Mouse ENCODE
Integrity signals
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Normalized TAD coverage across single-cell dataset reflects strong correlation between domains previously annotated as early- or late-replicating in mouse ESCs.
“we found normalized TAD coverage across the single-cell dataset reflects a strong correlation between domains previously annotated as early- or late-replicating in mouse ESCs15”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [15]
Pseudo-compartments are characterized by a gradient of epigenetic signatures.
“Analysis of RNA-seq, histone marks15 and Lamin association17 suggested pseudo-compartments are characterized by a gradient of epigenetic signatures”
From Cell-cycle dynamics of chromosomal organization at single-cell resolution (2017) · cites this paper as [15]
Cites
An encyclopedia of mouse DNA elements (Mouse ENCODE)
Mouse ENCODE Consortium, Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-8-418 · Cited by 446 · see citing works
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Phased diploid genome assembly with single-molecule real-time sequencing
Chin, C.-S., Peluso, P. S., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O’Malley, R. C., Figueroa-Balderas, R. E., Morales‐Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,847 · see citing works
Local regulation of gene expression by lncRNA promoters, transcription and splicing
Engreitz, J. M., Haines, J. E., Perez, E. M., Munson, G., Chen, J., Kane, M., McDonel, P. E., Guttman, M., & Lander, E. S. (2016) · Nature · doi:10.1038/nature20149 · Cited by 1,253 · see citing works
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
Dekker, J., Marti-Renom, M. A., & Mirny, L. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3454 · Cited by 1,068 · see citing works
Topologically associating domains are stable units of replication-timing regulation
Pope, B. D., Ryba, T., Dileep, V., Yue, F., Wu, W.-S., Denas, O., Vera, D. L., Wang, Y., Hansen, R. S., Canfield, T. K., et al. (2014) · Nature · doi:10.1038/nature13986 · Cited by 902 · see citing works
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Nagano, T., Lubling, Y., Várnai, C., Dudley, C., Leung, W., Baran, Y., Mendelson Cohen, N., Wingett, S., Fraser, P., & Tanay, A. (2017) · Nature · doi:10.1038/nature23001 · Cited by 794 · see citing works
Diabetic nephropathy—emerging epigenetic mechanisms
Kato, M. V., & Natarajan, R. D. (2014) · Nature Reviews Nephrology · doi:10.1038/nrneph.2014.116 · Cited by 316 · see citing works
Genome-wide identification and characterization of functional neuronal activity–dependent enhancers
Malik, A. N., Vierbuchen, T., Hemberg, M., Rubin, A. A., Ling, E., Couch, C. H., Stroud, H., Spiegel, I., Farh, K. K., Harmin, D. A., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3808 · Cited by 267 · see citing works
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum
Frank, C. L., Liu, F., Wijayatunge, R., Song, L., Biegler, M. T., Yang, M. G., Vockley, C. M., Safi, A., Gersbach, C. A., Crawford, G. E., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3995 · Cited by 167 · see citing works
Assessment of engineered cells using CellNet and RNA-seq
Radley, A., Schwab, R. M., Tan, Y., Kim, J., Lo, E. K. W., & Cahan, P. (2017) · Nature Protocols · doi:10.1038/nprot.2017.022 · Cited by 44 · see citing works
Gasper, W. C., Marinov, G. K., Pauli, F., Scott, M. T., Newberry, K. M., DeSalvo, G., Ou, S. K.-H., Myers, R., Vielmetter, J., & Wold, B. J. (2014) · Scientific Reports · doi:10.1038/srep05152 · Cited by 33 · see citing works
A novel DNA sequence motif in human and mouse genomes
Zhang, S., Du, F., & Ji, H. (2015) · Scientific Reports · doi:10.1038/srep10444
- Authors
- Stower, H.
- Corresponding author
- Stower, Hannah
- Venue
- Nature Reviews Genetics
- Published
- 2012-09-18
- Volume
- 13
- Issue
- 10
- Pages
- 675-675
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W2084216324
- Cited by
- 11
- References
- 1
- Citations by year
- 2017: 2 · 2016: 2 · 2015: 2 · 2014: 4 · 2013: 1
- FWCI
- 0.90
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature Reviews Genetics (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- mouse genome, DNA elements, regulatory elements, chromatin accessibility, epigenetic modifications, non-coding DNA, functional genomics
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.
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