The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Open accessAbstract
Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales. Structural features, such as loops and domains, are automatically annotated. Juicer is available as open source software at http://aidenlab.org/juicer/.
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Servant, N., Varoquaux, N., Lajoie, B. R., Viara, E., Chen, C.-J., Vert, J.-P., Heard, E., Dekker, J., & Barillot, E. (2015) · Genome Biology · doi:10.1186/s13059-015-0831-x · Cited by 2,565 · cited 1×
“Although pipelines for Hi-C data analysis exist (Lieberman-Aiden et al., 2009; Schmid et al., 2015; Servant et al., 2015; Sauria et al., 2015), these packages are not designed to process datasets at the terabase scale or to annotate the structural features that these maps reflect.”
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730
Self-citation
Research works printed but not linked: 7
- Durand, 2016, Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom, Cell Systems, 3, 99, 10.1016/j.cels.2015.07.012 · DOI · Paper page
- Grant, 2011, FIMO: scanning for occurrences of a given motif, Bioinformatics, 27, 1017, 10.1093/bioinformatics/btr064 · DOI · Paper page
- Knight, 2012, A fast algorithm for matrix balancing, IMA J. Numer. Anal., 33, 1029, 10.1093/imanum/drs019 · DOI · Paper page
- Lieberman-Aiden, 2009, Comprehensive mapping of long-range interactions reveals folding principles of the human genome, Science, 326, 289, 10.1126/science.1181369 · DOI · Paper page
- Rao, 2014, A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping, Cell, 159, 1665, 10.1016/j.cell.2014.11.021 · DOI · Paper page
- Sauria, 2015, HiFive: a tool suite for easy and efficient HiC and 5C data analysis, Genome Biol., 16, 237, 10.1186/s13059-015-0806-y · DOI
- Schmid, 2015, HiCdat: a fast and easy-to-use Hi-C data analysis tool, BMC Bioinformatics, 16, 277, 10.1186/s12859-015-0678-x · DOI
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Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883
Self-citationHiChIP: efficient and sensitive analysis of protein-directed genome architecture
Mumbach, M. R., Rubin, A. J., Flynn, R. A., Dai, C., Khavari, P. A., Greenleaf, W. J., & Chang, H. Y. (2016) · Nature Methods · doi:10.1038/nmeth.3999 · Cited by 1,139
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111
Self-citationWutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201798004 · Cited by 864
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
Metadata
- Authors
- Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L.
- Venue
- Cell Systems
- Publisher
- Elsevier BV
- Published
- 2016-07
- Volume
- 3
- Issue
- 1
- Pages
- 95-98
- ISSN
- 2405-4712 (ISSN-L)
- OpenAlex
- W2481029670
- Cited by
- 3,836
- References
- 2
- FWCI
- 39.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- creativecommons.org/licenses/by/4.0/ (vor, 14 d)
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- Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016). Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Systems. https://doi.org/10.1016/j.cels.2016.07.002
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