor microenvironment. FEBS Journal 282:9, pages 1801-1814.
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Galina Yu. Zheleznyakova, Emil K. Nilsson, Anton V. Kiselev, Marianna A. Maretina, Lyudmila I. Tishchenko, Robert Fredriksson, Vladislav S. Baranov & Helgi B. Schiöth. (2015) Methylation Levels of SLC23A2 and NCOR2 Genes Correlate with Spinal Muscular Atrophy Severity. PLOS ONE 10:3, pages e0121964.
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Changhua Zhuo, Ye Xu, Mingang Ying, Qingguo Li, Liyong Huang, Dawei Li, Sanjun Cai & Bin Li. (2015) FOXP3+ Tregs: heterogeneous phenotypes and conflicting impacts on survival outcomes in patients with colorectal cancer. Immunologic Research 61:3, pages 338-347.
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Tiffany J. Morris & Stephan Beck. (2015) Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods 72, pages 3-8.
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Eugene Andres Houseman, John Molitor & Carmen J. Marsit. (2014) Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics 30:10, pages 1431-1439.
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Peter Zimmermann, Stéphane Boeuf, Andrea Dickhut, Sandra Boehmer, Sven Olek & Wiltrud Richter. (2008) Correlation of COL10A1 induction during chondrogenesis of mesenchymal stem cells with demethylation of two CpG sites in the COL10A1 promoter. Arthritis & Rheumatism 58:9, pages 2743-2753.
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