TY - BOOK AU - Anthony, P. P. AU - DeMatos, P. PY - 2000 DA - 2000// TI - Secondary tumours of the liver. World Health Organization classification of tumours. Pathology & Genetics. Tumours of the digestive system PB - IARC Press CY - Lyon ID - Anthony2000 ER - TY - JOUR AU - Fujii, M. AU - Shimokawa, M. AU - Date, S. AU - Takano, A. AU - Matano, M. AU - Nanki, K. PY - 2016 DA - 2016// TI - A colorectal tumor Organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis JO - Cell Stem Cell VL - 18 UR - https://doi.org/10.1016/j.stem.2016.04.003 DO - 10.1016/j.stem.2016.04.003 ID - Fujii2016 ER - TY - JOUR AU - Brannon, A. R. AU - Vakiani, E. AU - Sylvester, B. E. AU - Scott, S. N. AU - McDermott, G. AU - Shah, R. H. PY - 2014 DA - 2014// TI - Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0454-7 DO - 10.1186/s13059-014-0454-7 ID - Brannon2014 ER - TY - JOUR AU - Vignot, S. AU - Lefebvre, C. AU - Frampton, G. M. AU - Meurice, G. AU - Yelensky, R. AU - Palmer, G. PY - 2015 DA - 2015// TI - Comparative analysis of primary tumour and matched metastases in colorectal cancer patients: evaluation of concordance between genomic and transcriptional profiles JO - Eur J Cancer VL - 51 UR - https://doi.org/10.1016/j.ejca.2015.02.012 DO - 10.1016/j.ejca.2015.02.012 ID - Vignot2015 ER - TY - JOUR AU - Moran, S. AU - Martinez-Cardus, A. AU - Sayols, S. AU - Musulen, E. AU - Balana, C. AU - Estival-Gonzalez, A. PY - 2016 DA - 2016// TI - Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis JO - Lancet Oncol VL - 17 UR - https://doi.org/10.1016/S1470-2045(16)30297-2 DO - 10.1016/S1470-2045(16)30297-2 ID - Moran2016 ER - TY - JOUR AU - Salgia, R. AU - Kulkarni, P. PY - 2018 DA - 2018// TI - The genetic/non-genetic duality of drug “resistance” in Cancer JO - Trends Cancer VL - 4 UR - https://doi.org/10.1016/j.trecan.2018.01.001 DO - 10.1016/j.trecan.2018.01.001 ID - Salgia2018 ER - TY - JOUR AU - Leung, M. L. AU - Davis, A. AU - Gao, R. AU - Casasent, A. AU - Wang, Y. AU - Sei, E. PY - 2017 DA - 2017// TI - Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.209973.116 DO - 10.1101/gr.209973.116 ID - Leung2017 ER - TY - JOUR AU - Lee, S. Y. AU - Haq, F. AU - Kim, D. AU - Jun, C. AU - Jo, H. J. AU - Ahn, S. M. PY - 2014 DA - 2014// TI - Comparative genomic analysis of primary and synchronous metastatic colorectal cancers JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0090459 DO - 10.1371/journal.pone.0090459 ID - Lee2014 ER - TY - JOUR AU - Suzuki, M. M. AU - Bird, A. PY - 2008 DA - 2008// TI - DNA methylation landscapes: provocative insights from epigenomics JO - Nat Rev Genet VL - 9 UR - https://doi.org/10.1038/nrg2341 DO - 10.1038/nrg2341 ID - Suzuki2008 ER - TY - JOUR AU - Jones, P. A. PY - 2012 DA - 2012// TI - Functions of DNA methylation: islands, start sites, gene bodies and beyond JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3230 DO - 10.1038/nrg3230 ID - Jones2012 ER - TY - JOUR AU - Reddington, J. P. AU - Pennings, S. AU - Meehan, R. R. PY - 2013 DA - 2013// TI - Non-canonical functions of the DNA methylome in gene regulation JO - Biochem J VL - 451 UR - https://doi.org/10.1042/BJ20121585 DO - 10.1042/BJ20121585 ID - Reddington2013 ER - TY - JOUR AU - Schubeler, D. PY - 2015 DA - 2015// TI - Function and information content of DNA methylation JO - Nature VL - 517 UR - https://doi.org/10.1038/nature14192 DO - 10.1038/nature14192 ID - Schubeler2015 ER - TY - JOUR AU - Parker, H. R. AU - Orjuela, S. AU - Martinho Oliveira, A. AU - Cereatti, F. AU - Sauter, M. AU - Heinrich, H. PY - 2018 DA - 2018// TI - The proto CpG island methylator phenotype of sessile serrated adenomas/polyps JO - Epigenetics VL - 13 UR - https://doi.org/10.1080/15592294.2018.1543504 DO - 10.1080/15592294.2018.1543504 ID - Parker2018 ER - TY - JOUR AU - Hackett, J. A. AU - Surani, M. A. PY - 2012 DA - 2012// TI - DNA methylation dynamics during the mammalian life cycle JO - Philos Trans R Soc B VL - 368 UR - https://doi.org/10.1098/rstb.2011.0328 DO - 10.1098/rstb.2011.0328 ID - Hackett2012 ER - TY - JOUR AU - Lee, H. J. AU - Hore, T. A. AU - Reik, W. PY - 2014 DA - 2014// TI - Reprogramming the methylome: erasing memory and creating diversity JO - Cell Stem Cell VL - 14 UR - https://doi.org/10.1016/j.stem.2014.05.008 DO - 10.1016/j.stem.2014.05.008 ID - Lee2014 ER - TY - JOUR AU - Truninger, K. AU - Menigatti, M. AU - Luz, J. AU - Russell, A. AU - Haider, R. AU - Gebbers, J. O. PY - 2005 DA - 2005// TI - Immunohistochemical analysis reveals high frequency of PMS2 defects in colorectal cancer JO - Gastroenterology VL - 128 UR - https://doi.org/10.1053/j.gastro.2005.01.056 DO - 10.1053/j.gastro.2005.01.056 ID - Truninger2005 ER - TY - JOUR AU - Phipps, A. I. AU - Limburg, P. J. AU - Baron, J. A. AU - Burnett-Hartman, A. N. AU - Weisenberger, D. J. AU - Laird, P. W. PY - 2015 DA - 2015// TI - Association between molecular subtypes of colorectal cancer and patient survival JO - Gastroenterology VL - 148 UR - https://doi.org/10.1053/j.gastro.2014.09.038 DO - 10.1053/j.gastro.2014.09.038 ID - Phipps2015 ER - TY - JOUR AU - Carethers, J. M. AU - Smith, E. J. AU - Behling, C. A. AU - Nguyen, L. AU - Tajima, A. AU - Doctolero, R. T. PY - 2004 DA - 2004// TI - Use of 5-fluorouracil and survival in patients with microsatellite-unstable colorectal cancer JO - Gastroenterology VL - 126 UR - https://doi.org/10.1053/j.gastro.2003.12.023 DO - 10.1053/j.gastro.2003.12.023 ID - Carethers2004 ER - TY - JOUR AU - Le, D. T. AU - Uram, J. N. AU - Wang, H. AU - Bartlett, B. R. AU - Kemberling, H. AU - Eyring, A. D. PY - 2015 DA - 2015// TI - PD-1 blockade in tumors with mismatch-repair deficiency JO - N Engl J Med VL - 372 UR - https://doi.org/10.1056/NEJMoa1500596 DO - 10.1056/NEJMoa1500596 ID - Le2015 ER - TY - JOUR AU - Guinney, J. AU - Dienstmann, R. AU - Wang, X. AU - Reyniès, A. AU - Schlicker, A. AU - Soneson, C. PY - 2015 DA - 2015// TI - The consensus molecular subtypes of colorectal cancer JO - Nat Med VL - 21 UR - https://doi.org/10.1038/nm.3967 DO - 10.1038/nm.3967 ID - Guinney2015 ER - TY - STD TI - Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, et al. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell, 2018. 33:721–735.e8. https://doi.org/10.1016/j.ccell.2018.03.010. ID - ref21 ER - TY - JOUR AU - Serre, D. AU - Lee, B. H. AU - Ting, A. H. PY - 2010 DA - 2010// TI - MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp992 DO - 10.1093/nar/gkp992 ID - Serre2010 ER - TY - JOUR AU - Li, H. PY - 2013 DA - 2013// TI - Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM JO - arXiv VL - 1303 ID - Li2013 ER - TY - JOUR AU - Lun, A. T. AU - Smyth, G. K. PY - 2016 DA - 2016// TI - csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1191 DO - 10.1093/nar/gkv1191 ID - Lun2016 ER - TY - STD TI - Lund SP, Nettleton D, McCarthy DJ, Smyth GK. Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Stat Appl Genet Mol Biol. 2012;11. https://doi.org/10.1515/1544-6115.1826. ID - ref25 ER - TY - JOUR AU - Cavalcante, R. G. AU - Sartor, M. A. PY - 2017 DA - 2017// TI - Annotatr: genomic regions in context JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx183 DO - 10.1093/bioinformatics/btx183 ID - Cavalcante2017 ER - TY - BOOK AU - Wickham, H. PY - 2016 DA - 2016// TI - ggplot2 -elegant graphics for data analysis PB - Springer-Verlag CY - New York ID - Wickham2016 ER - TY - JOUR AU - Lex, A. AU - Gehlenborg, N. AU - Strobelt, H. AU - Vuillemot, R. AU - Pfister, H. PY - 2014 DA - 2014// TI - UpSet: visualization of intersecting sets JO - IEEE Trans Vis Comput Graph VL - 20 UR - https://doi.org/10.1109/TVCG.2014.2346248 DO - 10.1109/TVCG.2014.2346248 ID - Lex2014 ER - TY - JOUR AU - Gardiner-Garden, M. AU - Frommer, M. PY - 1987 DA - 1987// TI - CpG islands in vertebrate genomes JO - J Mol Biol VL - 196 UR - https://doi.org/10.1016/0022-2836(87)90689-9 DO - 10.1016/0022-2836(87)90689-9 ID - Gardiner-Garden1987 ER - TY - STD TI - Affinito O, Palumbo D, Fierro A, Cuomo M, De Riso G, Monticelli A, et al. Nucleotide distance influences co-methylation between nearby CpG sites. Genomics. 2019. https://doi.org/10.1016/j.ygeno.2019.05.007. ID - ref30 ER - TY - JOUR AU - Zhang, W. AU - Spector, T. D. AU - Deloukas, P. AU - Bell, J. T. AU - Engelhardt, B. E. PY - 2015 DA - 2015// TI - Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0581-9 DO - 10.1186/s13059-015-0581-9 ID - Zhang2015 ER - TY - JOUR AU - De, S. AU - Michor, F. PY - 2011 DA - 2011// TI - DNA secondary structures and epigenetic determinants of cancer genome evolution JO - Nat Struct Mol Biol VL - 18 UR - https://doi.org/10.1038/nsmb.2089 DO - 10.1038/nsmb.2089 ID - De2011 ER - TY - JOUR AU - Ehrlich, M. PY - 2009 DA - 2009// TI - DNA hypomethylation in cancer cells JO - Epigenomics. VL - 1 UR - https://doi.org/10.2217/epi.09.33 DO - 10.2217/epi.09.33 ID - Ehrlich2009 ER - TY - JOUR AU - Tongelen, A. AU - Loriot, A. AU - Smet, C. PY - 2017 DA - 2017// TI - Oncogenic roles of DNA hypomethylation through the activation of cancer-germline genes JO - Cancer Lett VL - 396 UR - https://doi.org/10.1016/j.canlet.2017.03.029 DO - 10.1016/j.canlet.2017.03.029 ID - Tongelen2017 ER - TY - JOUR AU - Hur, K. AU - Cejas, P. AU - Feliu, J. AU - Moreno-Rubio, J. AU - Burgos, E. AU - Boland, C. R. PY - 2014 DA - 2014// TI - Hypomethylation of long interspersed nuclear element-1 (LINE-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis JO - Gut. VL - 63 UR - https://doi.org/10.1136/gutjnl-2012-304219 DO - 10.1136/gutjnl-2012-304219 ID - Hur2014 ER - TY - JOUR AU - Licht, J. D. PY - 2015 DA - 2015// TI - DNA methylation inhibitors in Cancer therapy: the immunity dimension JO - Cell VL - 162 UR - https://doi.org/10.1016/j.cell.2015.08.005 DO - 10.1016/j.cell.2015.08.005 ID - Licht2015 ER - TY - JOUR AU - Ju, H. X. AU - An, B. AU - Okamoto, Y. AU - Shinjo, K. AU - Kanemitsu, Y. AU - Komori, K. PY - 2011 DA - 2011// TI - Distinct profiles of epigenetic evolution between colorectal cancers with and without metastasis JO - Am J Pathol VL - 178 UR - https://doi.org/10.1016/j.ajpath.2010.12.045 DO - 10.1016/j.ajpath.2010.12.045 ID - Ju2011 ER - TY - JOUR AU - Konishi, K. AU - Watanabe, Y. AU - Shen, L. AU - Guo, Y. AU - Castoro, R. J. AU - Kondo, K. PY - 2011 DA - 2011// TI - DNA methylation profiles of primary colorectal carcinoma and matched liver metastasis JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0027889 DO - 10.1371/journal.pone.0027889 ID - Konishi2011 ER - TY - JOUR AU - Timp, W. AU - Bravo, H. C. AU - McDonald, O. G. AU - Goggins, M. AU - Umbricht, C. AU - Zeiger, M. PY - 2014 DA - 2014// TI - Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors JO - Genome Med VL - 6 UR - https://doi.org/10.1186/s13073-014-0061-y DO - 10.1186/s13073-014-0061-y ID - Timp2014 ER - TY - JOUR AU - Toyota, M. AU - Ho, C. AU - Ahuja, N. AU - Jair, K. W. AU - Li, Q. AU - Ohe-Toyota, M. PY - 1999 DA - 1999// TI - Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification JO - Cancer Res VL - 59 ID - Toyota1999 ER - TY - JOUR AU - Estecio, M. R. AU - Yan, P. S. AU - Huang, T. H. AU - Issa, J. P. PY - 2008 DA - 2008// TI - Methylated CpG Island Amplification and Microarray (MCAM) for High-Throughput Analysis of DNA Methylation JO - CSH Protoc VL - 2008 UR - https://doi.org/10.1101/pdb.prot4974 DO - 10.1101/pdb.prot4974 ID - Estecio2008 ER - TY - JOUR AU - Cohen, S. A. AU - Yu, M. AU - Baker, K. AU - Redman, M. AU - Wu, C. AU - Heinzerling, T. J. PY - 2017 DA - 2017// TI - The CpG island methylator phenotype is concordant between primary colorectal carcinoma and matched distant metastases JO - Clin Epigenetics VL - 9 UR - https://doi.org/10.1186/s13148-017-0347-1 DO - 10.1186/s13148-017-0347-1 ID - Cohen2017 ER - TY - JOUR AU - Piskol, R. AU - Huw, L. AU - Sergin, I. AU - Kljin, C. AU - Modrusan, Z. AU - Kim, D. PY - 2019 DA - 2019// TI - A clinically applicable gene-expression classifier reveals intrinsic and extrinsic contributions to consensus molecular subtypes in primary and metastatic Colon Cancer JO - Clin Cancer Res VL - 25 UR - https://doi.org/10.1158/1078-0432.CCR-18-3032 DO - 10.1158/1078-0432.CCR-18-3032 ID - Piskol2019 ER - TY - JOUR AU - Sharma, S. V. AU - Lee, D. Y. AU - Li, B. AU - Quinlan, M. P. AU - Takahashi, F. AU - Maheswaran, S. PY - 2010 DA - 2010// TI - A chromatin-mediated reversible drug-tolerant state in Cancer cell subpopulations JO - Cell VL - 141 UR - https://doi.org/10.1016/j.cell.2010.02.027 DO - 10.1016/j.cell.2010.02.027 ID - Sharma2010 ER - TY - JOUR AU - Roesch, A. AU - Vultur, A. AU - Bogeski, I. AU - Wang, H. AU - Zimmermann, K. M. AU - Speicher, D. PY - 2013 DA - 2013// TI - Overcoming intrinsic multidrug resistance in melanoma by blocking the mitochondrial respiratory chain of slow-cycling JARID1Bhigh cells JO - Cancer Cell VL - 23 UR - https://doi.org/10.1016/j.ccr.2013.05.003 DO - 10.1016/j.ccr.2013.05.003 ID - Roesch2013 ER - TY - JOUR AU - Tanaka, K. AU - Okamoto, A. PY - 2007 DA - 2007// TI - Degradation of DNA by bisulfite treatment JO - Bioorg Med Chem Lett VL - 17 UR - https://doi.org/10.1016/j.bmcl.2007.01.040 DO - 10.1016/j.bmcl.2007.01.040 ID - Tanaka2007 ER - TY - JOUR AU - Grunau, C. AU - Clark, S. J. AU - Rosenthal, A. PY - 2001 DA - 2001// TI - Bisulfite genomic sequencing: systematic investigation of critical experimental parameters JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.13.e65 DO - 10.1093/nar/29.13.e65 ID - Grunau2001 ER - TY - JOUR AU - Aberg, K. A. AU - Chan, R. F. AU - Shabalin, A. A. AU - Zhao, M. AU - Turecki, G. AU - Staunstrup, N. H. PY - 2017 DA - 2017// TI - A MBD-seq protocol for large-scale methylome-wide studies with (very) low amounts of DNA JO - Epigenetics VL - 12 UR - https://doi.org/10.1080/15592294.2017.1335849 DO - 10.1080/15592294.2017.1335849 ID - Aberg2017 ER - TY - JOUR AU - Cooper, D. N. AU - Taggart, M. H. AU - Bird, A. P. PY - 1983 DA - 1983// TI - Unmethylated domains in vertebrate DNA JO - Nucleic Acids Res VL - 11 UR - https://doi.org/10.1093/nar/11.3.647 DO - 10.1093/nar/11.3.647 ID - Cooper1983 ER - TY - JOUR AU - Bird, A. P. PY - 1986 DA - 1986// TI - CpG-rich islands and the function of DNA methylation JO - Nature VL - 321 UR - https://doi.org/10.1038/321209a0 DO - 10.1038/321209a0 ID - Bird1986 ER - TY - JOUR AU - Harris, R. A. AU - Wang, T. AU - Coarfa, C. AU - Nagarajan, R. P. AU - Hong, C. AU - Downey, S. L. PY - 2010 DA - 2010// TI - Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1682 DO - 10.1038/nbt.1682 ID - Harris2010 ER - TY - JOUR AU - Li, N. AU - Ye, M. AU - Li, Y. AU - Yan, Z. AU - Butcher, L. M. AU - Sun, J. PY - 2010 DA - 2010// TI - Whole genome DNA methylation analysis based on high throughput sequencing technology JO - Methods VL - 52 UR - https://doi.org/10.1016/j.ymeth.2010.04.009 DO - 10.1016/j.ymeth.2010.04.009 ID - Li2010 ER - TY - JOUR AU - Aberg, K. A. AU - Chan, R. F. AU - Xie, L. AU - Shabalin, A. A. AU - Oord, E. PY - 1708 DA - 1708// TI - Methyl-CpG-binding domain sequencing: MBD-seq JO - Methods Mol Biol VL - 2018 UR - https://doi.org/10.1007/978-1-4939-7481-8_10 DO - 10.1007/978-1-4939-7481-8_10 ID - Aberg1708 ER - TY - JOUR AU - Robinson, M. D. AU - Stirzaker, C. AU - Statham, A. L. AU - Coolen, M. W. AU - Song, J. Z. AU - Nair, S. S. PY - 2010 DA - 2010// TI - Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.110601.110 DO - 10.1101/gr.110601.110 ID - Robinson2010 ER -