| 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 | 7895 | 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 | 2390 | 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 | 1798 | 2017 |
| 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 | 1733 | 2015 |
| 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 | 1403 | 2016 |
| 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 | 757 | 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 | 548 | 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 | 351 | 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 | 292 | 2016 |
| 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 | 250 | 2018 |
| 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 | 243 | 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 | 171 | 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, ... | 80 | 2016 |
| 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, 1-17, 2017 | 62 | 2017 |
| Grammar-based compression of DNA sequences N Cherniavsky, R Ladner DIMACS Working Group on The Burrows-Wheeler Transform 21, 2004, 2004 | 61 | 2004 |
| 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 | 56 | 2021 |
| Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst 3: 99–101 NC Durand, JT Robinson, MS Shamim, I Machol, JP Mesirov, ES Lander, ... | 52 | 2016 |
| CTCF looping is established during gastrulation in medaka embryos R Nakamura, Y Motai, M Kumagai, CL Wike, H Nishiyama, Y Nakatani, ... Genome Research 31 (6), 968-980, 2021 | 47 | 2021 |
| The ENCODE uniform analysis pipelines BC Hitz, JW Lee, O Jolanki, MS Kagda, K Graham, P Sud, I Gabdank, ... Research Square, 2023 | 39 | 2023 |
| A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing PA Adastra, NC Durand, N Mitra, SG Pulido, R Mahajan, A Blackburn, ... Plos one 18 (11), e0294283, 2023 | 36 | 2023 |
