| A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping SSP Rao, MH Huntley, NC Durand, EK Stamenova, ID Bochkov, ... Cell 159 (7), 1665-1680, 2014 | 9889 | 2014 |
| Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments NC Durand, MS Shamim, I Machol, SSP Rao, MH Huntley, ES Lander, ... Cell systems 3 (1), 95-98, 2016 | 3590 | 2016 |
| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds O Dudchenko, SS Batra, AD Omer, SK Nyquist, M Hoeger, NC Durand, ... Science 356 (6333), 92-95, 2017 | 2642 | 2017 |
| Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom NC Durand, JT Robinson, MS Shamim, I Machol, JP Mesirov, ES Lander, ... Cell systems 3 (1), 99-101, 2016 | 2157 | 2016 |
| Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes AL Sanborn, SSP Rao, SC Huang, NC Durand, MH Huntley, AI Jewett, ... Proceedings of the National Academy of Sciences 112 (47), E6456-E6465, 2015 | 1987 | 2015 |
| Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations CP Fulco, J Nasser, TR Jones, G Munson, DT Bergman, V Subramanian, ... Nature genetics 51 (12), 1664-1669, 2019 | 1149 | 2019 |
| The energetics and physiological impact of cohesin extrusion L Vian, A Pękowska, SSP Rao, KR Kieffer-Kwon, S Jung, L Baranello, ... Cell 173 (5), 1165-1178. e20, 2018 | 664 | 2018 |
| Juicebox. js provides a cloud-based visualization system for Hi-C data JT Robinson, D Turner, NC Durand, H Thorvaldsdóttir, JP Mesirov, ... Cell systems 6 (2), 256-258. e1, 2018 | 527 | 2018 |
| The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 O Dudchenko, MS Shamim, SS Batra, NC Durand, NT Musial, R Mostofa, ... BioRxiv, 254797, 2018 | 363 | 2018 |
| Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture EM Darrow, MH Huntley, O Dudchenko, EK Stamenova, NC Durand, ... Proceedings of the National Academy of Sciences 113 (31), E4504-E4512, 2016 | 321 | 2016 |
| Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling G Nir, I Farabella, C Pérez Estrada, CG Ebeling, BJ Beliveau, HM Sasaki, ... PLoS genetics 14 (12), e1007872, 2018 | 295 | 2018 |
| Genetic determinants of co-accessible chromatin regions in activated T cells across humans RE Gate, CS Cheng, AP Aiden, A Siba, M Tabaka, D Lituiev, I Machol, ... Nature genetics 50 (8), 1140-1150, 2018 | 214 | 2018 |
| Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 NC Durand, MS Shamim, I Machol, SSP Rao, MH Huntley, ES Lander, ... | 169 | 2016 |
| The ENCODE uniform analysis pipelines BC Hitz, L Jin-Wook, O Jolanki, MS Kagda, K Graham, P Sud, I Gabdank, ... Biorxiv, 2023 | 141 | 2023 |
| An encyclopedia of enhancer-gene regulatory interactions in the human genome AR Gschwind, KS Mualim, A Karbalayghareh, MU Sheth, KK Dey, ... BioRxiv, 2023 | 108 | 2023 |
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| Chromatin architecture transitions from zebrafish sperm through early embryogenesis CL Wike, Y Guo, M Tan, R Nakamura, DK Shaw, N Díaz, ... Genome research 31 (6), 981-994, 2021 | 89 | 2021 |
| Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus) PA Larsen, RA Harris, Y Liu, SC Murali, CR Campbell, AD Brown, ... BMC biology 15 (1), 110, 2017 | 74 | 2017 |
| Grammar-based compression of DNA sequences N Cherniavsky, R Ladner DIMACS Working Group on The Burrows-Wheeler Transform 21, 2004, 2004 | 67 | 2004 |
| Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement V Garg, O Dudchenko, J Wang, AW Khan, S Gupta, P Kaur, K Han, ... Journal of Advanced Research 42, 315-329, 2022 | 66 | 2022 |
