The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Robust 4C-seq data analysis to screen for regulatory DNA interactions
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386
Self-citationA map of the cis-regulatory sequences in the mouse genome
Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361
Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus
Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344
Self-citationCTCF mediates long-range chromatin looping and local histone modification in the β-globin locus
Splinter, E., Heath, H., Kooren, J., Palstra, R.-J., Klous, P., Grosveld, F., Galjart, N., & de Laat, W. (2006) · Genes & Development · doi:10.1101/gad.399506 · Cited by 677
Self-citationVernimmen, D., Gobbi, M. D., Sloane‐Stanley, J. A., Wood, W. G., & Higgs, D. R. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601654 · Cited by 244
Lower, K. M., Hughes, J. R., De Gobbi, M., Henderson, S., Viprakasit, V., Fisher, C., Goriely, A., Ayyub, H., Sloane-Stanley, J., Vernimmen, D., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909331106 · Cited by 92
Cited by
Chromatin architecture reorganization during stem cell differentiation
Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature · doi:10.1038/nature14222 · Cited by 1,646
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E. D., Tanay, A., & Fraser, P. (2013) · Nature · doi:10.1038/nature12593 · Cited by 1,589
Self-citationSingle-cell sequencing-based technologies will revolutionize whole-organism science
Shapiro, E., Biezuner, T., & Linnarsson, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3542 · Cited by 1,177
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174
Long-range enhancer–promoter contacts in gene expression control
Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Weintraub, A. S., Li, C. H., Zamudio, A. V., Sigova, A. A., Hannett, N. M., Day, D. S., Abraham, B. J., Cohen, M. A., Nabet, B., Buckley, D. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.008 · Cited by 992
The cohesin release factor WAPL restricts chromatin loop extension
Haarhuis, J. H. I., van der Weide, R. H., Blomen, V. A., Yáñez-Cuna, J. O., Amendola, M., van Ruiten, M. S., Krijger, P. H. L., Teunissen, H., Medema, R. H., van Steensel, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.04.013 · Cited by 793
Non-coding recurrent mutations in chronic lymphocytic leukaemia
Puente, X. S., Beà, S., Valdés-Mas, R., Villamor, N., Gutiérrez-Abril, J., Martín-Subero, J. I., Munar, M., Rubio-Pérez, C., Jares, P., Aymerich, M., et al. (2015) · Nature · doi:10.1038/nature14666 · Cited by 829
Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
Vietri Rudan, M., Barrington, C., Henderson, S., Ernst, C., Odom, D. T., Tanay, A., & Hadjur, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.004 · Cited by 680
“Mouse primers were designed according to the genome-wide 4C-seq primer database from (van de Werken et al., 2012).”
MethodSelf-citationMoran, S., Arribas, C., & Esteller, M. (2016) · Epigenomics · doi:10.2217/epi.15.114 · Cited by 697
A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia
Gröschel, S., Sanders, M. A., Hoogenboezem, R., de Wit, E., Bouwman, B. A. M., Erpelinck, C., van der Velden, V. H. J., Havermans, M., Avellino, R., van Lom, K., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.019 · Cited by 687
Self-citationCTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation
Narendra, V., Rocha, P. P., An, D., Raviram, R., Skok, J. A., Mazzoni, E. O., & Reinberg, D. (2015) · Science · doi:10.1126/science.1262088 · Cited by 535
Enhancer loops appear stable during development and are associated with paused polymerase
Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature · doi:10.1038/nature13417 · Cited by 536
Topology of mammalian developmental enhancers and their regulatory landscapes
de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521
Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461
Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation
Shi, J., Whyte, W. A., Zepeda-Mendoza, C. J., Milazzo, J. P., Shen, C., Roe, J.-S., Minder, J. L., Mercan, F., Wang, E., Eckersley-Maslin, M. A., et al. (2013) · Genes & Development · doi:10.1101/gad.232710.113 · Cited by 463
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460
Gupta, R. M., Hadaya, J., Trehan, A., Zekavat, S. M., Roselli, C., Klarin, D., Emdin, C. A., Hilvering, C. R. E., Bianchi, V., Mueller, C., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.049 · Cited by 450
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., Zerbino, D., Schoenfelder, S., Javierre, B.-M., Osborne, C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0992-2 · Cited by 417
Cohesin-mediated interactions organize chromosomal domain architecture
Sofueva, S., Yaffe, E., Chan, W., Georgopoulou, D., Vietri Rudan, M., Mira‐Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., & Hadjur, S. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.237 · Cited by 394
Self-citationGenome-wide mapping and analysis of chromosome architecture
Schmitt, A. D., Hu, M., & Ren, B. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.104 · Cited by 344
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
Fang, R., Yu, M., Li, G., Chee, S., Liu, T., Schmitt, A. D., & Ren, B. (2016) · Cell Research · doi:10.1038/cr.2016.137 · Cited by 344
YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers
Galli, G. G., Carrara, M., Yuan, W.-C., Valdes-Quezada, C., Gurung, B., Pepe-Mooney, B., Zhang, T., Geeven, G., Gray, N. S., de Laat, W., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.09.001 · Cited by 290
Self-citationMultiplexed analysis of chromosome conformation at vastly improved sensitivity
Davies, J. O. J., Telenius, J. M., McGowan, S. J., Roberts, N. A., Taylor, S., Higgs, D. R., & Hughes, J. R. (2016) · Nature Methods · doi:10.1038/nmeth.3664 · Cited by 268
Capturing the Onset of PRC2-Mediated Repressive Domain Formation
Oksuz, O., Narendra, V., Lee, C.-H., Descostes, N., LeRoy, G., Raviram, R., Blumenberg, L., Karch, K., Rocha, P. P., Garcia, B. A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.023 · Cited by 266
Enhancer hubs and loop collisions identified from single-allele topologies
Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J. H. I., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0161-5 · Cited by 227
Self-citationSymmons, O., Pan, L., Remeseiro, S., Aktas, T., Klein, F., Huber, W., & Spitz, F. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.015 · Cited by 222
Cuartero, S., Weiss, F. D., Dharmalingam, G., Guo, Y., Ing-Simmons, E., Masella, S., Robles-Rebollo, I., Xiao, X., Wang, Y.-F., Barozzi, I., et al. (2018) · Nature Immunology · doi:10.1038/s41590-018-0184-1 · Cited by 210
LRP8-Reelin-regulated neuronal enhancer signature underlying learning and memory formation
Telese, F., Ma, Q., Perez, P. M., Notani, D., Oh, S., Li, W., Comoletti, D., Ohgi, K. A., Taylor, H., & Rosenfeld, M. G. (2015) · Neuron · doi:10.1016/j.neuron.2015.03.033 · Cited by 166
Epigenetic regulation: A new frontier for biomedical engineers
Chen, Z., Li, S., Subramaniam, S., Shyy, J. Y.-J., & Chien, S. (2017) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-071516-044720 · Cited by 163
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
Liu, N. Q., Maresca, M., van den Brand, T., Braccioli, L., Schijns, M. M. G. A., Teunissen, H., Bruneau, B. G., Nora, E. P., & de Wit, E. (2021) · Nature Genetics · doi:10.1038/s41588-020-00744-4 · Cited by 162
Self-citationPositively selected enhancer elements endow osteosarcoma cells with metastatic competence
Morrow, J. J., Bayles, I., Funnell, A. P. W., Miller, T. E., Saiakhova, A., Lizardo, M. M., Bartels, C. F., Kapteijn, M. Y., Hung, S., Mendoza, A., et al. (2018) · Nature Medicine · doi:10.1038/nm.4475 · Cited by 161
Enhancer release and retargeting activates disease-susceptibility genes
Oh, S., Shao, J., Mitra, J., Xiong, F., D’Antonio, M., Wang, R., Garcia-Bassets, I., Ma, Q., Zhu, X., Lee, J.-H., et al. (2021) · Nature · doi:10.1038/s41586-021-03577-1 · Cited by 148
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development
Wilderman, A., VanOudenhove, J., Kron, J., Noonan, J. P., & Cotney, J. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.129 · Cited by 139
A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening
Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A. Y., Dixon, J., Maliskova, L., Guan, K.-L., Shen, Y., & Ren, B. (2016) · Genome Research · doi:10.1101/gr.197152.115 · Cited by 122
17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells
Schmiedel, B. J., Seumois, G., Samaniego-Castruita, D., Cayford, J., Schulten, V., Chavez, L., Ay, F., Sette, A., Peters, B., & Vijayanand, P. (2016) · Nature Communications · doi:10.1038/ncomms13426 · Cited by 127
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., et al. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006982 · Cited by 121
Sams, D. S., Nardone, S., Getselter, D., Raz, D., Tal, M., Rayi, P. R., Kaphzan, H., Hakim, O., & Elliott, E. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.11.004 · Cited by 92
Epigenome editing strategies for the functional annotation of CTCF insulators
Tarjan, D. R., Flavahan, W. A., & Bernstein, B. E. (2019) · Nature Communications · doi:10.1038/s41467-019-12166-w · Cited by 88
3C-based technologies to study the shape of the genome
de Laat, W., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.11.005 · Cited by 84
DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
Redolfi, J., Zhan, Y., Valdes-Quezada, C., Kryzhanovska, M., Guerreiro, I., Iesmantavicius, V., Pollex, T., Grand, R. S., Mulugeta, E., Kind, J., et al. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0231-0 · Cited by 86
Self-citationGenetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma
McGeachie, M. J., Yates, K. P., Zhou, X., Guo, F., Sternberg, A. L., Van Natta, M. L., Wise, R. A., Szefler, S. J., Sharma, S., Kho, A. T., et al. (2016) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201602-0250oc · Cited by 25
Metadata
- Authors
- van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes-Quezada, C., Öz, Y., Bouwman, B. A. M., Verstegen, M. J. A. M., de Wit, E., Tanay, A., & de Laat, W.
- Venue
- Nature Methods
- Published
- 2012-09-09
- Volume
- 9
- Issue
- 10
- Pages
- 969-972
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W1991269963
- Cited by
- 390
- References
- 8
- FWCI
- 9.18
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
