TY - JOUR AU - Li, G. L. PY - 2012 DA - 2012// TI - Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation JO - Cell VL - 148 UR - https://doi.org/10.1016/j.cell.2011.12.014 DO - 10.1016/j.cell.2011.12.014 ID - Li2012 ER - TY - JOUR AU - Zhang, Y. B. PY - 2013 DA - 2013// TI - Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations JO - Nature VL - 504 UR - https://doi.org/10.1038/nature12716 DO - 10.1038/nature12716 ID - Zhang2013 ER - TY - JOUR AU - Roy, A. L. AU - Sen, R. AU - Roeder, R. G. PY - 2011 DA - 2011// TI - Enhancer-promoter communication and transcriptional regulation of Igh JO - Trends Immunol VL - 32 UR - https://doi.org/10.1016/j.it.2011.06.012 DO - 10.1016/j.it.2011.06.012 ID - Roy2011 ER - TY - JOUR AU - Dixon, J. R. PY - 2012 DA - 2012// TI - Topological domains in mammalian genomes identified by analysis of chromatin interactions JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11082 DO - 10.1038/nature11082 ID - Dixon2012 ER - TY - JOUR AU - Nora, E. P. PY - 2012 DA - 2012// TI - Spatial partitioning of the regulatory landscape of the X-inactivation centre JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11049 DO - 10.1038/nature11049 ID - Nora2012 ER - TY - JOUR AU - Sexton, T. PY - 2012 DA - 2012// TI - Three-dimensional folding and functional organization principles of the Drosophila genome JO - Cell VL - 148 UR - https://doi.org/10.1016/j.cell.2012.01.010 DO - 10.1016/j.cell.2012.01.010 ID - Sexton2012 ER - TY - JOUR AU - Hu, G. Q. PY - 2018 DA - 2018// TI - Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells JO - Immunity VL - 48 UR - https://doi.org/10.1016/j.immuni.2018.01.013 DO - 10.1016/j.immuni.2018.01.013 ID - Hu2018 ER - TY - JOUR AU - Krijger, P. H. L. PY - 2016 DA - 2016// TI - Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming JO - Cell Stem Cell VL - 18 UR - https://doi.org/10.1016/j.stem.2016.01.007 DO - 10.1016/j.stem.2016.01.007 ID - Krijger2016 ER - TY - JOUR AU - Jin, F. L. PY - 2013 DA - 2013// TI - A high-resolution map of the three-dimensional chromatin interactome in human cells JO - Nature VL - 503 UR - https://doi.org/10.1038/nature12644 DO - 10.1038/nature12644 ID - Jin2013 ER - TY - JOUR AU - Dixon, J. R. PY - 2015 DA - 2015// TI - Chromatin architecture reorganization during stem cell differentiation JO - Nature VL - 518 UR - https://doi.org/10.1038/nature14222 DO - 10.1038/nature14222 ID - Dixon2015 ER - TY - JOUR AU - Smith, E. M. AU - Lajoie, B. R. AU - Jain, G. AU - Dekker, J. PY - 2016 DA - 2016// TI - Invariant TAD boundaries constrain cell-type-specific looping interactions between promoters and distal elements around the CFTR locus JO - Am J Hum Genet VL - 98 UR - https://doi.org/10.1016/j.ajhg.2015.12.002 DO - 10.1016/j.ajhg.2015.12.002 ID - Smith2016 ER - TY - JOUR AU - Rao, S. S. PY - 2014 DA - 2014// TI - A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping JO - Cell VL - 159 UR - https://doi.org/10.1016/j.cell.2014.11.021 DO - 10.1016/j.cell.2014.11.021 ID - Rao2014 ER - TY - JOUR AU - Dixon, J. R. AU - Gorkin, D. U. AU - Ren, B. PY - 2016 DA - 2016// TI - Chromatin domains: the unit of chromosome organization JO - Mol Cell VL - 62 UR - https://doi.org/10.1016/j.molcel.2016.05.018 DO - 10.1016/j.molcel.2016.05.018 ID - Dixon2016 ER - TY - JOUR AU - Wang, X. T. AU - Cui, W. AU - Peng, C. PY - 2017 DA - 2017// TI - HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkx735 DO - 10.1093/nar/gkx735 ID - Wang2017 ER - TY - JOUR AU - Haddad, N. AU - Vaillant, C. AU - Jost, D. PY - 2017 DA - 2017// TI - IC-Finder: inferring robustly the hierarchical organization of chromatin folding JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkx036 DO - 10.1093/nar/gkx036 ID - Haddad2017 ER - TY - JOUR AU - Li, A. S. PY - 2018 DA - 2018// TI - Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-05691-7 DO - 10.1038/s41467-018-05691-7 ID - Li2018 ER - TY - JOUR AU - Yu, W. B. AU - He, B. AU - Tan, K. PY - 2017 DA - 2017// TI - Identifying topologically associating domains and subdomains by Gaussian mixture model and proportion test JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-00478-8 DO - 10.1038/s41467-017-00478-8 ID - Yu2017 ER - TY - JOUR AU - Yan, K. K. AU - Yardimci, G. G. AU - Yan, C. F. AU - Noble, W. S. AU - Gerstein, M. PY - 2017 DA - 2017// TI - HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx152 DO - 10.1093/bioinformatics/btx152 ID - Yan2017 ER - TY - JOUR AU - Yang, T. PY - 2017 DA - 2017// TI - HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.220640.117 DO - 10.1101/gr.220640.117 ID - Yang2017 ER - TY - JOUR AU - Lang, B. AU - Wu, B. AU - Liu, Y. AU - Liu, X. L. AU - Zhang, B. Y. PY - 2018 DA - 2018// TI - Fast graph similarity search via hashing and its application on image retrieval JO - Multimed Tools Appl VL - 77 UR - https://doi.org/10.1007/s11042-017-5194-8 DO - 10.1007/s11042-017-5194-8 ID - Lang2018 ER - TY - JOUR AU - Zufferey, M. AU - Tavernari, D. AU - Oricchio, E. AU - Ciriello, G. PY - 2018 DA - 2018// TI - Comparison of computational methods for the identification of topologically associating domains JO - Genome Biol VL - 19 UR - https://doi.org/10.1186/s13059-018-1596-9 DO - 10.1186/s13059-018-1596-9 ID - Zufferey2018 ER - TY - JOUR AU - Levy-Leduc, C. AU - Delattre, M. AU - Mary-Huard, T. AU - Robin, S. PY - 2014 DA - 2014// TI - Two-dimensional segmentation for analyzing Hi-C data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu443 DO - 10.1093/bioinformatics/btu443 ID - Levy-Leduc2014 ER - TY - JOUR AU - Li, Y. AU - Lui, K. O. AU - Zhou, B. PY - 2018 DA - 2018// TI - Reassessing endothelial-to-mesenchymal transition in cardiovascular diseases JO - Nat Rev Cardiol VL - 15 UR - https://doi.org/10.1038/s41569-018-0023-y DO - 10.1038/s41569-018-0023-y ID - Li2018 ER - TY - JOUR AU - Bonev, B. PY - 2017 DA - 2017// TI - Multiscale 3D genome rewiring during mouse neural development JO - Cell VL - 171 UR - https://doi.org/10.1016/j.cell.2017.09.043 DO - 10.1016/j.cell.2017.09.043 ID - Bonev2017 ER - TY - JOUR AU - Franke, M. PY - 2016 DA - 2016// TI - Formation of new chromatin domains determines pathogenicity of genomic duplications JO - Nature VL - 538 UR - https://doi.org/10.1038/nature19800 DO - 10.1038/nature19800 ID - Franke2016 ER - TY - JOUR AU - Dixon, J. R. PY - 2018 DA - 2018// TI - Integrative detection and analysis of structural variation in cancer genomes JO - Nat Genet VL - 50 UR - https://doi.org/10.1038/s41588-018-0195-8 DO - 10.1038/s41588-018-0195-8 ID - Dixon2018 ER - TY - JOUR AU - Zirkel, A. PY - 2018 DA - 2018// TI - HMGB2 loss upon senescence entry disrupts genomic organization and induces CTCF clustering across cell types JO - Mol Cell VL - 70 UR - https://doi.org/10.1016/j.molcel.2018.03.030 DO - 10.1016/j.molcel.2018.03.030 ID - Zirkel2018 ER - TY - JOUR AU - Mateo, L. J. PY - 2019 DA - 2019// TI - Visualizing DNA folding and RNA in embryos at single-cell resolution JO - Nature VL - 568 UR - https://doi.org/10.1038/s41586-019-1035-4 DO - 10.1038/s41586-019-1035-4 ID - Mateo2019 ER - TY - JOUR AU - Berlivet, S. PY - 2013 DA - 2013// TI - Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1004018 DO - 10.1371/journal.pgen.1004018 ID - Berlivet2013 ER - TY - JOUR AU - Phillips-Cremins, J. E. PY - 2013 DA - 2013// TI - Architectural protein subclasses shape 3D organization of genomes during lineage commitment JO - Cell VL - 153 UR - https://doi.org/10.1016/j.cell.2013.04.053 DO - 10.1016/j.cell.2013.04.053 ID - Phillips-Cremins2013 ER - TY - JOUR AU - Yu, M. AU - Ren, B. PY - 2017 DA - 2017// TI - The three-dimensional organization of mammalian genomes JO - Annu Rev Cell Dev Biol VL - 33 UR - https://doi.org/10.1146/annurev-cellbio-100616-060531 DO - 10.1146/annurev-cellbio-100616-060531 ID - Yu2017 ER - TY - STD TI - Barutcu AR, et al. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biol. 2015;16. https://doi.org/10.1186/s13059-015-0768-0. ID - ref32 ER - TY - JOUR AU - Nagano, T. PY - 2017 DA - 2017// TI - Cell-cycle dynamics of chromosomal organization at single-cell resolution JO - Nature VL - 547 UR - https://doi.org/10.1038/nature23001 DO - 10.1038/nature23001 ID - Nagano2017 ER - TY - JOUR AU - Taberlay, P. C. PY - 2016 DA - 2016// TI - Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.201517.115 DO - 10.1101/gr.201517.115 ID - Taberlay2016 ER - TY - JOUR AU - Rafique, S. AU - Thomas, J. S. AU - Sproul, D. AU - Bickmore, W. A. PY - 2015 DA - 2015// TI - Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0719-9 DO - 10.1186/s13059-015-0719-9 ID - Rafique2015 ER - TY - JOUR AU - Wu, P. Z. PY - 2017 DA - 2017// TI - 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-01793-w DO - 10.1038/s41467-017-01793-w ID - Wu2017 ER - TY - JOUR AU - Bianco, S. PY - 2018 DA - 2018// TI - Polymer physics predicts the effects of structural variants on chromatin architecture JO - Nat Genet VL - 50 UR - https://doi.org/10.1038/s41588-018-0098-8 DO - 10.1038/s41588-018-0098-8 ID - Bianco2018 ER - TY - JOUR AU - Fryzlewicz, P. PY - 2014 DA - 2014// TI - Wild binary segmentation for multiple change-point detection JO - Ann Stat VL - 42 UR - https://doi.org/10.1214/14-Aos1245 DO - 10.1214/14-Aos1245 ID - Fryzlewicz2014 ER - TY - JOUR AU - Barry, D. AU - Hartigan, J. A. PY - 1993 DA - 1993// TI - A Bayesian analysis for change point problems JO - J Am Stat Assoc VL - 88 UR - https://doi.org/10.1080/01621459.1993.10594323 DO - 10.1080/01621459.1993.10594323 ID - Barry1993 ER - TY - JOUR AU - Sanborn, A. L. PY - 2015 DA - 2015// TI - Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1518552112 DO - 10.1073/pnas.1518552112 ID - Sanborn2015 ER - TY - JOUR AU - Durand, N. C. PY - 2016 DA - 2016// TI - Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments JO - Cell Syst VL - 3 UR - https://doi.org/10.1016/j.cels.2016.07.002 DO - 10.1016/j.cels.2016.07.002 ID - Durand2016 ER - TY - JOUR AU - Robinson, J. T. PY - 2018 DA - 2018// TI - Juicebox.js provides a cloud-based visualization system for Hi-C data JO - Cell Syst VL - 6 UR - https://doi.org/10.1016/j.cels.2018.01.001 DO - 10.1016/j.cels.2018.01.001 ID - Robinson2018 ER - TY - JOUR AU - Forcato, M. PY - 2017 DA - 2017// TI - Comparison of computational methods for Hi-C data analysis JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4325 DO - 10.1038/nmeth.4325 ID - Forcato2017 ER - TY - JOUR AU - Chen, K. F. PY - 2013 DA - 2013// TI - DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing JO - Genome Res VL - 23 UR - https://doi.org/10.1101/gr.142067.112 DO - 10.1101/gr.142067.112 ID - Chen2013 ER - TY - JOUR AU - Chen, K. PY - 2015 DA - 2015// TI - Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3385 DO - 10.1038/ng.3385 ID - Chen2015 ER - TY - JOUR AU - Kent, W. J. PY - 2002 DA - 2002// TI - The human genome browser at UCSC JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.229102 DO - 10.1101/gr.229102 ID - Kent2002 ER - TY - STD TI - Guangyu W, Qingshu M, Bo X, Shuo Z, Jie L, Dongyu Z, Yanqiang L, Xin W, Lili Z, John PC, Qi C, Kaifu C. TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription. Github. 2019. https://doi.org/10.5281/zenodo.3553025. ID - ref47 ER - TY - STD TI - Guangyu W, Qingshu M, Bo X, Shuo Z, Jie L, Dongyu Z, Yanqiang L, Xin W, Lili Z, John PC, Qi C, Kaifu C. TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription. zenodo. 2019. https://doi.org/10.5281/zenodo.3553025. ID - ref48 ER -