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JESSE DIXON - Publications

Affiliations: 
Salk Institute, La Jolla, California 
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40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.408
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  0.39
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  0.581
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  0.378
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  0.375
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  0.39
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  0.475
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  0.373
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  0.541
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  0.566
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  0.439
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  0.579
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  0.517
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  0.415
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  0.425
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  0.479
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  0.645
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  0.33
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  0.55
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  0.356
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  0.445
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  0.377
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  0.387
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  0.614
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  0.502
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  0.551
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  0.764
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  0.439
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  0.537
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  0.683
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  0.75
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  0.597
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  0.634
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  0.772
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  0.577
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  0.755
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  0.747
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  0.378
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