| Year |
Citation |
Score |
| 2024 |
Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, ... ... Dixon JR, et al. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature. PMID 39385032 DOI: 10.1038/s41586-024-08030-7 |
0.38 |
|
| 2023 |
Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Dixon JR, et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature. 624: 366-377. PMID 38092913 DOI: 10.1038/s41586-023-06805-y |
0.59 |
|
| 2023 |
Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR. Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. Nature Communications. 14: 6943. PMID 37932264 DOI: 10.1038/s41467-023-42647-y |
0.385 |
|
| 2023 |
Liu H, Zeng Q, Zhou J, Bartlett A, Wang BA, Berube P, Tian W, Kenworthy M, Altshul J, Nery JR, Chen H, Castanon RG, Zu S, Li YE, Lucero J, ... ... Dixon JR, et al. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. Biorxiv : the Preprint Server For Biology. PMID 37131654 DOI: 10.1101/2023.04.16.536509 |
0.584 |
|
| 2023 |
Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, ... ... Dixon JR, et al. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nature Communications. 14: 2300. PMID 37085539 DOI: 10.1038/s41467-023-38044-0 |
0.379 |
|
| 2023 |
Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA. Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics. PMID 36944735 DOI: 10.1038/s41588-023-01318-w |
0.371 |
|
| 2023 |
Liu Z, Lee DS, Liang Y, Zheng Y, Dixon JR. Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. Biorxiv : the Preprint Server For Biology. PMID 36865315 DOI: 10.1101/2023.02.22.529589 |
0.385 |
|
| 2022 |
Xu Z, Lee DS, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir KC, Tyndale S, Futreal PA, McVicker G, ... ... Dixon JR, et al. Structural variants drive context-dependent oncogene activation in cancer. Nature. PMID 36477537 DOI: 10.1038/s41586-022-05504-4 |
0.474 |
|
| 2022 |
Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. The Journal of Biological Chemistry. 102117. PMID 35691341 DOI: 10.1016/j.jbc.2022.102117 |
0.369 |
|
| 2022 |
Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, ... ... Dixon JR, et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genomics. 2. PMID 35419551 DOI: 10.1016/j.xgen.2022.100107 |
0.537 |
|
| 2022 |
Song F, Xu J, Dixon J, Yue F. Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. Methods in Molecular Biology (Clifton, N.J.). 2301: 143-161. PMID 34415534 DOI: 10.1007/978-1-0716-1390-0_7 |
0.599 |
|
| 2021 |
Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, ... ... Dixon JR, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8 |
0.576 |
|
| 2021 |
Reid DA, Reed PJ, Schlachetzki JCM, Nitulescu II, Chou G, Tsui EC, Jones JR, Chandran S, Lu AT, McClain CA, Ooi JH, Wang TW, Lana AJ, Linker SB, Ricciardulli AS, ... ... Dixon JR, et al. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons. Science (New York, N.Y.). 372: 91-94. PMID 33795458 DOI: 10.1126/science.abb9032 |
0.436 |
|
| 2021 |
Kubo N, Ishii H, Xiong X, Bianco S, Meitinger F, Hu R, Hocker JD, Conte M, Gorkin D, Yu M, Li B, Dixon JR, Hu M, Nicodemi M, Zhao H, et al. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nature Structural & Molecular Biology. PMID 33398174 DOI: 10.1038/s41594-020-00539-5 |
0.572 |
|
| 2020 |
Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer MW. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. Genes & Development. PMID 32499403 DOI: 10.1101/Gad.335794.119 |
0.511 |
|
| 2020 |
Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nature Genetics. PMID 32024999 DOI: 10.1038/S41588-019-0564-Y |
0.413 |
|
| 2019 |
Xu Z, Dixon JR. Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies. Briefings in Functional Genomics. PMID 31875884 DOI: 10.1093/bfgp/elz026 |
0.424 |
|
| 2019 |
Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nature Methods. PMID 31501549 DOI: 10.1038/S41592-019-0547-Z |
0.48 |
|
| 2019 |
Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, ... ... Dixon JR, et al. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. Nature Genetics. 51: 1252-1262. PMID 31367015 DOI: 10.1038/S41588-019-0472-1 |
0.637 |
|
| 2019 |
Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31235599 DOI: 10.1073/Pnas.1901423116 |
0.331 |
|
| 2019 |
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Cell Systems. PMID 31229558 DOI: 10.1016/J.Cels.2019.05.011 |
0.546 |
|
| 2019 |
Barbosa K, Deshpande A, Chen BR, Ghosh A, Sun Y, Dutta S, Weetall M, Dixon J, Armstrong SA, Bohlander SK, Deshpande AJ. Acute Myeloid Leukemia Driven by the CALM-AF10 Fusion Gene is Dependent on BMI1. Experimental Hematology. PMID 31022428 DOI: 10.1016/J.Exphem.2019.04.003 |
0.353 |
|
| 2019 |
Okonechnikov K, Hübner J, Chapman O, Chakraborty A, Bump R, Chandran S, Kraft K, Acuna Hidalgo R, Mundlos S, Coufal N, Levy M, Crawford J, Ay F, Mesirov J, Pajtler K, ... Dixon J, et al. GENE-15. TARGETING OF EPENDYMOMA AS INFORMED BY ONCOGENIC 3D GENOME ORGANIZATION Neuro-Oncology. 21: vi100-vi100. DOI: 10.1093/Neuonc/Noz175.417 |
0.442 |
|
| 2019 |
Okonechnikov K, Hübner J, Kraft K, Hidalgo RA, Bump R, Chandran S, Mundlos S, Mesirov J, Pajtler K, Dixon J, Pfister S, Kool M, Chavez L. GENE-02. CHROMOSOME CONFORMATION ANALYSIS OF EPENDYMOMA IDENTIFIES PUTATIVE TUMOR DEPENDENCY GENES ACTIVATED BY DISTAL ONCOGENIC ENHANCERS Neuro-Oncology. 21: ii80-ii81. DOI: 10.1093/Neuonc/Noz036.073 |
0.375 |
|
| 2018 |
Gatchalian J, Malik S, Ho J, Lee DS, Kelso TWR, Shokhirev MN, Dixon JR, Hargreaves DC. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. Nature Communications. 9: 5139. PMID 30510198 DOI: 10.1038/S41467-018-07528-9 |
0.382 |
|
| 2018 |
Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8 |
0.64 |
|
| 2017 |
Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y, Ma J, Zhang X, Zhang K, Wang Y, Zhang MQ, ... ... Dixon JR, et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 547: 232-235. PMID 28703188 DOI: 10.1038/Nature23263 |
0.495 |
|
| 2016 |
Dixon JR, Gorkin DU, Ren B. Chromatin Domains: The Unit of Chromosome Organization. Molecular Cell. 62: 668-80. PMID 27259200 DOI: 10.1016/J.Molcel.2016.05.018 |
0.544 |
|
| 2016 |
Diao Y, Li B, Meng Z, Jung I, Lee A, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9 mediated genetic screening. Genome Research. PMID 26813977 DOI: 10.1101/Gr.197152.115 |
0.765 |
|
| 2015 |
Selvaraj S, Schmitt AD, Dixon JR, Ren B. Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. Bmc Genomics. 16: 900. PMID 26541200 DOI: 10.1186/S12864-015-1949-7 |
0.435 |
|
| 2015 |
Ren B, Dixon JR. A CRISPR Connection between Chromatin Topology and Genetic Disorders. Cell. 161: 955-7. PMID 26000472 DOI: 10.1016/J.Cell.2015.04.047 |
0.532 |
|
| 2015 |
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 518: 331-6. PMID 25693564 DOI: 10.1038/Nature14222 |
0.768 |
|
| 2015 |
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Dixon JR, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248 |
0.679 |
|
| 2014 |
Li Y, Rivera CM, Ishii H, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. Plos One. 9: e114485. PMID 25486255 DOI: 10.1371/Journal.Pone.0114485 |
0.747 |
|
| 2014 |
Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, et al. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research. 24: 920-9. PMID 24752179 DOI: 10.1101/Gr.168930.113 |
0.592 |
|
| 2014 |
Zuin J, Dixon JR, van der Reijden MI, Ye Z, Kolovos P, Brouwer RW, van de Corput MP, van de Werken HJ, Knoch TA, van IJcken WF, Grosveld FG, Ren B, Wendt KS. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 996-1001. PMID 24335803 DOI: 10.1073/Pnas.1317788111 |
0.627 |
|
| 2013 |
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 503: 290-4. PMID 24141950 DOI: 10.1038/Nature12644 |
0.77 |
|
| 2013 |
Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. Bayesian inference of spatial organizations of chromosomes. Plos Computational Biology. 9: e1002893. PMID 23382666 DOI: 10.1371/Journal.Pcbi.1002893 |
0.574 |
|
| 2012 |
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. A map of the cis-regulatory sequences in the mouse genome. Nature. 488: 116-20. PMID 22763441 DOI: 10.1038/Nature11243 |
0.752 |
|
| 2012 |
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 485: 376-80. PMID 22495300 DOI: 10.1038/Nature11082 |
0.743 |
|
| 2010 |
Barish GD, Yu RT, Karunasiri M, Ocampo CB, Dixon J, Benner C, Dent AL, Tangirala RK, Evans RM. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. Genes & Development. 24: 2760-5. PMID 21106671 DOI: 10.1101/Gad.1998010 |
0.375 |
|
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