Popay, T.M., Pant, A., Munting, F., Tastemel, M., Black, M.E., Haghani, N., Dixon, J.R. Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation. (2026) Nature Genetics. DOI: 10.1038/s41588-026-02516-y

Zhou, J., Wu, Y., Liu, H., Tian, W., Castanon, R.G., Bartlett, A., Zhang, Z., Yao, G., Shi, D., Clock, B., Marcotte, S., Nery, J.R., Liem, M., Claffey, N., Boggeman, L., Barragan, C., Drigo, R.A.E., Weimer, A.K., Shi, M., Cooper-Knock, J., Zhang, S., Snyder, M.P., Preissl, S., Ren, B., O'Connor, C., Chen, S., Luo, C., Dixon, J.R., Ecker, J.R. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. (2025) bioRxiv. DOI: 10.1101/2025.03.23.644697

Ashkin, E.L., Tang, Y.J., Xu, H., Hung, K.L., Belk, J.A., Cai, H., Lopez, S.S., Dolcen, D.N., Hebert, J.D., Li, R., Ruiz, P.A., Keal, T., Andrejka, L., Chang, H.Y., Petrov, D.A., Dixon, J.R., Xu, Z., Winslow, M.M. A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis. (2025) Journal of Experimental Medicine. 222(1). DOI: 10.1084/jem.20240765

Heffel, M.G., Zhou, J., Zhang, Y., Lee, D.S., Hou, K., Pastor-Alonso, O., Abuhanna, K.D., Galasso, J., Kern, C., Tai, C.Y., Garcia-Padilla, C., Nafisi, M., Zhou, Y., Schmitt, A.D., Li, T., Haeussler, M., Wick, B., Zhang, M.J., Xie, F., Ziffra, R.S., Mukamel, E.A., Eskin, E., Nowakowski, T.J., Dixon, J.R., Pasaniuc, B., Ecker, J.R., Zhu, Q., Bintu, B., Paredes, M.F., Luo, C. Temporally distinct 3D multi-omic dynamics in the developing human brain. (2024) Natur. DOI: 10.1038/s41586-024-08030-7

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J.R., Chen, H., Castanon, R.G., Zu, S., Li, Y.E., Lucero, J., Osteen, J.K., Pinto-Duarte, A., Lee, J., Rink, J., Cho, S., Emerson, N., Nunn, M., O'Connor, C., Wu, Z., Stoica, I., Yao, Z., Smith, K.A., Tasic, B., Luo, C., Dixon, J.R., Zeng, H., Ren, B., Behrens, M.M., Ecker, J.R. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. (2023) Natur. 624(7991):366-377. DOI: 10.1038/s41586-023-06805-y

Liu, Z., Lee, D.S., Liang, Y., Zheng, Y., Dixon, J.R. Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity. (2023) Nature Communications. 14(1):6943. DOI: 10.1038/s41467-023-42647-y

Chapman, O.S., Luebeck, J., Sridhar, S., Wong, I.T., Dixit, D., Wang, S., Prasad, G., Rajkumar, U., Pagadala, M.S., Larson, J.D., He, B.J., Hung, K.L., Lange, J.T., Dehkordi, S.R., Chandran, S., Adam, M., Morgan, L., Wani, S., Tiwari, A., Guccione, C., Lin, Y., Dutta, A., Lo, Y.Y., Juarez, E., Robinson, J.T., Korshunov, A., Michaels, J.A., Cho, Y.J., Malicki, D.M., Coufal, N.G., Levy, M.L., Hobbs, C., Scheuermann, R.H., Crawford, J.R., Pomeroy, S.L., Rich, J.N., Zhang, X., Chang, H.Y., Dixon, J.R., Bagchi, A., Deshpande, A.J., Carter, H., Fraenkel, E., Mischel, P.S., Wechsler-Reya, R.J., Bafna, V., Mesirov, J.P., Chavez, L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. (2023) Nature Genetics. DOI: 10.1038/s41588-023-01551-3

Okonechnikov, K., Camgöz, A., Chapman, O., Wani, S., Park, D.E., Hübner, J.M., Chakraborty, A., Pagadala, M., Bump, R., Chandran, S., Kraft, K., Acuna-Hidalgo, R., Reid, D., Sikkink, K., Mauermann, M., Juarez, E.F., Jenseit, A., Robinson, J.T., Pajtler, K.W., Milde, T., Jäger, N., Fiesel, P., Morgan, L., Sridhar, S., Coufal, N.G., Levy, M., Malicki, D., Hobbs, C., Kingsmore, S., Nahas, S., Snuderl, M., Crawford, J., Wechsler-Reya, R.J., Davidson, T.B., Cotter, J., Michaiel, G., Fleischhack, G., Mundlos, S., Schmitt, A., Carter, H., Michealraj, K.A., Kumar, S.A., Taylor, M.D., Rich, J., Buchholz, F., Mesirov, J.P., Pfister, S.M., Ay, F., Dixon, J.R., Kool, M., Chavez, L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. (2023) Nature Communications. 14(1):2300. DOI: 10.1038/s41467-023-38044-0

Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J.R., Chen, H., Castanon, R.G., Zu, S., Li, Y.E., Lucero, J., Osteen, J.K., Pinto-Duarte, A., Lee, J., Rink, J., Cho, S., Emerson, N., Nunn, M., O'Connor, C., Yao, Z., Smith, K.A., Tasic, B., Zeng, H., Luo, C., Dixon, J.R., Ren, B., Behrens, M.M., Ecker, J.R. Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain. (2023) bioRxiv. DOI: 10.1101/2023.04.16.536509

Liu, Z., Lee, D.S., Liang, Y., Zheng, Y., Dixon, J.R. Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity. (2023) bioRxiv. DOI: 10.1101/2023.02.22.529589

Xu, Z., Lee, D.S., Chandran, S., Le, V.T., Bump, R., Yasis, J., Dallarda, S., Marcotte, S., Clock, B., Haghani, N., Cho, C.Y., Akdemir, K.C., Tyndale, S., Futreal, P.A., McVicker, G., Wahl, G.M., Dixon, J.R. Structural variants drive context-dependent oncogene activation in cancer. (2022) Natur. DOI: 10.1038/s41586-022-05504-4

Shah, R., Gallardo, C.M., Jung, Y.H., Clock, B., Dixon, J.R., McFadden, W.M., Majumder, K., Pintel, D.J., Corces, V.G., Torbett, B.E., Tedbury, P.R., Sarafianos, S.G. Activation of HIV-1 proviruses increases downstream chromatin accessibility. (2022) iScience. 25(12):105490. DOI: 10.1016/j.isci.2022.105490

Popay, T.M., Dixon, J.R. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. (2022) Journal of Biological Chemistry.:102117 DOI: 10.1016/j.jbc.2022.102117

Luo, C., Liu, H., Xie, F., Armand, E.J., Siletti, K., Bakken, T.E., Fang, R., Doyle, W.I., Stuart, T., Hodge, R.D., Hu, L., Wang, B.A., Zhang, Z., Preissl, S., Lee, D.S., Zhou, J., Niu, S.Y., Castanon, R., Bartlett, A., Rivkin, A., Wang, X., Lucero, J., Nery, J.R., Davis, D.A., Mash, D.C., Satija, R., Dixon, J.R., Linnarsson, S., Lein, E., Behrens, M.M., Ren, B., Mukamel, E.A., Ecker, J.R. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. (2022) Zellgenom. 2(3). DOI: 10.1016/j.xgen.2022.100107

Liu, H., Zhou, J., Tian, W., Luo, C., Bartlett, A., Aldridge, A., Lucero, J., Osteen, J.K., Nery, J.R., Chen, H., Rivkin, A., Castanon, R.G., Clock, B., Li, Y.E., Hou, X., Poirion, O.B., Preissl, S., Pinto-Duarte, A., O'Connor, C., Boggeman, L., Fitzpatrick, C., Nunn, M., Mukamel, E.A., Zhang, Z., Callaway, E.M., Ren, B., Dixon, J.R., Behrens, M.M., Ecker, J.R. DNA methylation atlas of the mouse brain at single-cell resolution. (2021) Natur. 598(7879):120-128. DOI: 10.1038/s41586-020-03182-8

Song, F., Xu, J., Dixon, J., Yue, F. Analysis of Hi-C Data for Discovery of Structural Variations in Cancer. (2021) Methods in Molecular Biology. 2301:143-161. DOI: 10.1007/978-1-0716-1390-0_7

Reid, D.A., Reed, P.J., Schlachetzki, J.C.M., Nitulescu, I.I., Chou, G., Tsui, Chandran, S., Jones, J.R., Lu, A.T., McClain, C.A., Ooi, J.H., Wang, T.W., Lana, Linker, S.B., Ricciardulli, A.S., Lau, S., Schafer, S., Horvath, S., Dixon, J.R., Hah, N., Glass, C.K., Gage, F.H. Incorporation of a nucleoside analog maps genome repair sites in postmitotic human neurons. (2021) Wissenschaft. 372(6537):91-94. DOI: 10.1126/science.abb9032

Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J.D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J.R., Hu, M., Nicodemi, M., Zhao, H., Ren, B. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. (2021) Nature Structural & Molecular Biology. DOI: 10.1038/s41594-020-00539-5

Akdemir, K.C., Le, V.T., Kim, J.M., Killcoyne, S., King, D.A., Lin, Y.P., Tian, Y., Inoue, A., Amin, S.B., Robinson, F.S., Nimmakayalu, M., Herrera, R.E., Lynn, E.J., Chan, K., Seth, S., Klimczak, L.J., Gerstung, M., Gordenin, D.A., O'Brien, J., Li, L., Deribe, Y.L., Verhaak, R.G., Campbell, P.J., Fitzgerald, R., Morrison, A.J., Dixon, J.R., Andrew Futreal, P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. (2020) Nature Genetics. DOI: 10.1038/s41588-020-0708-0

Kang, H., Shokhirev, M.N., Xu, Z., Chandran, S., Dixon, J.R., Hetzer, M.W. Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. (2020) Genes & Development. DOI: 10.1101/gad.335794.119

Akdemir, K.C., Le, V.T., Chandran, S., Li, Y., Verhaak, R.G., Beroukhim, R., Campbell, P.J., Chin, L., Dixon, J.R., Futreal, P.A. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. (2020) Nature Genetics. DOI: 10.1038/s41588-019-0564-y

Dixon, J.R. TADs for Life: Chromatin Domain Organization Regulates Lifespan in C. elegans. (2019) Developmental Cell. 51(2):131-132. DOI: 10.1016/j.devcel.2019.09.021

Lee, D.S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J.R., Fitzpatrick, C., O'Connor, C., Dixon, J.R., Ecker, J.R. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. (2019) Nature Methods. DOI: 10.1038/s41592-019-0547-z

Song, M., Yang, X., Ren, X., Maliskova, L., Li, B., Jones, I.R., Wang, C., Jacob, F., Wu, K., Traglia, M., Tam, T.W., Jamieson, K., Lu, S.Y., Ming, G.L., Li, Y., Yao, J., Weiss, L.A., Dixon, J.R., Judge, L.M., Conklin, B.R., Song, H., Gan, L., Shen, Y. Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes. (2019) Nature Genetics. 51(8):1252-1262. DOI: 10.1038/s41588-019-0472-1

Yang, Y., Zhang, Y., Ren, B., Dixon, J.R., Ma, J. Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. (2019) Cell Systems. DOI: 10.1016/j.cels.2019.05.011

Zhou, J., Ma, J., Chen, Y., Cheng, C., Bao, B., Peng, J., Sejnowski, T.J., Dixon, J.R., Ecker, J.R. Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation. (2019) Proceedings of the National Academy of Sciences of the United States of America. DOI: 10.1073/pnas.1901423116

Barbosa, K., Deshpande, A., Chen, B.R., Ghosh, A., Sun, Y., Dutta, S., Weetall, M., Dixon, J., Armstrong, S.A., Bohlander, S.K., Deshpande, A.J. Acute Myeloid Leukemia Driven by the CALM-AF10 Fusion Gene is Dependent on BMI1. (2019) Experimental Hematology.:42-54 DOI: 10.1016/j.exphem.2019.04.003

Gatchalian, J., Malik, S., Ho, J., Lee, D.S., Kelso, T.W.R., Shokhirev, M.N., Dixon, J.R., Hargreaves, D.C. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. (2018) Nature Communications. 9(1):5139. DOI: 10.1038/s41467-018-07528-9

Dixon, J.R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardımcı, G.G., Chakraborty, A., Bann, D.V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J.C., Ozadam, H., Lajoie, B.R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D.T., Stamatoyannopoulos, J.A., Broach, J.R., Hardison, R.C., Ay, F., Noble, W.S., Dekker, J., Gilbert, D.M., Yue, F. Integrative detection and analysis of structural variation in cancer genomes. (2018) Nature Genetics.:1388-1403 DOI: 10.1038/s41588-018-0195-8

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, M.Q., Gao, J., Dixon, J.R., Wang, X., Zeng, J., Xie, W. Allelic reprogramming of 3D chromatin architecture during early mammalian development. (2017) Natur. 547(7662):232-235. DOI: 10.1038/nature23263

Dixon, J.R., Gorkin, D.U., Ren, B. Chromatin Domains: The Unit of Chromosome Organization. (2016) Molecular Cell. 62(5):668-80. DOI: 10.1016/j.molcel.2016.05.018

Diao, Y., Li, B., Meng, Z., Jung, I., Lee, A.Y., Dixon, J., Maliskova, L., Guan, K.L., Shen, Y., Ren, B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. (2016) Genome Research. 26(3):397-405. DOI: 10.1101/gr.197152.115

Selvaraj, S., Schmitt, A.D., Dixon, J.R., Ren, B. Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. (2015) BMC Genomics. 16:900. DOI: 10.1186/s12864-015-1949-7

Ren, B., Dixon, J.R. A CRISPR Connection between Chromatin Topology and Genetic Disorders. (2015) Cell. 161(5):955-957. DOI: 10.1016/j.cell.2015.04.047

Dixon, J.R.*, Jung, I.*, Selvaraj, S.*, Shen, Y., Antosiewicz-Bourget, J.E., Lee, A.Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., Diao, Y., Liang, J., Zhao, H., Lobanenkov, V.V., Ecker, J.R., Thomson, J.A., Ren, B. Chromatin architecture reorganization during stem cell differentiation. (2015) Natur. 518(7539):331-6. DOI: 10.1038/nature14222

Li, Y., Rivera, C.M., Ishii, H., Jin, F., Selvaraj, S., Lee, A.Y., Dixon, J.R., Ren, B. CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells. (2014) PLOS One. 9(12):e114485. DOI: 10.1371/journal.pone.0114485

Attanasio, C., Nord, A.S., Zhu, Y., Blow, M.J., Biddie, S.C., Mendenhall, E.M., Dixon, J., Wright, C., Hosseini, R., Akiyama, J.A., Holt, A., Plajzer-Frick, I., Shoukry, M., Afzal, V., Ren, B., Bernstein, B.E., Rubin, E.M., Visel, A., Pennacchio, L.A. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. (2014) Genome Research. 24(6):920-9. DOI: 10.1101/gr.168930.113

Zuin, J.*, Dixon, J.R.*, van der Reijden, M.I., Ye, Z., Kolovos, P., Brouwer, R.W., van de Corput, M.P., van de Werken, H.J., Knoch, T.A., van IJcken, W.F., Grosveld, F.G., Ren, B., Wendt, K.S. Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(3):996-1001. DOI: 10.1073/pnas.1317788111

Selvaraj, S.*, Dixon, J.R.*, Bansal, V., Ren, B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. (2013) Nature Biotechnology. 31(12):1111-8. DOI: 10.1038/nbt.2728

Jin, F., Li, Y., Dixon, J.R., Selvaraj, S., Ye, Z., Lee, A.Y., Yen, C.A., Schmitt, A.D., Espinoza, C.A., Ren, B. A high-resolution map of the three-dimensional chromatin interactome in human cells. (2013) Natur. 503(7475):290-4. DOI: 10.1038/nature12644

Hu, M., Deng, K., Qin, Z., Dixon, J., Selvaraj, S., Fang, J., Ren, B., Liu, J.S. Bayesian inference of spatial organizations of chromosomes. (2013) PLOS Computational Biology. 9(1):e1002893. DOI: 10.1371/journal.pcbi.1002893

Shen, Y., Yue, F., McCleary, D.F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V.V., Ren, B. A map of the cis-regulatory sequences in the mouse genome. (2012) Natur. 488(7409):116-20. DOI: 10.1038/nature11243

Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., Ren, B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. (2012) Natur. 485(7398):376-80. DOI: 10.1038/nature11082

Barish, G.D., Yu, R.T., Karunasiri, M., Ocampo, C.B., Dixon, J., Benner, C., Dent, A.L., Tangirala, R.K., Evans, R.M. Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. (2010) Genes & Development. 24(24):2760-5. DOI: 10.1101/gad.1998010

Pagliarini, D.J., Wiley, S.E., Kimple, M.E., Dixon, J.R., Kelly, P., Worby, C.A., Casey, P.J., Dixon, J.E. Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic beta cells. (2005) Molecular Cell. 19(2):197-207. DOI: 10.1016/j.molcel.2005.06.008