The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
Open accessAbstract
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.
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
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Self-citationGenome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 1×
“Additionally, specific patterns of post-translational histone modifications [42,43] have been connected with distinct classes of regions such as promoters and enhancers [3,44–47] as well as regions subject to programmed repression by Polycomb complexes [48,49] or other mechanisms [46,50,51].”
BackgroundGenome-scale DNA methylation maps of pluripotent and differentiated cells
Meissner, A., Mikkelsen, T. S., Gu, H., Wernig, M., Hanna, J., Sivachenko, A., Zhang, X., Bernstein, B. E., Nusbaum, C., Jaffe, D. B., et al. (2008) · Nature · doi:10.1038/nature07107 · Cited by 2,536
Bernstein, B. E., Meissner, A., & Lander, E. S. (2007) · Cell · doi:10.1016/j.cell.2007.01.033 · Cited by 2,086
A vision for the future of genomics research
Collins, F. S., Green, E. D., Guttmacher, A. E., Guyer, M. S., & on behalf of the US National Human Genome Research Institute (2003) · Nature · doi:10.1038/nature01626 · Cited by 1,752
A census of human transcription factors: function, expression and evolution
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573
Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454
Genome-wide analysis of mammalian promoter architecture and evolution
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1789 · Cited by 1,350
Transcriptional Regulatory Elements in the Human Genome
Maston, G. A., Evans, S. K., & Green, M. R. (2006) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.7.080505.115623 · Cited by 937 · cited 1×
“, promoters, enhancers, silencers, and insulators) that collectively modulate the magnitude, timing, and cell-specificity of gene expression [35].”
BackgroundComplete sequencing and characterization of 21,243 full-length human cDNAs
Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. (2004) · Nature Genetics · doi:10.1038/ng1285 · Cited by 925
The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer
Pomerantz, M. M., Ahmadiyeh, N., Jia, L., Herman, P., Verzi, M. P., Doddapaneni, H., Beckwith, C. A., Chan, J. A., Hills, A., Davis, M., et al. (2009) · Nature Genetics · doi:10.1038/ng.403 · Cited by 663
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559
Pique-Regi, R., Degner, J. F., Pai, A. A., Gaffney, D. J., Gilad, Y., & Pritchard, J. K. (2011) · Genome Research · doi:10.1101/gr.112623.110 · Cited by 521
Wu, J. Q., Habegger, L., Noisa, P., Szekely, A., Qiu, C., Hutchison, S., Raha, D., Egholm, M., Lin, H., Weissman, S., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914114107 · Cited by 189
The problem of neuronal cell types: a physiological genomics approach
Nelson, S. B., Sugino, K., & Hempel, C. M. (2006) · Trends in Neurosciences · doi:10.1016/j.tins.2006.05.004 · Cited by 157
Research works printed but not linked: 95
- 2004, The ENCODE (ENCyclopedia Of DNA Elements) Project., Science, 306, 636, 10.1126/science.1105136 · DOI · Paper page
- F Chiaromonte, 2003, The share of human genomic DNA under selection estimated from human-mouse genomic alignments., Cold Spring Harb Symp Quant Biol, 68, 245, 10.1101/sqb.2003.68.245 · DOI · Paper page
- E. A Stone, 2005, Trade-offs in detecting evolutionarily constrained sequence by comparative genomics., Annu Rev Genomics Hum Genet, 6, 143, 10.1146/annurev.genom.6.080604.162146 · DOI
- S. C Parker, 2009, Local DNA topography correlates with functional noncoding regions of the human genome., Science, 324, 389, 10.1126/science.1169050 · DOI
- S Asthana, 2007, Widely distributed noncoding purifying selection in the human genome., Proc Natl Acad Sci U S A, 104, 12410, 10.1073/pnas.0705140104 · DOI
- B Wold, 2008, Sequence census methods for functional genomics., Nature Meth, 5, 19, 10.1038/nmeth1157 · DOI · Paper page
- K. R Rosenbloom, 2010, ENCODE whole-genome data in the UCSC Genome Browser., Nucleic Acids Res, 38, D620, 10.1093/nar/gkp961 · DOI · Paper page
- B Rhead, 2010, The UCSC Genome Browser database: update 2010., Nucleic Acids Res, 38, D613, 10.1093/nar/gkp939 · DOI · Paper page
- C. B Lozzio, 1975, Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome., Blood, 45, 321, 10.1182/blood.V45.3.321.321 · DOI · Paper page
- J. A Thomson, 1998, Embryonic stem cell lines derived from human blastocysts., Science, 282, 1145, 10.1126/science.282.5391.1145 · DOI · Paper page
- G. O Gey, 1952, Tissue culture studies of the proliferative capacity of cervical carcinoma and normal epithelium., Cancer Res, 12, 264
- B. B Knowles, 1980, Human hepatocellular carcinoma cell lines secrete the major plasma proteins and hepatitis B surface antigen., Science, 209, 497, 10.1126/science.6248960 · DOI · Paper page
- E. A Jaffe, 1973, Culture of human endothelial cells derived from umbilical veins: Identification by morphologic and immunologic criteria., J Clin Invest, 52, 2745, 10.1172/JCI107470 · DOI · Paper page
- 2004, Finishing the euchromatic sequence of the human genome., Nature, 431, 931, 10.1038/nature03001 · DOI · Paper page
- R Guigó, 2006, EGASP: the human ENCODE Genome Annotation Assessment Project., Genome Biol, 7, S2 1, 10.1186/gb-2006-7-s1-s2 · DOI
- J Harrow, 2006, GENCODE: producing a reference annotation for ENCODE., Genome Biol, 7, S4 1, 10.1186/gb-2006-7-s1-s4 · DOI · Paper page
- Z Zhang, 2006, PseudoPipe: an automated pseudogene identification pipeline., Bioinformatics, 22, 1437, 10.1093/bioinformatics/btl116 · DOI
- P Flicek, 2010, Ensembl's 10th year., Nucleic Acids Res, 38, D557, 10.1093/nar/gkp972 · DOI · Paper page
- D Kampa, 2004, Novel RNAs identified from a comprehensive analysis of the transcriptome of human chromosomes 21 and 22., Genome Res, 14, 331, 10.1101/gr.2094104 · DOI · Paper page
- M Schmid, 2010, Nuclear quality control of RNA polymerase II transcripts., J Wiley Interdisciplinary Review
- J. P Bachellerie, 2002, The expanding snoRNA world., Biochimie, 84, 775, 10.1016/S0300-9084(02)01402-5 · DOI · Paper page
- P Kapranov, 2007, Genome-wide transcription and the implications for genomic organization., Nat Rev Genet, 8, 413, 10.1038/nrg2083 · DOI · Paper page
- M. J Fullwood, 2009, Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses., Genome Res, 19, 521, 10.1101/gr.074906.107 · DOI · Paper page
- T Shiraki, 2003, Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage., Proc Natl Acad Sci U S A, 100, 15776, 10.1073/pnas.2136655100 · DOI · Paper page
- E Valen, 2009, Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE., Genome Res, 19, 255, 10.1101/gr.084541.108 · DOI
- M. A Frohman, 1988, Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer., Proc Natl Acad Sci U S A, 85, 8998, 10.1073/pnas.85.23.8998 · DOI · Paper page
- M. C Giddings, 2003, Genome-based peptide fingerprint scanning., Proc Natl Acad Sci U S A, 100, 20, 10.1073/pnas.0136893100 · DOI
- G. E Merrihew, 2008, Use of shotgun proteomics for the identification, confirmation, and correction of C elegans gene annotations., Genome Res, 18, 1660, 10.1101/gr.077644.108 · DOI
- C Wu, 1980, The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I., Nature, 286, 854, 10.1038/286854a0 · DOI · Paper page
- M. A Keene, 1981, DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription., Proc Natl Acad Sci U S A, 78, 143, 10.1073/pnas.78.1.143 · DOI
- J. D McGhee, 1981, A 200 base pair region at the 5′ end of the chicken adult beta-globin gene is accessible to nuclease digestion., Cell, 27, 45, 10.1016/0092-8674(81)90359-7 · DOI · Paper page
- D. S Gross, 1988, Nuclease hypersensitive sites in chromatin., Annu Rev Biochem, 57, 159, 10.1146/annurev.bi.57.070188.001111 · DOI · Paper page
- P. G Giresi, 2007, FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin., Genome Res, 17, 877, 10.1101/gr.5533506 · DOI · Paper page
- R. K Auerbach, 2009, Mapping accessible chromatin regions using Sono-Seq., Proc Natl Acad Sci U S A, 106, 14926, 10.1073/pnas.0905443106 · DOI
- G Liang, 2004, Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome., Proc Natl Acad Sci U S A, 11, 7357, 10.1073/pnas.0401866101 · DOI · Paper page
- R Schneider, 2004, Histone H3 lysine 4 methylation patterns in higher eukaryotic genes., Nat Cell Biol, 6, 73, 10.1038/ncb1076 · DOI · Paper page
- B. E Bernstein, 2005, Genomic maps and comparative analysis of histone modifications in human and mouse., Cell, 28, 169, 10.1016/j.cell.2005.01.001 · DOI · Paper page
- L. A Boyer, 2006, Polycomb complexes repress developmental regulators in murine embryonic stem cells., Nature, 18, 349, 10.1038/nature04733 · DOI · Paper page
- T. I Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells., Cell, 21, 301, 10.1016/j.cell.2006.02.043 · DOI · Paper page
- B. D Strahl, 2000, The language of covalent histone modifications., Nature, 6, 41, 10.1038/47412 · DOI · Paper page
- P. J Sabo, 2004, Discovery of functional noncoding elements by digital analysis of chromatin structure., Proc Natl Acad Sci U S A, 101, 16837, 10.1073/pnas.0407387101 · DOI
- A. P Boyle, 2008, High-resolution mapping and characterization of open chromatin across the genome., Cell, 25, 311, 10.1016/j.cell.2007.12.014 · DOI · Paper page
- P. J Sabo, 2006, Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays., Nat Methods, 3, 511, 10.1038/nmeth890 · DOI · Paper page
- M Sekimata, 2009, CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus., Immunity, 31, 551, 10.1016/j.immuni.2009.08.021 · DOI
- P. G Giresi, 2009, Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)., Methods, 48, 233, 10.1016/j.ymeth.2009.03.003 · DOI
- K. J Gaulton, 2010, A map of open chromatin in human pancreatic islets., Nat Genet, 42, 255, 10.1038/ng.530 · DOI · Paper page
- D. S Johnson, 2007, Genome-wide mapping of in vivo protein-DNA interactions., Science, 316, 1497, 10.1126/science.1141319 · DOI · Paper page
- I Poser, 2008, BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals., Nat Methods, 5, 409, 10.1038/nmeth.1199 · DOI · Paper page
- S Hua, 2009, Genomic antagonism between retinoic acid and estrogen signaling in breast cancer., Cell, 137, 1259, 10.1016/j.cell.2009.04.043 · DOI · Paper page
- D Raha, 2010, ChIP-seq: a method for global identification of regulatory elements in the genome., Curr Protoc Mol Biol Chapter, 21, Unit 2119 1, 10.1002/0471142727.mb2119s91 · DOI
- T. H Kim, 2007, Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome., Cell, 128, 1231, 10.1016/j.cell.2006.12.048 · DOI · Paper page
- R Jaenisch, 1997, DNA methylation and imprinting: Why bother?, Trends Genet, 13, 323, 10.1016/S0168-9525(97)01180-3 · DOI · Paper page
- H Noushmehr, 2010, Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma., Cancer Cell, 17, 510, 10.1016/j.ccr.2010.03.017 · DOI · Paper page
- A. E Teschendorff, 2010, Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer., Genome Res, 20, 440, 10.1101/gr.103606.109 · DOI · Paper page
- L Laurent, 2010, Dynamic changes in the human methylome during differentiation., Genome Res, 20, 320, 10.1101/gr.101907.109 · DOI · Paper page
- V. K Rakyan, 2010, Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains., Genome Res, 20, 434, 10.1101/gr.103101.109 · DOI · Paper page
- A. L Brunner, 2009, Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver., Genome Res, 19, 1044, 10.1101/gr.088773.108 · DOI · Paper page
- D. J Galas, 1978, DNAse footprinting: a simple method for the detection of protein-DNA binding specificity., Nucleic Acids Res, 5, 3157, 10.1093/nar/5.9.3157 · DOI · Paper page
- E. C Strauss, 1992, In vivo protein-DNA interactions at hypersensitive site 3 of the human beta-globin locus control region., Proc Natl Acad Sci U S A, 89, 5809, 10.1073/pnas.89.13.5809 · DOI
- A. P Boyle, 2011, High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells., Genome Res
- Y Lu, 2010, Common genetic variants near the Brittle Cornea Syndrome locus ZNF469 influence the blinding disease risk factor central corneal thickness., PLoS Genet, 6, e1000947, 10.1371/journal.pgen.1000947 · DOI
- R McDaniell, 2010, Heritable individual-specific and allele-specific chromatin signatures in humans., Science, 328, 235, 10.1126/science.1184655 · DOI · Paper page
- M Kasowski, 2010, Variation in transcription factor binding among humans., Science, 328, 232, 10.1126/science.1183621 · DOI · Paper page
- R Redon, 2006, Global variation in copy number in the human genome., Nature, 444, 444, 10.1038/nature05329 · DOI · Paper page
- J. O Korbel, 2007, Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome., Proc Natl Acad Sci U S A, 104, 10110, 10.1073/pnas.0703834104 · DOI
- D. F Conrad, 2010, Mutation spectrum revealed by breakpoint sequencing of human germline CNVs., Nat Genet, 42, 385, 10.1038/ng.564 · DOI · Paper page
- A Miele, 2008, Long-range chromosomal interactions and gene regulation., Mol Biosyst, 4, 1046, 10.1039/b803580f · DOI
- J Dostie, 2006, Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements., Genome Res, 16, 1299, 10.1101/gr.5571506 · DOI · Paper page
- B. R Lajoie, 2009, My5C: web tools for chromosome conformation capture studies., Nat Methods, 6, 690, 10.1038/nmeth1009-690 · DOI
- T. E Baroni, 2008, Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling., Methods Mol Biol, 419, 93, 10.1007/978-1-59745-033-1_6 · DOI
- J. D Keene, 2006, RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts., Nat Protoc, 1, 302, 10.1038/nprot.2006.47 · DOI · Paper page
- S. A Tenenbaum, 2000, Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays., Proc Natl Acad Sci U S A, 97, 14085, 10.1073/pnas.97.26.14085 · DOI · Paper page
- S. A Tenenbaum, 2002, Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays., Methods, 26, 191, 10.1016/S1046-2023(02)00022-1 · DOI · Paper page
- N. D Trinklein, 2007, Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome., Genome Res, 17, 720, 10.1101/gr.5716607 · DOI
- J. M Lin, 2007, Transcription factor binding and histone modifications in human bidirectional promoters., Genome Res, 17, 818, 10.1101/gr.5623407 · DOI
- P. J Collins, 2007, The ets-related transcription factor GABP directs bidirectional transcription., PLoS Genet, 3, e208, 10.1371/journal.pgen.0030208 · DOI
- H. M Petrykowska, 2008, Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus., Genome Research, 18, 1238, 10.1101/gr.073817.107 · DOI
- J. M Landolin, 2010, Sequence features that drive human promoter function and tissue specificity., Genome Res, 20, 890, 10.1101/gr.100370.109 · DOI
- J Khatun, 2008, Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification., Bioinformatics, 24, 674, 10.1093/bioinformatics/btn011 · doi:10.1093/bioinformatics/btn011
- B Paten, 2008, Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs., Genome Res, 8, 1814, 10.1101/gr.076554.108 · DOI · Paper page
- B Paten, 2008, Genome-wide nucleotide-level mammalian ancestor reconstruction., Genome Res, 18, 1829, 10.1101/gr.076521.108 · DOI
- G. M Cooper, 2005, Distribution and intensity of constraint in mammalian genomic sequence., Genome Res, 15, 901, 10.1101/gr.3577405 · DOI · Paper page
- S Asthana, 2007, Analysis of sequence conservation at nucleotide resolution., PLoS Comput Biol, 3, e254, 10.1371/journal.pcbi.0030254 · DOI
- K. S Pollard, 2010, Detection of nonneutral substitution rates on mammalian phylogenies., Genome Res, 20, 110, 10.1101/gr.097857.109 · DOI · Paper page
- J Rozowsky, 2009, PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls., Nat Biotechnol, 27, 66, 10.1038/nbt.1518 · DOI · Paper page
- E Birney, 2009, Prepublication data sharing., Nature, 461, 168, 10.1038/461168a · DOI · Paper page
- D Wokolorczyk, 2008, A range of cancers is associated with the rs6983267 marker on chromosome 8., Cancer Res, 68, 9982, 10.1158/0008-5472.CAN-08-1838 · DOI
- K Curtin, 2009, Meta association of colorectal cancer confirms risk alleles at 8q24 and 18q21., Cancer Epidemiol Biomarkers Prev, 18, 616, 10.1158/1055-9965.EPI-08-0690 · DOI
- A. A Al Olama, 2009, Multiple loci on 8q24 associated with prostate cancer susceptibility., Nat Genet, 41, 1058, 10.1038/ng.452 · DOI · Paper page
- L Jia, 2009, Functional enhancers at the gene-poor 8q24 cancer-linked locus., PLoS Gene, 5, e1000597, 10.1371/journal.pgen.1000597 · DOI
- S Tuupanen, 2009, The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling., Nat Genet, 41, 885, 10.1038/ng.406 · DOI · Paper page
- J. B Wright, 2010, Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells., Mol Cell Biol, 30, 1411, 10.1128/MCB.01384-09 · DOI · Paper page
- J. M Kidd, 2010, Characterization of missing human genome sequences and copy-number polymorphic insertions., Nat Methods, 7, 365, 10.1038/nmeth.1451 · DOI
- Q Li, 2011, Measuring reproducibility of high-throughput experiments., Annals of Applied Statistics
- D Reisman, 1996, A novel transcript encoded within the 10-kb first intron of the human p53 tumor suppressor gene (D17S2179E) is induced during differentiation of myeloid leukemia cells., Genomics, 38, 364, 10.1006/geno.1996.0639 · doi:10.1006/geno.1996.0639
Cited by
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationA 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citationBuenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Metadata
- Authors
- The ENCODE Project Consortium
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-04-19
- Volume
- 9
- Issue
- 4
- Pages
- e1001046
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W1544691147
- Cited by
- 1,506
- References
- 26
- FWCI
- 81.00
- Type
- journal article
- Language
- en
- Open access
- gold
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.