{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T14:50:46Z","timestamp":1753887046187,"version":"3.41.2"},"reference-count":41,"publisher":"Index Copernicus","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Despite enormous progress in molecular analysis of cancer cell genomes, the mechanism of tumorigenesis remains unclear. The information present in the genome is not limited to the DNA sequence itself. Indeed, a significant portion of this information is concealed in the spatial structure of chromatin. Ongoing scientific studies that focus on the three-dimensional structure of chromatin raise hopes of arriving at a general explanation of the cancer transformation phenomenon.<\/jats:p>","DOI":"10.1515\/bams-2018-0002","type":"journal-article","created":{"date-parts":[[2018,4,12]],"date-time":"2018-04-12T08:50:02Z","timestamp":1523523002000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromatin 3D \u2013 will it make understanding of cancer transformation finally possible?"],"prefix":"10.5604","volume":"14","author":[{"given":"Gra\u017cyna","family":"Drabik","sequence":"first","affiliation":[{"name":"Department of Transplantation , Polish-American Institute of Pediatrics, Jagiellonian University \u2013 Medical College , Krak\u00f3w , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jolanta","family":"Kaszuba-Zwoi\u0144ska","sequence":"additional","affiliation":[{"name":"Chair of Pathophysiology, Jagiellonian University \u2013 Medical College , Krak\u00f3w , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zdzis\u0142aw","family":"Wi\u015bniowski","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , Krak\u00f3w , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leszek","family":"Konieczny","sequence":"additional","affiliation":[{"name":"Chair of Medical Biochemistry, Jagiellonian University \u2013 Medical College , Krak\u00f3w , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irena","family":"Roterman","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Telemedicine , Jagiellonian University \u2013 Medical College , \u0141azarza 16 , 31-530 Krak\u00f3w , Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"3689","published-online":{"date-parts":[[2018,3,30]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, et al. Comparison of algorithms for the detection of cancer drivers at subgene resolution. Nat Methods 2017;14:782\u20138.10.1038\/nmeth.436428714987","key":"2023010916541022745_j_bams-2018-0002_ref_001_w2aab3b7b3b1b6b1ab1b4b1Aa","DOI":"10.1038\/nmeth.4364"},{"unstructured":"Fraser M, Sabelnykova VY, Yamaguchi TN, Heisler LE, Livingstone J, Huang V, et al. Genomic hallmarks of localized, non-indolent prostate cancer. Nature 2017;541:359\u201364.10.1038\/nature2078828068672","key":"2023010916541022745_j_bams-2018-0002_ref_002_w2aab3b7b3b1b6b1ab1b4b2Aa"},{"doi-asserted-by":"crossref","unstructured":"Lan X, J\u00f6rg DJ, Cavalli FM, Richards LM, Nguyen LV, Vanner RJ, et al. Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature 2017;549:227\u201332.2885417110.1038\/nature23666","key":"2023010916541022745_j_bams-2018-0002_ref_003_w2aab3b7b3b1b6b1ab1b4b3Aa","DOI":"10.1038\/nature23666"},{"doi-asserted-by":"crossref","unstructured":"Smith MP, Harper DA. Causes of the Cambrian explosion. Science 2013;341:1355\u20136.10.1126\/science.123945024052300","key":"2023010916541022745_j_bams-2018-0002_ref_004_w2aab3b7b3b1b6b1ab1b4b4Aa","DOI":"10.1126\/science.1239450"},{"doi-asserted-by":"crossref","unstructured":"Piwowar M, Dygut J, Piwowar P, Konieczny L, Roterman I. Attempt at a systemic outlook on aging and carcinogenesis. BAMS 2014;19:101\u201315.","key":"2023010916541022745_j_bams-2018-0002_ref_005_w2aab3b7b3b1b6b1ab1b4b5Aa","DOI":"10.1515\/bams-2014-0012"},{"unstructured":"Pollack RE, Teebor GW. Relationship of contact inhibition to tumor transplantability, morphology, and growth rate. Cancer Res 1969;29:1770\u20132.5350078","key":"2023010916541022745_j_bams-2018-0002_ref_006_w2aab3b7b3b1b6b1ab1b4b6Aa"},{"doi-asserted-by":"crossref","unstructured":"GTEx Consortium; Laboratory, Data Analysis & Coordinating Center (LDACC) \u2013 Analysis Working Group; Statistical Methods groups \u2013 Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH\/NCI; et al. Genetic effects on gene expression across human tissues. Nature 2017;550:204\u201313.29022597","key":"2023010916541022745_j_bams-2018-0002_ref_007_w2aab3b7b3b1b6b1ab1b4b7Aa","DOI":"10.1038\/nature24277"},{"unstructured":"Peifer M, Hertwig F, Roels F, Dreidax D, Gartlgruber M, Menon R, et al. Telomerase activation by genomic rearrangements in high-risk neuroblastoma. Nature 2015;526:700\u20134.10.1038\/nature1498026466568","key":"2023010916541022745_j_bams-2018-0002_ref_008_w2aab3b7b3b1b6b1ab1b4b8Aa"},{"doi-asserted-by":"crossref","unstructured":"de Lange T. Activation of telomerase in a human tumor. Proc Natl Acad Sci U S A 1994;91:2882\u20135.10.1073\/pnas.91.8.2882","key":"2023010916541022745_j_bams-2018-0002_ref_009_w2aab3b7b3b1b6b1ab1b4b9Aa","DOI":"10.1073\/pnas.91.8.2882"},{"doi-asserted-by":"crossref","unstructured":"Shay JW, Reddel RR, Wright WE. Cancer and telomeres \u2013 an ALTernative to telomerase. Science 2012;336:1388\u201390.10.1126\/science.122239422700908","key":"2023010916541022745_j_bams-2018-0002_ref_010_w2aab3b7b3b1b6b1ab1b4c10Aa","DOI":"10.1126\/science.1222394"},{"doi-asserted-by":"crossref","unstructured":"Els\u00e4sser SJ, Allis CD, Lewis PW. Cancer. New epigenetic drivers of cancers. Science 2011;331:1145\u20136.10.1126\/science.120328021385704","key":"2023010916541022745_j_bams-2018-0002_ref_011_w2aab3b7b3b1b6b1ab1b4c11Aa","DOI":"10.1126\/science.1203280"},{"doi-asserted-by":"crossref","unstructured":"Vander Heiden MG, Cantley LC, Thompson CB. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 2009;324:1029\u201333.10.1126\/science.116080919460998","key":"2023010916541022745_j_bams-2018-0002_ref_012_w2aab3b7b3b1b6b1ab1b4c12Aa","DOI":"10.1126\/science.1160809"},{"doi-asserted-by":"crossref","unstructured":"Vander Heiden MG, Locasale JW, Swanson KD, Sharfi H, Heffron GJ, Amador-Noguez D, et al. Evidence for an alternative glycolytic pathway in rapidly proliferating cells. Science 2010;329:1492\u20139.2084726310.1126\/science.1188015","key":"2023010916541022745_j_bams-2018-0002_ref_013_w2aab3b7b3b1b6b1ab1b4c13Aa","DOI":"10.1126\/science.1188015"},{"doi-asserted-by":"crossref","unstructured":"Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 2017;543:122\u20135.10.1038\/nature2135628178237","key":"2023010916541022745_j_bams-2018-0002_ref_014_w2aab3b7b3b1b6b1ab1b4c14Aa","DOI":"10.1038\/nature21356"},{"doi-asserted-by":"crossref","unstructured":"Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014;505:495\u2013501.10.1038\/nature1291224390350","key":"2023010916541022745_j_bams-2018-0002_ref_015_w2aab3b7b3b1b6b1ab1b4c15Aa","DOI":"10.1038\/nature12912"},{"doi-asserted-by":"crossref","unstructured":"Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013;502:333\u20139.10.1038\/nature1263424132290","key":"2023010916541022745_j_bams-2018-0002_ref_016_w2aab3b7b3b1b6b1ab1b4c16Aa","DOI":"10.1038\/nature12634"},{"doi-asserted-by":"crossref","unstructured":"Weinstein JN, Akbani R, Broom BM, Wang W, Verhaak RG, McConkey D, et al. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014;507:315\u201322.10.1038\/nature1296524476821","key":"2023010916541022745_j_bams-2018-0002_ref_017_w2aab3b7b3b1b6b1ab1b4c17Aa","DOI":"10.1038\/nature12965"},{"doi-asserted-by":"crossref","unstructured":"Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 2013;3:2650.2408484910.1038\/srep02650","key":"2023010916541022745_j_bams-2018-0002_ref_018_w2aab3b7b3b1b6b1ab1b4c18Aa","DOI":"10.1038\/srep02952"},{"doi-asserted-by":"crossref","unstructured":"Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, et al. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330\u20137.2281069610.1038\/nature11252","key":"2023010916541022745_j_bams-2018-0002_ref_019_w2aab3b7b3b1b6b1ab1b4c19Aa","DOI":"10.1038\/nature11252"},{"doi-asserted-by":"crossref","unstructured":"Tokheim CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Karchin R. Evaluating the evaluation of cancer driver genes. Proc Natl Acad Sci U S A 2016;113:14330\u20135.10.1073\/pnas.161644011327911828","key":"2023010916541022745_j_bams-2018-0002_ref_020_w2aab3b7b3b1b6b1ab1b4c20Aa","DOI":"10.1073\/pnas.1616440113"},{"doi-asserted-by":"crossref","unstructured":"Zhu J, Sammons MA, Donahue G, Dou Z, Vedadi M, Getlik M, et al. Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth. Nature 2015;525:206\u201311.10.1038\/nature1525126331536","key":"2023010916541022745_j_bams-2018-0002_ref_021_w2aab3b7b3b1b6b1ab1b4c21Aa","DOI":"10.1038\/nature15251"},{"unstructured":"Konieczny L, Roterman I, Spolnik P. Systems biology \u2013 strategy of living organism. Heidelberg Dordrecht, London, NY:  Springer, 2012.","key":"2023010916541022745_j_bams-2018-0002_ref_022_w2aab3b7b3b1b6b1ab1b4c22Aa"},{"doi-asserted-by":"crossref","unstructured":"Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, et al. 3D chromosome regulatory landscape of human pluripotent cells. Cell Stem Cell 2016;18:262\u201375.2668646510.1016\/j.stem.2015.11.007","key":"2023010916541022745_j_bams-2018-0002_ref_023_w2aab3b7b3b1b6b1ab1b4c23Aa","DOI":"10.1016\/j.stem.2015.11.007"},{"doi-asserted-by":"crossref","unstructured":"Davies JO, Telenius JM, McGowan SJ, Roberts NA, Taylor S, Higgs DR, et al. Multiplexed analysis of chromosome conformation at vastly improved sensitivity. Nat Methods 2016;13:74\u201380.10.1038\/nmeth.366426595209","key":"2023010916541022745_j_bams-2018-0002_ref_024_w2aab3b7b3b1b6b1ab1b4c24Aa","DOI":"10.1038\/nmeth.3664"},{"doi-asserted-by":"crossref","unstructured":"Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, et al. The 4D nucleome project. Nature 2017;549:219\u201326.2890591110.1038\/nature23884","key":"2023010916541022745_j_bams-2018-0002_ref_025_w2aab3b7b3b1b6b1ab1b4c25Aa","DOI":"10.1038\/nature23884"},{"doi-asserted-by":"crossref","unstructured":"Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 2012;9:999\u20131003.10.1038\/nmeth.214822941365","key":"2023010916541022745_j_bams-2018-0002_ref_026_w2aab3b7b3b1b6b1ab1b4c26Aa","DOI":"10.1038\/nmeth.2148"},{"doi-asserted-by":"crossref","unstructured":"Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013;14:390\u2013403.10.1038\/nrg345423657480","key":"2023010916541022745_j_bams-2018-0002_ref_027_w2aab3b7b3b1b6b1ab1b4c27Aa","DOI":"10.1038\/nrg3454"},{"doi-asserted-by":"crossref","unstructured":"van Arensbergen J, van Steensel B, Bussemaker HJ. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol 2014;24:695\u2013702.2516091210.1016\/j.tcb.2014.07.004","key":"2023010916541022745_j_bams-2018-0002_ref_028_w2aab3b7b3b1b6b1ab1b4c28Aa","DOI":"10.1016\/j.tcb.2014.07.004"},{"doi-asserted-by":"crossref","unstructured":"Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays 2013;35:818\u201328.10.1002\/bies.20130004023832846","key":"2023010916541022745_j_bams-2018-0002_ref_029_w2aab3b7b3b1b6b1ab1b4c29Aa","DOI":"10.1002\/bies.201300040"},{"doi-asserted-by":"crossref","unstructured":"Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature 2012;489:109\u201313.10.1038\/nature1127922955621","key":"2023010916541022745_j_bams-2018-0002_ref_030_w2aab3b7b3b1b6b1ab1b4c30Aa","DOI":"10.1038\/nature11279"},{"doi-asserted-by":"crossref","unstructured":"Pennisi E. An enhanced view of gene control. Science 2015;348:1407\u20138.2611369510.1126\/science.348.6242.1407","key":"2023010916541022745_j_bams-2018-0002_ref_031_w2aab3b7b3b1b6b1ab1b4c31Aa","DOI":"10.1126\/science.348.6242.1407"},{"doi-asserted-by":"crossref","unstructured":"Terakawa T, Bisht S, Eeftens JM, Dekker C, Haering CH, Greene EC. The condensin complex is a mechanochemical motor that translocates along DNA. Science 2017;358:672\u20136.10.1126\/science.aan651628882993","key":"2023010916541022745_j_bams-2018-0002_ref_032_w2aab3b7b3b1b6b1ab1b4c32Aa","DOI":"10.1126\/science.aan6516"},{"doi-asserted-by":"crossref","unstructured":"Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 2017;551:51\u20136.29094699","key":"2023010916541022745_j_bams-2018-0002_ref_033_w2aab3b7b3b1b6b1ab1b4c33Aa","DOI":"10.1038\/nature24281"},{"doi-asserted-by":"crossref","unstructured":"Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, et al. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell 2014;159:374\u201387.10.1016\/j.cell.2014.09.03025303531","key":"2023010916541022745_j_bams-2018-0002_ref_034_w2aab3b7b3b1b6b1ab1b4c34Aa","DOI":"10.1016\/j.cell.2014.09.030"},{"doi-asserted-by":"crossref","unstructured":"McCord RP. How to build a cohesive genome in 3D. Nature 2017;551:38\u201340.28976964","key":"2023010916541022745_j_bams-2018-0002_ref_035_w2aab3b7b3b1b6b1ab1b4c35Aa","DOI":"10.1038\/nature24145"},{"doi-asserted-by":"crossref","unstructured":"Willis NA, Frock RL, Menghi F, Duffey EE, Panday A, Camacho V, et al. Mechanism of tandem duplication formation in BRCA1-mutant cells. Nature 2017;551:590\u20135.29168504","key":"2023010916541022745_j_bams-2018-0002_ref_036_w2aab3b7b3b1b6b1ab1b4c36Aa","DOI":"10.1038\/nature24477"},{"doi-asserted-by":"crossref","unstructured":"Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Sch\u00f6pflin R, et al. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature 2016;538:265\u20139.10.1038\/nature1980027706140","key":"2023010916541022745_j_bams-2018-0002_ref_037_w2aab3b7b3b1b6b1ab1b4c37Aa","DOI":"10.1038\/nature19800"},{"doi-asserted-by":"crossref","unstructured":"Menghi F, Inaki K, Woo X, Kumar PA, Grzeda KR, Malhotra A, et al. The tandem duplicator phenotype as a distinct genomic configuration in cancer. Proc Natl Acad Sci U S A 2016;113:E2373\u201382.10.1073\/pnas.152001011327071093","key":"2023010916541022745_j_bams-2018-0002_ref_038_w2aab3b7b3b1b6b1ab1b4c38Aa","DOI":"10.1073\/pnas.1520010113"},{"doi-asserted-by":"crossref","unstructured":"Lupi\u00e1\u00f1ez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 2015;161:1012\u201325.2595977410.1016\/j.cell.2015.04.004","key":"2023010916541022745_j_bams-2018-0002_ref_039_w2aab3b7b3b1b6b1ab1b4c39Aa","DOI":"10.1016\/j.cell.2015.04.004"},{"doi-asserted-by":"crossref","unstructured":"Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 2016;351:1454\u20138.2694086710.1126\/science.aad9024","key":"2023010916541022745_j_bams-2018-0002_ref_040_w2aab3b7b3b1b6b1ab1b4c40Aa","DOI":"10.1126\/science.aad9024"},{"unstructured":"Ferguson-Smith M. Essential medical genetics. Oxford:  Blackwell Science, 1997.","key":"2023010916541022745_j_bams-2018-0002_ref_041_w2aab3b7b3b1b6b1ab1b4c41Aa"}],"container-title":["Bio-Algorithms and Med-Systems"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.degruyter.com\/view\/j\/bams.2018.14.issue-1\/bams-2018-0002\/bams-2018-0002.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/bams-2018-0002\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.degruyter.com\/document\/doi\/10.1515\/bams-2018-0002\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T10:08:18Z","timestamp":1719223698000},"score":1,"resource":{"primary":{"URL":"https:\/\/bamsjournal.com\/resources\/html\/article\/details?id=616716"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,3,1]]},"references-count":41,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,2,21]]},"published-print":{"date-parts":[[2018,3,28]]}},"alternative-id":["10.1515\/bams-2018-0002"],"URL":"https:\/\/doi.org\/10.1515\/bams-2018-0002","relation":{},"ISSN":["1896-530X","1895-9091"],"issn-type":[{"type":"electronic","value":"1896-530X"},{"type":"print","value":"1895-9091"}],"subject":[],"published":{"date-parts":[[2018,3,1]]},"article-number":"20180002"}}