The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Unlocking the secrets of the genome
Open accessAbstract
Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that. The National Human Genome Research Institute's modENCODE project (the model organism ENCyclopedia Of DNA Elements) was set up in 2007 with the goal of identifying all the sequence-based functional elements in the genomes of two important experimental organisms, Caenorhabditis elegans and Drosophila melanogaster. Armed with modENCODE data, geneticists will be able to undertake the comprehensive molecular studies of regulatory networks that hold the key to how complex multicellular organisms arise from the list of instructions coded in the genome. In this issue, modENCODE team members outline their plan of campaign. Data from the project are to be made available on http://www.modencode.org and elsewhere as the work progresses.
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
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
Exploring genetic interactions and networks with yeast
Boone, C., Bussey, H., & Andrews, B. J. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2085 · Cited by 661
Cited by
miRBase: integrating microRNA annotation and deep-sequencing data
Kozomara, A., & Griffiths-Jones, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1027 · Cited by 3,634
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
Self-citationChIP–seq: advantages and challenges of a maturing technology
Park, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2641 · Cited by 2,217
Construction of a human cell landscape at single-cell level
Han, X., Zhou, Z., Fei, L., Sun, H., Wang, R., Chen, Y., Chen, H., Wang, J., Tang, H., Ge, W., et al. (2020) · Nature · doi:10.1038/s41586-020-2157-4 · Cited by 1,087
Synthetic spike-in standards for RNA-seq experiments
Jiang, L., Schlesinger, F., Davis, C. A., Zhang, Y., Li, R., Salit, M., Gingeras, T. R., & Oliver, B. (2011) · Genome Research · doi:10.1101/gr.121095.111 · Cited by 653
Piercing the dark matter: bioinformatics of long-range sequencing and mapping
Sedlazeck, F. J., Lee, H., Darby, C. A., & Schatz, M. C. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0003-4 · Cited by 530
Tau promotes neurodegeneration through global chromatin relaxation
Frost, B., Hemberg, M., Lewis, J., & Feany, M. B. (2014) · Nature Neuroscience · doi:10.1038/nn.3639 · Cited by 495
“These five genes are classified as moderately to highly expressed (modEncode Project 31 ) in Drosophila heads despite their heterochromatic environment, while the six genes with increased expression in tau transgenic Drosophila are classified as heterochromatically silenced, with no to low baseline…”
Annotating non-coding regions of the genome.
Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464
Self-citationEnhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
Whalen, S., Truty, R. M., & Pollard, K. S. (2016) · Nature Genetics · doi:10.1038/ng.3539 · Cited by 456
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Yu, Y., Fuscoe, J. C., Zhao, C., Guo, C., Jia, M., Qing, T., Bannon, D. I., Lancashire, L., Bao, W., Du, T., et al. (2014) · Nature Communications · doi:10.1038/ncomms4230 · Cited by 395
RPN-6 determines C. elegans longevity under proteotoxic stress conditions
Vilchez, D., Morantte, I., Liu, Z., Douglas, P. M., Merkwirth, C., Rodrigues, A. P. C., Manning, G., & Dillin, A. (2012) · Nature · doi:10.1038/nature11315 · Cited by 413
Ulianov, S. V., Khrameeva, E. E., Gavrilov, A. A., Flyamer, I. M., Kos, P., Mikhaleva, E. A., Penin, A. A., Logacheva, M. D., Imakaev, M. V., Chertovich, A., et al. (2016) · Genome Research · doi:10.1101/gr.196006.115 · Cited by 388
Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family
Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.011 · Cited by 365
Cloud computing for genomic data analysis and collaboration
Langmead, B., & Nellore, A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.113 · Cited by 310
“…most visibly in projects such as the ICGC and the related Pan-Cancer Analysis of Whole Genomes (PCAWG) effort 21 , the National Cancer Institute (NCI) Cancer Genomics Cloud (CGC) Pilots 22–24 and the Encyclopedia of DNA Elements (ENCODE and Model Organism ENCODE (modENCODE)) projects 25,26 .”
BackgroundRNA-seq: technical variability and sampling
McIntyre, L. M., Lopiano, K. K., Morse, A. M., Amin, V., Oberg, A. L., Young, L. J., & Nuzhdin, S. V. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-293 · Cited by 285
piRNA-mediated transgenerational inheritance of an acquired trait
Grentzinger, T., Armenise, C., Brun, C., Mugat, B., Serrano, V., Pelisson, A., & Chambeyron, S. (2012) · Genome Research · doi:10.1101/gr.136614.111 · Cited by 162
MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains
Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002327 · Cited by 130
Gisselbrecht, S. S., Palagi, A., Kurland, J. V., Rogers, J. M., Ozadam, H., Zhan, Y., Dekker, J., & Bulyk, M. L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.10.004 · Cited by 128
Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101
Viswanatha, R., Li, Z., Hu, Y., & Perrimon, N. (2018) · eLife · doi:10.7554/elife.36333 · Cited by 79
Haenni, S., Ji, Z., Hoque, M., Rust, N., Sharpe, H., Eberhard, R., Browne, C., Hengartner, M. O., Mellor, J., Tian, B., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks282 · Cited by 71
Order and stochasticity in the folding of individual Drosophila genomes
Ulianov, S. V., Zakharova, V. V., Galitsyna, A. A., Kos, P. I., Polovnikov, K. E., Flyamer, I. M., Mikhaleva, E. A., Khrameeva, E. E., Germini, D., Logacheva, M. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20292-z · Cited by 64
Chinmo is the larval member of the molecular trinity that directs Drosophila metamorphosis
Truman, J. W., & Riddiford, L. M. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2201071119 · Cited by 53
H3K4me2 regulates the recovery of protein biosynthesis and homeostasis following DNA damage
Wang, S., Meyer, D. H., & Schumacher, B. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-00513-1 · Cited by 49
Kazemian, M., Suryamohan, K., Chen, J.-Y., Zhang, Y., Samee, M. A. H., Halfon, M. S., & Sinha, S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu184 · Cited by 42
GDAP2 mutations implicate susceptibility to cellular stress in a new form of cerebellar ataxia
Eidhof, I., Baets, J., Kamsteeg, E.-J., Deconinck, T., van Ninhuijs, L., Martin, J.-J., Schüle, R., Züchner, S., De Jonghe, P., Schenck, A., et al. (2018) · Brain · doi:10.1093/brain/awy198 · Cited by 25
Collaboration between mitochondria and the nucleus is key to long life in Caenorhabditis elegans
Chang, H.-W., Shtessel, L., & Lee, S. S. (2015) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2014.10.576 · Cited by 15
Metadata
- Authors
- modENCODE Consortium, Celniker, S. E., Dillon, L. A. L., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L., White, K. P., & Waterston, R. H.
- Venue
- Nature
- Published
- 2009-06-17
- Volume
- 459
- Issue
- 7249
- Pages
- 927-930
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2150904790
- Cited by
- 781
- References
- 4
- FWCI
- 28.09
- Type
- journal article
- Language
- en
- Open access
- hybrid
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.