Pre-print PublicationsFunded by NIH 4DN program
Pre-prints
| Title | Authors | DOI | Date |
|---|---|---|---|
| Daniel, B., Chen, A. Y., Sandor, K., Zhang, W., Miao, Z., Lareau, C. A., Yost, K. E., Chang, H., Satpathy, A. | 10.1101/2024.02.29.582872 | 2024-03-04 | |
Zhao, R., Xu, M., Wondisford, A. R., Lackner, R. M., Salsman, J., Dellaire, G., Chenoweth, D. M., O'Sullivan, R. J., Zhao, X., Zhang, H. | 10.1101/2024.02.29.582813 | 2024-02-29 | |
Chandrashekar, H., Simandi, Z., Choi, H., Ryu, H.-S., Waldman, A. J., Nikish, A., Muppidi, S. S., Gong, W., Paquet, D., Phillips-Cremins, J. E. | 10.1101/2024.02.27.582395 | 2024-02-27 | |
Hamazaki, N., Yang, W., Kubo, C., Qiu, C., Martin, B. K., Garge, R. K., Regalado, S. G., Nichols, E., Lee, C., Daza, R. M., Srivatsan, S., Shendure, J. | 10.1101/2024.02.10.579769 | 2024-02-12 | |
| Chilinski, M., Plewczynski, D. | 10.1101/2024.02.01.578389 | 2024-02-05 | |
Stein, J., Ericsson, M., Nofal, M., Magni, L., Aufmkolk, S., McMillan, R. B., Breimann, L., Herlihy, C. P., Lee, S. D., Willemin, A., Wohlmann, J., Arguedas-Jimenez, L., Yin, P., Pombo, A., Church, G. M., Wu, C.-t. | 10.1101/2024.02.05.576943 | 2024-02-05 | |
| Niu, Z., O'Farrell, A., Li, J., Reffsin, S., Jain, N., Dardani, I., Goyal, Y., Raj, A. | 10.1101/2024.01.31.578123 | 2024-01-31 | |
Hildebrand, E. M., Polovnikov, K., Dekker, B., Liu, Y., Lafontaine, D. L., Fox, A. N., Li, Y., Venev, S. V., Mirny, L. A., Dekker, J. | 10.1101/2022.10.15.511838 | 2024-01-30 | |
| Pseudotime analysis for time-series single-cell sequencing and imaging data | Li, G., Kim, H.-J., Pendyala, S., Zhang, R., Disteche, C. M., Vert, J.-P., Deng, X., Fowler, D. M., Noble, W. S. | 10.1101/2023.11.03.565575 | 2024-01-26 |
| Brumbaugh-Reed, E. H., Aoki, K., Toettcher, J. E. | 10.1101/2024.01.16.575860 | 2024-01-17 | |
| LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin | Korsak, S., Plewczynski, D. | 10.1101/2024.01.10.574968 | 2024-01-12 |
| Machine learning reveals the diversity of human 3D chromatin contact patterns | Gilbertson, E. N., Brand, C. M., McArthur, E., Rinker, D. C., Kuang, S., Pollard, K. S., Capra, J. A. | 10.1101/2023.12.22.573104 | 2023-12-23 |
| Perez, A. A., Goronzy, I. N., Blanco, M. R., Guo, J. K., Guttman, M. | 10.1101/2023.12.14.571730 | 2023-12-18 | |
| Electrostatic encoding of genome organization principles within single native nucleosomes | Park, S., Athreya, A., Carrizo, G., Benning, N., Mitchener, M., Bhanu, N., Garcia, B., Zhang, B., Muir, T. W., Pearce, E., Ha, T. | 10.1101/2023.12.08.570828 | 2023-12-09 |
| Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation | Titus, K. R., Simandi, Z., Chandrashekar, H., Paquet, D., Phillips-Cremins, J. E. | 10.1101/2023.12.04.569731 | 2023-12-05 |
| Zhou, Z., Narlikar, G. J. | 10.1101/2023.12.04.569983 | 2023-12-05 | |
| Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles | Andronov, L., Han, M., Zhu, Y., Roy, A. R., Barentine, A. E. S., Garhyan, J., Qi, L. S., Moerner, W. E. | 10.1101/2023.11.07.566110 | 2023-11-29 |
| Gunsalus, L. M., Keiser, M. J., Pollard, K. S. | 10.1101/2023.11.22.568268 | 2023-11-22 | |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene | Cote, A. J., O'Farrell, A., Dardani, I., Dunagin, M., Cote, C. J., Wan, Y., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Patel, R., Pham, K., Boyden, E. S., Berger, S., Phillips-Cremins, J., Churchman, L. S., Raj, A. | 10.1101/2020.04.06.028092 | 2023-11-13 |
| Genome folding principles revealed in condensin-depleted mitotic chromosomes | Zhao, H., Lin, Y., Lin, E., Liu, F., Shu, L., Jing, D., Wang, B., Wang, M., Shan, F., Zhang, L., Lam, J., Midla, S., Giardine, B., Keller, C., Hardison, R., Blobel, G., Zhang, H. | 10.1101/2023.11.09.566494 | 2023-11-13 |
| Gjoni, K., Pollard, K. S. | 10.1101/2023.11.03.565556 | 2023-11-05 | |
Kumar, P., Gholamalamdari, O., Zhang, Y., Zhang, L., Vertii, A., van Schaik, T., Peric-Hupkes, D., Sasaki, T., Gilbert, D. M., van Steensel, B., Ma, J., Kaufman, P. D., Belmont, A. S. | 10.1101/2023.10.29.564613 | 2023-11-01 | |
| Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning | Kuang, S., Pollard, K. S. | 0.1101/2023.10.22.563498 | 2023-10-24 |
| Sinha, J., Nickels, J. F., Thurm, A. R., Ludwig, C. H., Archibald, B. N., Hinks, M. M., Wan, J., Fang, D., Bintu, L. | 10.1101/2023.10.13.562147 | 2023-10-14 | |
| Single-cell chromatin state transitions during epigenetic memory formation | Fujimori, T., Rios-Martinez, C., Thurm, A. R., Hinks, M. M., Doughty, B. R., Sinha, J., Le, D., Hafner, A., Greenleaf, W. J., Boettiger, A. N., Bintu, L. | 10.1101/2023.10.03.560616 | 2023-10-05 |
| HybriSeq: Probe-based Device-free Single-cell RNA Profiling | Foyt, D., Brown, D., Zhou, S., Huang, B. | 10.1101/2023.09.27.559406 | 2023-09-29 |
Yang, X., Jones, I. R., Chen, P. B., Yang, H., Ren, X., Zheng, L., Li, B., Li, Y. E., Sun, Q., Wen, J., Beaman, C., Cui, X., Li, Y., Wang, W., Hu, M., Ren, B., Shen, Y. | 10.1101/2023.08.30.555359 | 2023-08-30 | |
| ChromaFold predicts the 3D contact map from single-cell chromatin accessibility | Gao, V. R., Yang, R., Das, A., Luo, R., Luo, H., McNally, D. R., Karagiannidis, I., Rivas, M. A., Wang, Z.-m., Barisic, D., Karbalayghareh, A., Wong, W., Zhan, Y., Chin, C. R., Noble, W. S., Bilmes, J. A., Apostolou, E., Kharas, M., Beguelin, W., Viny, A. D., Huangfu, D., Rudensky, A., Melnick, A., Leslie, C. S. | 10.1101/2023.07.27.550836 | 2023-07-28 |
| Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells | Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., Vercellone, F., Conte, M., Fontana, A., Nicodemi, M. | 10.1101/2023.07.27.550709 | 2023-07-28 |
| Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum | Zhao, Z., Parra, O. P., Musella, F., Scrutton-Alvarado, N., Fujita, S.-i., Alber, F., Yang, Y., Yamada, T. | 10.1101/2023.07.19.549737 | 2023-07-25 |
| Zhou, T., Zhang, R., Jia, D., Doty, R. T., Munday, A. D., Gao, D., Xin, L., Abkowitz, J. L., Duan, Z., Ma, J. | 10.1101/2023.07.20.549578 | 2023-07-25 | |
| A genome-wide single-cell 3D genome atlas of lung cancer progression | Liu, M., Jin, S., Agabiti, S. S., Jensen, T. B., Yang, T., Radda, J. S. D., Ruiz, C. F., Baldissera, G., Muzumdar, M. D., Wang, S. | 10.1101/2023.07.23.550157 | 2023-07-24 |
Murphy, D., Salataj, E., Di Giammartino, D. C., Rodriguez-Hernaez, J., Kloetgen, A., Garg, V., Char, E., Uyehara, C. M., Ee, L.-s., Lee, U., Stadtfeld, M., Hadjantonakis, A.-K., Tsirigos, A., Polyzos, A., Apostolou, E. | 10.1101/2023.07.19.549714 | 2023-07-19 | |
| High throughput PRIME editing screens identify functional DNA variants in the human genome | Ren, X., Yang, H., Nierenberg, J. L., Sun, Y., Chen, J., Beaman, C., Pham, T., Nobuhara, M., Takagi, M. A., Narayan, V., Li, Y., Ziv, E., Shen, Y. | 10.1101/2023.07.12.548736 | 2023-07-12 |
| Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states | Reffsin, S., Miller, J., Ayyanathan, K., Dunagin, M. C., Jain, N., Schultz, D. C., Cherry, S., Raj, A. | 10.1101/2023.07.06.547955 | 2023-07-07 |
| Luo, Z., Wen, X., Zhao, W., Nguyen, T., Wan, X., Richard, J. L. C., Zhong, S. | 10.1101/2023.06.28.546457 | 2023-06-29 | |
| Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells | Pulecio, J., Tayyebi, Z., Liu, D., Wong, W., Luo, R., Damodaran, J. R., Kaplan, S., Cho, H., Yan, J., Murphy, D. J., Rickert, R., Shukla, A., Zhong, A., Gonzalez, F., Yang, D., Li, W., Zhou, T., Apostolou, E., Leslie, C., Huangfu, D. | 10.1101/2023.06.14.544990 | 2023-06-14 |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene | Cote, A. J., O'Farrell, A., Dardani, I., Dunagin, M., Cote, C. J., Wan, Y., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Patel, R., Pham, K., Boyden, E. S., Berger, S., Phillips-Cremins, J., Churchman, L. S., Raj, A. | 10.1101/2020.04.06.028092 | 2023-06-13 |
SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress | Wolin, E., Guo, J. K., Blanco, M. R., Perez, A. A., Goronzy, I. N., Abdou, A. A., Gorhe, D., Guttman, M., Jovanovic, M. | 10.1101/2023.06.05.543769 | 2023-06-07 |
| scGHOST: Identifying single-cell 3D genome subcompartments | Xiong, K., Zhang, R., Ma, J. | 10.1101/2023.05.24.542032 | 2023-05-25 |
| High-resolution spatial multi-omics reveals cell-type specific nuclear compartments | Takei, Y., Yang, Y., White, J., Yun, J., Prasad, M., Ombelets, L. J., Schindler, S., Cai, L. | 10.1101/2023.05.07.539762 | 2023-05-09 |
| The temporal progression of immune remodeling during metastasis | McGinnis, C. S., Mao, Z., Reticker-Flynn, N. E., Winkler, J., Satpathy, A. T. | 10.1101/2023.05.04.539153 | 2023-05-07 |
| CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation | Fang, H., Tronco, A. R., Bonora, G., Nguyen, T., Thakur, J., Berletch, J. B., Filippova, G.N., Henikoff, S., Shendure, J., Noble, W. S., Disteche, C.M., Deng, X. | 10.1101/2023.05.04.539469 | 2023-05-04 |
Zemke, N. R., Armand, E. J., Wang, W., Lee, S., Zhou, J., Li, Y. E., Liu, H., Tian, W., Nery, J. R., Castanon, R. G., Bartlett, A., Osteen, J. K., Li, D., Zhuo, X., Xu, V., Miller, M., Krienen, F. M., Zhang, Q., Taskin, N., Ting, J., Feng, G., McCarroll, S. A., Callaway, E. M., Wang, T., Behrens, M., Lein, E. S., Ecker, J. R., Ren, B. | 10.1101/2023.04.08.536119 | 2023-04-08 | |
| Chilinski, M., Lipinski, J., Agarwal, A., Ruan, Y., Plewczynski, D. | 10.1101/2023.04.06.535849 | 2023-04-06 | |
| Comparing chromatin contact maps at scale: methods and insights | Gunsalus, L. M., McArthur, E., Gjoni, K., Kuang, S., Pittman, M., Capra, J. A., Pollard, K. S. | 10.1101/2023.04.04.535480 | 2023-04-04 |
Southerland, K. W., Xu, Y., Peters, D. T., Wei, X., Lin, X., Xiang, Y., Fei, K., Olivere, L. A., Morowitz, J. M., Otto, J., Kontos, C. D., Diao, Y. | 10.1101/2023.04.01.535211 | 2023-04-03 | |
| Nucleolar structure connects with global nuclear organization | Wang, C., Ma, H., Baserga, S., Pederson, T., Huang, S. | 10.1101/2023.03.30.534966 | 2023-03-31 |
| Faber, G. P., Hauschner, H., Atrash, M. K., Bilinsky, L., Shav-Tal, Y. | 10.1101/2023.03.21.533670 | 2023-03-24 | |
| Liu, Z., Lee, D.-S., Liang, Y., Zheng, Y., Dixon, J. | 10.1101/2023.02.22.529589 | 2023-03-21 | |
| Ho, E. K., Oatman, H. R., McFann, S. E., Yang, L., Johnson, H. E., Shvartsman, S. Y., Toettcher, J. E. | 10.1101/2023.03.09.531972 | 2023-03-10 | |
Luo, R., Yan, J., Oh, J. W., Xi, W., Shigaki, D., Wong, W., Cho, H., Murphy, D., Cutler, R., Rosen, B. P., Pulecio, J., Yang, D., Glenn, R., Chen, T., Li, Q. V., Vierbuchen, T., Sidoli, S., Apostolou, E., Huangfu, D., Beer, M. A. | 10.1101/2023.03.07.531569 | 2023-03-09 | |
| Aguilar, R., Camplisson, C.K., Lin, Q., Miga, K. H., Noble, W. S., Beliveau, B. J. | 10.1101/2023.03.06.530899 | 2023-03-07 | |
| Liu, Z., Lee, D.-S., Liang, Y., Zheng, Y., Dixon, J. | 10.1101/2023.02.22.529589 | 2023-02-23 | |
| Zhan, Y., Yildirim, A., Boninsegna, L., Alber, F. | 10.1101/2023.02.18.528138 | 2023-02-19 | |
Attar, S., Browning, V. E.., Liu, Y. Nichols, E.K., Tsue, A. F., Shechner, D.M., Shendure, J., Lieberman, J.A., Akilesh, S., Beliveau, B.J. | 10.1101/2023.01.30.526264 | 2023-02-01 | |
| Brueckner, D. B., Chen, H., Barinov, L., Zoller, B., Gregor, T. | 10.1101/2023.01.18.524527 | 2023-01-20 | |
Jain, N., Goyal, Y., Dunagin, M. C., Cote, C. J., Mellis, I. A., Emert, B., Jiang, C. L., Dardani, I. P., Reffsin, S., Raj, A. | 10.1101/2023.02.10.527870 | 2023-02-10 | |
| Hung, T-C., Kingsley, D.M., Boettiger, A.N. | 10.1101/2023.02.06.527380 | 2023-02-06 | |
| Deep learning enables fast, gentle STED microscopy | Ebrahimi, V., Stephan, T., Kim, J., Carravilla, P., Eggeling, C., Jakobs, S.,Kyu Young Han, K.Y. | 10.1101/2023.01.26.525571 | 2023-01-27 |
Singh, B. N., Tran, H., Kramer, J., Kirishenko, E., Changela, N., Wang, F., Feng, Y., Kumar, D., Tu, M., Lan, J., Bizet, M., Fuks, F., Steward, R. | 10.1101/2023.01.03.522592 | 2023-01-19 | |
| Programmable Drug Control of Receptor Valency Modulates the Potency of Cell Therapeutics | Finn, P., Chavez, M., Chen, X., Wang, H., Rane, D. A., Gurjar, J., Qi, L. S. | 10.1101/2023.01.04.522664 | 2023-01-04 |
| 3D genome organization around nuclear speckles drives mRNA splicing efficiency | Bhat, P., Chow, A., Emert, B., Ettlin, O., Quinodoz, S.A., Takei, Y., Huang, W., Blanco, M.R., Guttman, M. | 10.1101/2023.01.04.522632 | 2023-04-01 |
| Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+ | Zou, R. S., Liu, Y., Reyes Gaido, O. E., Konig, M. F., Mog, B. J., Shen, L. L., Aviles-Vazquez, F., Marin-Gonzalez, A., Ha, T. | 10.1101/2022.10.29.514376 | 2022-10-30 |
| Remodeling and compaction of the inactive X is regulated by Xist during female B cell activation | Anguera, M., Sierra, I., Nguyen, S. C., Barnett, R. J., Cook, A., Ryu, H.-S., Beethem, Z., Phillips-Cremins, J. E., Joyce, E. F. | 10.1101/2022.10.19.512821 | 2022-10-21 |
| Structural elements facilitate extreme long-range gene regulation at a human disease locus | Chen, L.-F., Long, H. K., Park, M., Swigut, T., Boettiger, A. N., Wysocka, J. | 10.1101/2022.10.20.513057 | 2022-10-21 |
Hildebrand, E. M., Polovnikov, K., Dekker, B., Liu, Y., Lafontaine, D. L., Fox, A. N., Li, Y., Venev, S. V., Mirny, L. A., Dekker, J. | 10.1101/2022.10.15.511838 | 2022-10-16 | |
| Murphy, S. E., Boettiger, A. | 10.1101/2022.10.14.512199 | 2022-10-14 | |
| Okafor, A. E., Lin, X., Situ, C., Wei, X., Wei, X., Wu, Z., Diao, Y. | 10.1101/2022.09.16.508339 | 2022-09-17 | |
| Sun, T., Xu, Y., Xiang, Y., Soderblom, E. J., Diao, Y. | 10.1101/2022.09.08.507172 | 2022-09-12 | |
| Phase separation of Myc differentially regulates gene transcription | Yang, J., Chung, C.-I., Koach, J., Liu, H., Zhao, Q., Yang, X., Shen, Y., Weiss, W. A., Shu, X. | 10.1101/2022.06.28.498043 | 2022-09-07 |
| Development and application of an uncapped mRNA platform | Liu, B., Ni, P., Cai, L., Shi, X., Ji, S., Ke, Z., Zhang, S., Hu, B., Yang, B., Xu, Y., Long, W., Fang, Z., Hu, H., Wang, Y., Zhang, W., Geng, H., Xu, Y., Zheng, X., Wang, Z., Zhang, B., Pan, K., Zhou, K., Cui, Y., Wang, H., Liu, B. | 10.1101/2022.06.05.494796 | 2022-08-28 |
| In silico discovery of repetitive elements as key sequence determinants of 3D genome folding | Gunsalus, L. M., Keiser, M. J., Pollard, K. S. | 10.1101/2022.08.11.503410 | 2022-08-12 |
| Loop stacking organizes genome folding from TADs to chromosomes | Hafner, A., Park, M., Berger, S. E., Nora, E., Boettiger, A. N. | 10.1101/2022.07.13.499982 | 2022-07-29 |
| Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut | Bara, A. M., Chen, L., Ma, C., Underwood, J., Moreci, R. S., Sumigray, K., Sun, T., Diao, Y., Verzi, M., Lechler, T. | 10.1101/2022.07.26.501624 | 2022-07-28 |
Nair, S., Barrett, A., Li, D., Raney, B. J., Lee, B. T., Kerpedjiev, P., Ramalingam, V., Pampari, A., Lekschas, F., Wang, T., Haeussler, M., Kundaje, A. | 10.1101/2022.05.26.493621 | 2022-05-31 | |
Rodrigues, A., MacQuarrie, K. L., Freeman, E., Willis, A. B., Xu, Z., Alvarez, A. A., Ma, Y., Perez White, B. E., Foltz, D. R., Huang, S. | 10.1101/2022.05.21.492846 | 2022-05-21 | |
| The association of MEG3 lncRNA with nuclear speckles in living cells | Hasenson, S., Alkalay, E., Atrash, M. K., Boocholez, A., Gershbaum, J., Hochberg-Laufer, H., Shav-Tal, Y. | 10.1101/2022.05.11.491451 | 2022-05-11 |
| A unique epigenomic landscape defines CD8+ tissue-resident memory T cells | Buquicchio, F. A., Fonseca, R., Belk, J. A., Evrard, M., Obers, A., Qi, Y., Daniel, B., Yost, K. E., Satpathy, A. T., Mackay, L. K. | 10.1101/2022.05.04.490680 | 2022-05-06 |
| Multi-scale phase separation by explosive percolation with single chromatin loop resolution | Sengupta, K., Denkiewicz, M., Chilinski, M., Szczepinska, T., Mollah, A. F., Korsak, S., D'Souza, R., Ruan, Y., Plewczynski, D. | 10.1101/2022.04.28.489670 | 2022-04-29 |
| CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing | Yang, Y., Wang, Y., Zhang, Y., Ma, J. | 10.1101/2022.04.21.488684 | 2022-04-22 |
Belk, J., Yao, W., Ly, N., Freitas, K., Chen, Y.-T., Shi, Q., Valencia, A., Shifrut, E., Kale, N., Yost, K., Duffy, C., Hwee, M., Miao, Z., Ashworth, A., Mackall, C., Marson, A., Carnevale, J., Vardhana, S., Satpathy, A. | 10.1101/2022.04.20.488974 | 2022-04-21 | |
| Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi | Zhang, R., Zhou, T., Ma, J. | 10.1101/2022.04.18.488683 | 2022-04-19 |
| NIPBL and WAPL balance cohesin activity to regulate chromatin folding and gene expression | Luppino, J. M., Field, A., Nguyen, S. C., Park, D. S., Shah, P. P., Lan, Y., Yunker, R., Jain, R., Adelman, K., Joyce, E. F. | 10.1101/2022.04.19.488785 | 2022-04-19 |
Alavattam, K. G., Mitzelfelt, K. A., Bonora, G., Fields, P. A., Yang, X., Chiu, H. S., Pabon, L., Bertero, A., Palpant, N. J., Noble, W. S., Murry, C. E. | 10.1101/2022.04.15.488491 | 2022-04-16 | |
| Reducing peptide sequence bias in quantitative mass spectrometry data with machine learning | Dincer, A. B., Lu, Y., Schweppe, D., Oh, S., Noble, W. S. | 10.1101/2022.04.11.487945 | 2022-04-12 |
| High-throughput Oligopaint screen identifies druggable regulators of genome folding | Park, D. S., Nguyen, S. C., Isenhart, R., Shah, P. P., Kim, W., Barnett, R. J., Chandra, A., Luppino, J. M., Harke, J., Wai, M., Yang, R., Lan, Y., Yoon, S., Yunker, R., Vahedi, G., Phillips-Cremins, J. E., Jain, R., Joyce, E. F. | 10.1101/2022.04.08.487672 | 2022-04-10 |
| A spatial genome aligner for multiplexed DNA-FISH | Jia, B. B., Jussila, A. P., Kern, J. C., Zhu, Q., Ren, B. | 10.1101/2022.03.25.485845 | 2022-03-27 |
| clampFISH 2.0 enables rapid, scalable amplified RNA detection in situ | Dardani, I., Emert, B. L., Goyal, Y., Jiang, C. L., Kaur, A., Lee, J., Rouhanifard, S. H., Alicea, G. M., Fane, M. E., Xiao, M., Herlyn, M., Weeraratna, A. T., Raj, A. | 10.1101/2022.03.16.484659 | 2022-03-17 |
Henn, D., Zhao, D., Chen, K., Trotsyuk, A., Bonham, C. A., Fischer, K. S., Kehl, T., Fehlmann, T., Sivaraj, D., Greco, A. H., Moortgat Illouz, S. E., Padmanabhan, J., Barrera, J. A., Kneser, U., Lenhof, H.-P., Januszyk, M., Levi, B., Keller, A., Longaker, M. T., Qi, L. S., Gurtner, G. C. | 10.1101/2022.03.14.484360 | 2022-03-15 | |
| Fang, W., Bell, C. M., Sapirstein, A., Asami, S., Leeper, K., Zack, D. J., Ji, H., Kalhor, R. | 10.1101/2022.02.13.480215 | 2022-02-14 | |
| Choudhary, M. N., Quaid, K., Xing, X., Schmidt, H., Wang, T. | 10.1101/2022.02.01.475239 | 2022-02-03 | |
| Li, D., Purushotham, D., Harrison, J. K., Wang, T. | 10.1101/2022.01.18.476849 | 2022-01-21 | |
| Zou, R. S., Marin-Gonzalez, A., Liu, Y., Liu, H. B., Shen, L., Dveirin, R., Luo, J. X. J., Kalhor, R., Ha, T. | 10.1101/2022.01.18.476836 | 2022-01-20 | |
| Reliance of neuronal gene expression on cohesin scales with chromatin loop length | Calderon, L., Weiss, F. D., Beagan, J. A., Oliveira, M. S., Wang, Y.-F., Carroll, T., Dharmalingam, G., Gong, W., Tossell, K., de Paola, V., Whilding, C., Ungless, M. A., Fisher, A. G., Phillips-Cremins, J. E., Merkenschlager, M. | 10.1101/2021.02.24.432639 | 2022-01-02 |
| Divergent clonal differentiation trajectories of T cell exhaustion | Daniel, B., Yost, K. E., Sandor, K., Xia, Y., Qi, Y., Hiam-Galvez, K. J., Meier, S. L., Belk, J., Giles, J. R., Wherry, E. J., Chang, H., Egawa, T., Satpathy, A. | 10.1101/2021.12.16.472900 | 2021-12-17 |
Abdulhay, N. J., Hsieh, L. J., McNally, C. P., Ketavarapu, M., Kasinathan, S., Nanda, A. S., Ostrowski, M. S., Wu, K., Moore, C. M., Goodarzi, H., Narlikar, G. J., Ramani, V. | 10.1101/2021.12.10.472156 | 2021-12-11 | |
| Chromatin interaction aware gene regulatory modeling with graph attention networks | Karbalayghareh, A., Sahin, M., Leslie, C. S. | 10.1101/2021.03.31.437978 | 2021-12-10 |
| Xu, M., Chigumira, T., Chen, Z., Tones, J., Zhao, R., Dahl, K. N., Chenoweth, D. M., Zhang, H. | 10.1101/2021.12.03.471109 | 2021-12-04 | |
| Boe, R. H., Ayyappan, V., Schuh, L., Raj, A. | 10.1101/2021.11.26.470134 | 2021-11-26 | |
Wang, J., Lareau, C. A., Bautista, J. L., Gupta, A. R., Sandor, K., Germino, J., Yin, Y., Arvedson, M. P., Reeder, G. C., Cramer, N. T., Xie, F., Ntranos, V., Satpathy, A. T., Anderson, M. S., Gardner, J. M. | 10.1101/2021.11.05.467513 | 2021-11-06 | |
| Conte, M., Irani, E., Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., Nicodemi, M. | 10.1101/2021.11.02.466589 | 2021-11-02 | |
| CTCF blocks anti-sense transcription initiation at divergent gene promoters | Luan, J., Syrett, C. M., Vermunt, M. W., Cote, A., Tome, J. M., Zhang, H., Huang, A., Luppino, J. M., Keller, C. A., Giardine, B. M., Zhang, S., Dunagin, M. C., Zhang, Z., Joyce, E. F., Lis, J. T., Raj, A., Hardison, R. C., Blobel, G. A. | 10.1101/2021.10.30.465508 | 2021-10-30 |
| Kinetic principles underlying pioneer function of GAGA transcription factor in live cells | Tang, X., Li, T., Liu, S., Wisniewski, J., Zheng, Q., Lavis, L., Rong, Y., Wu, C. | 10.1101/2021.10.21.465351 | 2021-10-23 |
| The 4D Nucleome Data Portal: a resource for searching and visualizing curated nucleomics data | Reiff, S. B., Schroeder, A. J., Kirli, K., Cosolo, A., Bakker, C., Mercado, L., Lee, S. B., Veit, A. D., Balashov, A. K., Vitzthum, C., Ronchetti, W., Pitman, K. M., Johnson, J., Ehmsen, S. R., Kerpedjiev, P., Abdennur, N. A., Imakaev, M., Ozturk, S. U., Camoglu, U., Mirny, L., Gehlenborg, N., Alver, B. H., Park, P. J. | 10.1101/2021.10.14.464435 | 2021-10-15 |
| Singh, A. P., Wu, P., Ryabichko, S., Raimundo, J., Swan, M., Wieschaus, E., Gregor, T., Toettcher, J. E. | 10.1101/2021.10.13.464280 | 2021-10-14 | |
| Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer | Kersten, K., Hu, K. H., Combes, A. J., Samad, B., Harwin, T., Ray, A., Rao, A. A., Cai, E., Marchuk, K., Artichoker, J., Courau, T., Shi, Q., Belk, J., Satpathy, A. T., Krummel, M. F. | 10.1101/2021.09.27.461866 | 2021-09-28 |
| Regional and clonal T cell dynamics at single cell resolution in immune checkpoint blockade | Pai, J. A., Chow, A., Sauter, J., Mattar, M., Rizvi, H., Woo, H. J., Shah, N., Uddin, F., Quintanal-Villalonga, A., Chan, J. M., Manoj, P., Allaj, V., Baine, M., Chaft, J. E., Plodkowski, A. J., Won, H., Wells, D., Donoghue, M. T. A., de Stanchina, E., Sen, T., Wolchok, J. D., Houck-Loomis, B., Merghoub, T., Rudin, C. M., Satpathy, A. T., Hellmann, M. D. | 10.1101/2021.09.27.461389 | 2021-09-27 |
| Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs | Lee, S., Vitzthum, C., Alver, B. H., Park, P. J. | 10.1101/2021.08.24.457552 | 2021-08-26 |
| Liu, Y., Dekker, J. | 10.1101/2021.08.24.457555 | 2021-08-26 | |
Xia, Y., Sandor, K., Pai, J. A., Daniel, B., Raju, S., Wu, R., Hsiung, S., Qi, Y., Yangdon, T., Okamoto, M., Schreiber, R. D., Murphy, K. M., Satpathy, A. T., Egawa, T. | 10.1101/2021.08.06.455141 | 2021-08-09 | |
Jiang, C. L., Goyal, Y., Jain, N., Wang, Q., Truitt, R. E., Cote, A. J., Emert, B., Mellis, I. A., Kiani, K., Yang, W., Jain, R., Raj, A. | 10.1101/2021.08.08.455532 | 2021-08-08 | |
| Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers | Spracklin, G., Abdennur, N. A., Imakaev, M., Chowdhury, N., Pradhan, S., Mirny, L., Dekker, J. | 10.1101/2021.08.05.455340 | 2021-08-06 |
| SARS-CoV-2 Restructures the Host Chromatin Architecture | Wang, R., Lee, J.-H., Xiong, F., Kim, J., Al Hasani, L., Yuan, X., Shivshankar, P., Krakowiak, J., Qi, C., Wang, Y., Eltzschig, H. K., Li, W. | 10.1101/2021.07.20.453146 | 2021-07-21 |
| Mapping the nuclear microenvironment of genes at a genome-wide scale | Yildirim, A., Hua, N., Boninsegna, L., Polles, G., Gong, K., Hao, S., Li, W., Zhou, X. J., Alber, F. | 10.1101/2021.07.11.451976 | 2021-07-12 |
Daniel, B., Belk, J. A., Meier, S. L., Chen, A. Y., Sandor, K., Qi, Y., Kitano, H., Wheeler, J. R., Foster, D. S., Januszyk, M. S., Longaker, M. T., Chang, H. Y., Satpathy, A. T. | 10.1101/2021.06.24.449850 | 2021-06-25 | |
| Sharma, A., Akshay, A., Rogne, M., Eskeland, R. | 10.1101/2021.06.21.449316 | 2021-06-22 | |
Calandrelli, R., Wen, X., Nguyen, T. C., Chen, C.-J., Qi, Z., Chen, W., Yan, Z., Wu, W., Zaleta-Rivera, K., Hu, R., Yu, M., Wang, Y., Ma, J., Ren, B., Zhong, S. | 10.1101/2021.06.10.447969 | 2021-06-11 | |
| Multi-color super-resolution imaging to study human coronavirus RNA during cellular infection | Wang, J., Han, M., Wang, H., Moeckl, L., Zeng, L., Moerner, W. E., Qi, L. S. | 10.1101/2021.06.09.447760 | 2021-06-09 |
| Systematic reconstruction of the cellular trajectories of mammalian embryogenesis | Qiu, C., Cao, J., Li, T., Srivatsan, S., Huang, X., Calderon, D., Noble, W. S., Disteche, C. M., Spielmann, M., Moens, C. B., Trapnell, C., Shendure, J. | 10.1101/2021.06.08.447626 | 2021-06-09 |
| Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9 | Gao, Y., Han, M., Shang, S., Wang, H., Qi, L. S. | 10.1101/2021.06.06.447300 | 2021-06-07 |
Rigano, A., Ehmsen, S., Ozturk, S. U., Ryan, J., Balashov, A., Hammer, M., Kirli, K., Bellve, K., Boehm, U., Brown, C. M., Chambers, J. J., Coleman, R. A., Cosolo, A., Faklaris, O., Fogarty, K., Guilbert, T., Hamacher, A. B., Itano, M. S., Keeley, D. P., Kunis, S., Lacoste, J., Laude, A., Ma, W., Marcello, M., Montero-Llopis, P., Nelson, G., Nitschke, R., Pimentel, J. A., Weidtkamp-Peters, S., Park, P. J., Alver, B., Grunwald, D., Strambio-De-Castillia, C. | 10.1101/2021.05.31.446382 | 2021-05-31 | |
| Cell-type specialization in the brain is encoded by specific long-range chromatin topologies | Winick-Ng, W., Kukalev, A., Harabula, I., Zea Redondo, L., Meijer, M., Serebreni, L., Bianco, S., Szabo, D., Chiariello, A. M., Irastorza Azcarate, I., Fiorillo, L., Musella, F., Thieme, C., Irani, E., Torlai Triglia, E., Kolodziejczyk, A. A., Abentung, A., Apostolova, G., Paul, E. J., Franke, V., Kempfer, R., Akalin, A., Teichmann, S., Dechant, G., Ungless, M. A., Nicodemi, M., Castelo-Branco, G., Pombo, A. | 10.1101/2020.04.02.020990 | 2021-05-11 |
| Takei, Y., Zheng, S., Yun, J., Shah, S., Pierson, N., White, J., Schindler, S., Tischbirek, C., Yuan, G.-C., Cai, L. | 10.1101/2021.04.26.441547 | 2021-04-27 | |
Hammer, M., Huisman, M., Rigano, A., Boehm, U., Chambers, J. J., Gaudreault, N., North, A. J., Pimentel, J. A., Sudar, D., Bajcsy, P., Brown, C. M., Corbett, A. D., Faklaris, O., Lacoste, J., Laude, A., Nelson, G., Nitschke, R., Farzam, F., Smith, C., Grunwald, D., Strambio-De-Castillia, C.. | 10.1101/2021.04.25.441198 | 2021-04-26 | |
| A perspective on Microscopy Metadata: data provenance and quality control | Maximiliaan Huisman, Mathias Hammer, Alex Rigano, Ulrike Boehm, James J. Chambers, Nathalie Gaudreault, Alison J. North, Jaime A. Pimentel, Damir Sudar, Peter Bajcsy, Claire M. Brown, Alexander D. Corbett, Orestis Faklaris, Judith Lacoste, Alex Laude, Glyn Nelson, Roland Nitschke, David Grunwald, Caterina Strambio-De-Castillia | arXiv:1910.11370 | 2021-04-26 |
| Stripenn detects architectural stripes from chromatin conformation data using computer vision | Yoon, S., Vahedi, G. | 10.1101/2021.04.16.440239 | 2021-04-18 |
| Quantification of durable CRISPR-based gene silencing activity | Nakamura, M., Ivec, A., Gao, Y., Qi, L. S. | 10.1101/2021.03.31.436355 | 2021-03-31 |
| Esposito, A., Bianco, S., Chiariello, A. M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R., Nicodemi, M. | 10.1101/2021.03.01.433416 | 2021-03-01 | |
| Disruption of nuclear architecture as a cause of COVID-19 induced anosmia | Zazhytska, M., Kodra, A., Hoagland, D. A., Fullard, J., Shayya, H. J., Omer, A., Firestein, S., Gong, Q., Canoll, P., Goldman, J. E., Roussos, P., tenOever, B. R., Overdevest, J. B., Lomvardas, S. | 10.1101/2021.02.09.430314 | 2021-02-09 |
| Jin, X., Fudenberg, G., Pollard, K. S. | 10.1101/2021.01.06.425599 | 2021-01-07 | |
| Cohesin-mediated loop anchors confine the location of human replication origins | Emerson, D. J., Zhao, P. A., Klein, K., Ge, C., Zhou, L., Sasaki, T., Yang, L., Venvev, S. V., Gibcus, J. H., Dekker, J., Gilbert, D. M., Phillips-Cremins, J. E. | 10.1101/2021.01.05.425437 | 2021-01-06 |
| Systematic evaluation of chromosome conformation capture assays | Akgol Oksuz, B., Yang, L., Abraham, S., Venev, S. V., Krietenstein, N., Parsi, K. M., Ozadam, H., Oomen, M. E., Nand, A., Mao, H., Genga, R. M. J., Maehr, R., Rando, O., Mirny, L., Gibcus, J. H., Dekker, J. | 10.1101/2020.12.26.424448 | 2020-12-27 |
| Mechanical frustration of phase separation in the cell nucleus by chromatin | Zhang, Y., Lee, D. S. W., Meir, Y., Brangwynne, C. P., Wingreen, N. S. | 10.1101/2020.12.24.424222 | 2020-12-24 |
| Multi-omics analysis of chromatin accessibility and interactions with transcriptome by HiCAR | Wei, X., Xiang, Y., Shan, R., Peters, D. T., Sun, T., Lin, X., Li, W., Diao, Y. | 10.1101/2020.11.02.366062 | 2020-12-19 |
Sanborn, A. L., Yeh, B. T., Feigerle, J. T., Hao, C. V., Townshend, R. J. L., Aiden, E. L., Dror, R. O., Kornberg, R. D. | 10.1101/2020.12.18.423551 | 2020-12-18 | |
| SnapHiC: a computational pipeline to map chromatin contacts from single cell Hi-C data | Yu, M., Abnousi, A., Zhang, Y., Li, G., Lee, L., Chen, Z., Fang, R., Wen, J., Sun, Q., Li, Y., Ren, B., Hu, M. | 10.1101/2020.12.13.422543 | 2020-12-15 |
| Multiscale and integrative single-cell Hi-C analysis with Higashi | Zhang, R., Zhou, T., Ma, J. | 10.1101/2020.12.13.422537 | 2020-12-15 |
| SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity | Chidester, B., Zhou, T., Ma, J. | 10.1101/2020.11.29.383067 | 2020-11-30 |
Jimenez Sabinina, V., Hossain, M. J., Heriche, J.-K., Hoess, P., Nijmeijer, B., Mosalaganti, S., Kueblbeck, M., Callegari, A., Szymborska, A., Beck, M., Ries, J., Ellenberg, J. | 10.1101/2020.11.27.386599 | 2020-11-27 | |
| DANGO: Predicting higher-order genetic interactions | Zhang, R., Ma, J., Ma, J. | 10.1101/2020.11.26.400739 | 2020-11-27 |
| Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells | Swygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T. | 10.1101/2020.11.24.396713 | 2020-11-24 |
Bonora, G., Ramani, V., Singh, R., Fang, H., Jackson, D., Srivatsan, S., Qiu, R., Lee, C., Trapnell, C., Shendure, J., Duan, Z., Deng, X., Noble, W. S., Disteche, C. M. | 10.1101/2020.11.20.390765 | 2020-11-20 | |
| Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors | Ypsilanti, A. R., Pattabiraman, K., Catta-Preta, R., Golonzhka, O., Lindtner, S., Tang, K., Jones, I., Abnousi, A., Juric, I., Hu, M., Shen, Y., Dickel, D. E., Visel, A., Pennachio, L. A., Hawrylycz, M., Thompson, C., Zeng, H., Barozzi, I., Nord, A. S., Rubenstein, J. L. R. | 10.1101/2020.11.03.366914 | 2020-11-04 |
| Lagler, T. M., Yang, Y., Abnousi, A., Hu, M., Li, Y. | 10.1101/2020.10.28.359869 | 2020-10-29 | |
| HiCRep.py: Fast comparison of Hi-C contact matrices in Python | Lin, D., Sanders, J., Noble, W. S. | 10.1101/2020.10.27.357756 | 2020-10-28 |
| DNA-loop extruding SMC complexes can traverse one another in vivo | Brandão, H. B., Ren, Z., Karaboja, X., Mirny, L. A., Wang, X. | 10.1101/2020.10.26.356329 | 2020-10-27 |
| Deep learning enables fast and dense single-molecule localization with high accuracy | Speiser, A., Müller, L.-R., Matti, U., Obara, C. J., Legant, W. R., Kreshuk, A., Macke, J. H., Ries, J., Turaga, S. C. | 10.1101/2020.10.26.355164 | 2020-10-26 |
| MCM complexes are barriers that restrict cohesin-mediated loop extrusion | Dequeker, B. J. H., Brandao, H. B., Scherr, M. J., Gassler, J., Powell, S., Gaspar, I., Flyamer, I. M., Tang, W., Stocsits, R., Davidson, I. F., Peters, J.-M., Duderstadt, K. E., Mirny, L. A., Tachibana, K. | 10.1101/2020.10.15.340356 | 2020-10-15 |
| HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics | Strom, A. R., Biggs, R. J., Banigan, E. J., Wang, X., Chiu, K., Herman, C., Collado, J., Yue, F., Ritland Politz, J. C., Tait, L. J., Scalzo, D., Telling, A., Groudine, M., Brangwynne, C. P., Marko, J., Stephens, A. D. | 10.1101/2020.10.09.331900 | 2020-10-09 |
| Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia | Janssens, D., Meers, M. P., Wu, S. J., Babaeva, E., Meshinchi, S., Sarthy, J. F., Ahmad, K., Henikoff, S. | 10.1101/2020.10.06.328948 | 2020-10-08 |
| Coarse-Grained Modelling of DNA Plectoneme Pinning in the Presence of Base-Pair Mismatches | Desai, P. R., Brahmachari, S., Marko, J. F., Das, S., Neuman, K. C. | 10.1101/2019.12.20.885533 | 2020-10-04 |
| PYMEVisualize: an open-source tool for exploring 3D super-resolution data | Marin, Z., Graff, M., Barentine, A. E. S., Soeller, C., Chung, K. K. H., Fuentes, L. A., Baddeley, D. | 10.1101/2020.09.29.315671 | 2020-09-30 |
| DMA-tudor interaction modules control the specificity of in vivo condensates | Courchaine, E. M., Barentine, A. E. S., Straube, K., Bewersdorf, J., Neugebauer, K. M. | 10.1101/2020.09.15.297994 | 2020-09-16 |
| Marko, J. F., Qiao, H., Liu, N., Biggs, R. J., Peng, Y. | 10.1101/2020.08.31.276402 | 2020-09-01 | |
Bashkirova, E., Monahan, K., Campbell, C. E., Osinski, J. M., Tan, L., Schieren, I., Barnea, G., Xie, S., Gronostajski, R. M., Lomvardas, S. | 10.1101/2020.08.30.274035 | 2020-08-30 | |
Geusz, R. J., Wang, A., Lam, D. K., Vinckier, N. K., Alysandratos, K.-D., Roberts, D. A., Wang, J., Kefalopoulou, S., Qiu, Y., Chiou, J., Gaulton, K. J., Ren, B., Kotton, D. N., Sander, M. | 10.1101/2020.08.28.263020 | 2020-08-29 | |
| RNA promotes the formation of spatial compartments in the nucleus | Quinodoz, S. A., Bhat, P., Ollikainen, N., Jachowicz, J. W., Banerjee, A. K., Chovanec, P., Blanco, M. R., Chow, A., Markaki, Y., Plath, K., Guttman, M. | 10.1101/2020.08.25.267435 | 2020-08-25 |
| Epigenetic memory as a time integral over prior history of Polycomb phase separation | Eeftens, J. M., Kapoor, M., Brangwynne, C. P. | 10.1101/2020.08.19.254706 | 2020-08-19 |
Arrastia, M. V., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S., Selck, D. A., Guttman, M., Ismagilov, R. F. | 10.1101/2020.08.11.242081 | 2020-08-12 | |
| Shao, W., Wang, T. | 10.1101/2020.07.31.231027 | 2020-07-31 | |
Beagrie, R. A., Thieme, C. J., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kramer, D. C., Chiariello, A. M., Bianco, S., Kukalev, A., Li, Y., Kempfer, R., Scialdone, A., Welch, L. A., Nicodemi, M., Pombo, A. | 10.1101/2020.07.31.230284 | 2020-07-31 | |
| Single-Molecule Micromanipulation Studies Of Methylated DNA | Zaichuk, T., Marko, J. | 10.1101/2020.07.29.227199 | 2020-07-30 |
| PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies | Bokota, G., Sroka, J., Basu, S., Das, N., Trzaskoma, P., Yushkevich, Y., Grabowska, A., Magalska, A., Plewczynski, D. | 10.1101/2020.07.16.206789 | 2020-07-17 |
Feng, Y., Wang, Y., Wang, X., He, X., Yang, C., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., Xie, W., Ma, H. | 10.1101/2020.07.15.204719 | 2020-07-16 | |
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A., Yu, M., Hu, R., Juric, I., Hu, M., Nicodemi, M., Zhuang, X., Ren, B. | 10.1101/2020.07.07.192526 | 2020-07-08 | |
| Unsupervised manifold alignment for single-cell multi-omics data | Singh, R., Demetci, P., Bonora, G., Ramani, V., Lee, C., Fang, H., Duan, Z., Deng, X., Shendure, J., Disteche, C., Noble, W. S. | 10.1101/2020.06.13.149195 | 2020-06-15 |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity | Mellis, I. A., Edelstein, H. I., Truitt, R., Beck, L. E., Symmons, O., Goyal, Y., Dunagin, M. C., Linares Saldana, R. A., Shah, P. P., Yang, W., Jain, R., Raj, A. | 10.1101/2020.06.11.147207 | 2020-06-12 |
| Lee, D. S. W., Wingreen, N. S., Brangwynne, C. P. | 10.1101/2020.06.03.128561 | 2020-06-04 | |
| Sanford, E. M., Emert, B. L., Cote, A., Raj, A. | 10.1101/2020.05.26.116962 | 2020-05-27 | |
| Conte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., Nicodemi, M. | 10.1101/2020.05.16.099275 | 2020-05-16 | |
| Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance | Schep, R., Brinkman, E. K., Leemans, C., Vergara, X., Morris, B., van Schaik, T., Manzo, S. G., Peric Hupkes, D., van den Berg, J., Beijersbergen, R., Medema, R. H., van Steensel, B. | 10.1101/2020.05.05.078436 | 2020-05-05 |
| Gromov-Wasserstein optimal transport to align single-cell multi-omics data | Demetci, P., Santorella, R., Sandstede, B., Noble, W. S., Singh, R. | 10.1101/2020.04.28.066787 | 2020-04-29 |
| The qBED track: a novel genome browser visualization for point processes | Moudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T., Mitra, R. D. | 10.1101/2020.04.27.060061 | 2020-04-29 |
| Jain, D., Chu, C., Alver, B. H., Lee, S., Lee, E. A., Park, P. J. | 10.1101/2020.04.27.060145 | 2020-04-28 | |
| Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin | Fiorillo, L., Musella, F., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Conte, M., Prisco, A., Pombo, A., Nicodemi, M. | 10.1101/2020.04.24.059915 | 2020-04-25 |
| Chen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C. | 10.1101/2020.04.10.036442 | 2020-04-11 | |
Cote, A. J., Cote, C. J., Bayatpour, S., Drexler, H. L., Alexander, K. A., Chen, F., Wassie, A. T., Boyden, E. S., Berger, S., Churchman, L. S., Raj, A. | 10.1101/2020.04.06.028092 | 2020-04-07 | |
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. | 10.1101/2020.03.21.001693 | 2020-03-23 | |
| Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell Lines | Cheng, R. R., Contessoto, V., Aiden, E. L., Wolynes, P. G., Di Pierro, M., Onuchic, J. N. | 10.1101/2020.03.21.001917 | 2020-03-22 |
| Accurate 4Pi single-molecule localization using an experimental PSF model | Li, Y., Buglakova, E., Zhang, Y., Thevathasan, J. V., Bewersdorf, J., Ries, J. | 10.1101/2020.03.18.997163 | 2020-03-19 |
| EMU: reconfigurable graphical user interfaces for Micro-Manager | Deschamps, J., Ries, J. | 10.1101/2020.03.18.997494 | 2020-03-19 |
| Emert, B., Cote, C., Torre, E. A., Dardani, I. P., Jiang, C., Jain, N., Shaffer, S. M., Raj, A. | 10.1101/2020.03.18.996660 | 2020-03-19 | |
| Detecting chromatin interactions along and between sister chromatids with SisterC | Oomen, M. E., Hedger, A. K., Watts, J. K., Dekker, J. | 10.1101/2020.03.10.986208 | 2020-03-11 |
| SPIN reveals genome-wide landscape of nuclear compartmentalization | Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Hupkes, D. P., Chen, Y., Gilbert, D. M., van Steensel, B., Belmont, A. S., Ma, J. | 10.1101/2020.03.09.982967 | 2020-03-10 |
| Ruan, Y. | 10.1101/2020.03.05.979070 | 2020-03-06 | |
| Regulation of gene expression by repression condensates during development | Treen, N., Shimobayashi, S. F., Eeftens, J., Brangwynne, C. P., Levine, M. | 10.1101/2020.03.03.975680 | 2020-03-04 |
| An Improved 4’-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNA | Wielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J. T., Lin, H. | 10.1101/2020.02.29.971317 | 2020-02-29 |
| Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer | Iyyanki, T. S., Zhang, B., Jin, Q., Yang, H., Liu, T., Wang, X., Song, F., Luan, Y., Yamashita, H., Wang, L., Warrick, J., Raman, J., Meeks, J., DeGraff, D. J., Yue, F. | 10.1101/2020.02.26.966697 | 2020-02-29 |
| Wang, J., Singh, A., Ozer, A., Zipfel, W. R. | 10.1101/2020.02.27.968578 | 2020-02-28 | |
Yang, H., Zhang, H., Luan, Y., Liu, T., Roberts, K. G., Qian, M., Zhang, B., Yang, W., Perez-Andreu, V., Xu, J., Iyyanki, S., Kuang, D., Reshmi, S. C., Gastier-Foster, J., Smith, C., Pui, C., Evans, W. E., Hunger, S. P., Platanias, L. C., Relling, M. V., Mullighan, C. G., Loh, M. L., Yue, F., Yang, J. J. | 10.1101/2020.02.23.961672 | 2020-02-25 | |
| CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization | Feng, Y., Wang, Y., Yang, C., Naseri, A., Pederson, T., Zheng, J., Xiao, X., Zhang, S., Xie, W., Ma, H. | 10.1101/2020.02.18.954610 | 2020-02-19 |
| Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping | Welch, L. R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W. F., Welch, J. D., Pombo, A. | 10.1101/2020.02.10.941047 | 2020-02-13 |
| Exploring the coronavirus epidemic using the new WashU Virus Genome Browser | Flynn, J., Purushotham, D., Choudhary, M. N., Zhuo, X., Fan, C., Matt, G., Li, D., Wang, T. | 10.1101/2020.02.07.939124 | 2020-02-11 |
Trzaskoma, P., Ruszczycki, B., Lee, B., Pels, K. K., Krawczyk, K., Bokota, G., Szczepankiewicz, A. A., Aaron, J., Walczak, A., Sliwinska, M., Magalska, A., Kadloff, M., Wolny, A., Parteka, Z., Arabasz, S., Kiss- Arabasz, M., Plewczynski, D., Ruan, Y., Wilczynski, G. M. | 10.1101/2020.02.05.935106 | 2020-02-06 | |
| GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data | Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F. | 10.1101/2020.01.30.927061 | 2020-01-31 |
| Probing multi-way chromatin interaction with hypergraph representation learning | Zhang, R., Ma, J. | 10.1101/2020.01.22.916171 | 2020-01-23 |
| Ma, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A. | 10.1101/2020.01.16.909333 | 2020-01-17 | |
Shaffer, S. M., Emert, B. L., Reyes-Hueros, R., Cote, C., Harmange, G., Sizemore, A. E., Gupte, R., Torre, E., Singh, A., Bassett, D. S., Raj, A. | 10.1101/379016 | 2019-12-21 | |
| Cell cycle dynamics of lamina associated DNA | van Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B. | 10.1101/2019.12.19.881979 | 2019-12-19 |
| Lekschas, F., Peterson, B., Haehn, D., Ma, E., Gehlenborg, N., Pfister, H. | 10.1101/597518 | 2019-12-12 | |
Humble, E., Dobrynin, P., Senn, H., Chuven, J., Scott, A. F., Mohr, D. W., Dudchenko, O., Omer, A. D., Colaric, Z., Lieberman Aiden, E., Wildt, D., Oliagi, S., Tamazian, G., Pukazhenthi, B., Ogden, R., Koepfli, K.-P. | 10.1101/867341 | 2019-12-08 | |
| Efficient Homology-directed Repair with Circular ssDNA Donors | Iyer, S., Mir, A., Ibraheim, R., Lee, J., VegaBadillo, J., Roscoe, B., Zhu, L. J., Liu, P., Luk, K., Mintzer, E., de Brito, J. S., Zamore, P., Sontheimer, E. J., Wolfe, S. | 10.1101/864199 | 2019-12-05 |
| High-Resolution 3D Fluorescent Imaging of Intact Tissues | El-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R. | 10.1101/855254 | 2019-11-26 |
Kim, H.-J., Yardimici, G. G., Bonora, G., Ramani, V., Liu, J., Qiu, R., Lee, C., Hesson, J., Ware, C. B., Shendure, J., Duan, Z., Noble, W. S. | 10.1101/534800 | 2019-11-18 | |
| Genetic screening for single-cell variability modulators driving therapy resistance | Torre, E. A., Arai, E., Bayatpour, S., Beck, L. E., Emert, B. L., Shaffer, S. M., Mellis, I. A., Fane, M., Alicea, G., Budinich, K. A., Weeraratna, A., Shi, J., Raj, A. | 10.1101/638809 | 2019-11-10 |
| Hyper-SAGNN: a self-attention based graph neural network for hypergraphs | Zhang, R., Zou, Y., Ma, J. | - | 2019-11-06 |
| Biswas, J., Rahman, R., Gupta, V., Rosbash, M., Singer, R. | 10.1101/829606 | 2019-11-04 | |
| TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles | Zhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Ma, J., Belmont, A. S. | 10.1101/824433 | 2019-10-30 |
| Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures | Brahmachari, S., Marko, J. F. | 10.1101/616102 | 2019-10-25 |
Huisman, M., Hammer, M., Rigano, A., Farzam, F., Gopinathan, R., Smith, C., Grunwald, D., Strambio-De-Castillia, C. | - | 2019-10-24 | |
| Cohesin depleted cells pass through mitosis and reconstitute a functional nuclear architecture | Cremer, M., Brandstetter, K., Maiser, A., Rao, S. S., Schmid, V., Mitra, N., Mamberti, S., Klein, K. N., Gilbert, D. M., Leonhardt, H., Cardoso, M. C., Lieberman Aiden, E., Harz, H., Cremer, T. | 10.1101/816611 | 2019-10-24 |
| Chromosome organization by one-sided and two-sided loop extrusion | Banigan, E. J., van den Berg, A. A., Brandao, H. B., Marko, J. F., Mirny, L. A. | 10.1101/815340 | 2019-10-22 |
| Composition dependent phase separation underlies directional flux through the nucleolus | Riback, J. A., Zhu, L., Ferrolino, M. C., Tolbert, M., Mitrea, D. M., Sanders, D. W., Wei, M.-T., Kriwacki, R. W., Brangwynne, C. P. | 10.1101/809210 | 2019-10-22 |
| A cost-efficient open source laser engine for microscopy | Schroeder, D., Deschamps, J., Dasgupta, A., Matti, U., Ries, J. | 10.1101/796482 | 2019-10-15 |
| Co-opted transposons help perpetuate conserved higher-order chromosomal structures | Choudhary, M. N., Friedman, R. Z., Wang, J. T., Jang, H. S., Zhuo, X., Wang, T. | 10.1101/485342 | 2019-10-14 |
| Architectural RNA is required for heterochromatin organization | Thakur, J., Fang, H., Llagas, T., Disteche, C. M., Henikoff, S. | 10.1101/784835 | 2019-09-27 |
Wutz, G., St. Hilaire, B. T. G., Ladurner, R., Stocsits, R., Nagasaka, K., Pignard, B., Sanborn, A., Tang, W., Varnai, C., Ivanov, M., Schoenfelder, S., van der Lelij, P., Huang, X., Duernberger, G., Roitinger, E., Mechtler, K., Davidson, I. F., Fraser, P., Aiden, E. L., Peters, J. M. | 10.1101/779058 | 2019-09-23 | |
| Kordon, M., Zarebski, M., Solarczyk, K., Ma, H., Pederson, T., Dobrucki, J. W. | 10.1101/772269 | 2019-09-18 | |
| Chromatin is frequently unknotted at the megabase scale | Goundaroulis, D., Aiden, E. L., Stasiak, A. | 10.1101/762872 | 2019-09-09 |
| Zhao, P.A., Sasaki, T., Gilbert, D. M. | 10.1101/755629 | 2019-09-05 | |
| NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells | Yang, L., Ghosh, R. P., Franklin, J. M., You, C., Liphardt, J. | 10.1101/749754 | 2019-08-28 |
| PBAF regulates compartmentalization of actively transcribing chromatin hubs | Kenworthy, C. A., Liou, S.-H., Chandris, P., Wong, V., Dziuba, P., Lavis, L. D., Liu, W.-L., Singer, R. H., Coleman, R. A. | 10.1101/111674 | 2019-08-22 |
| Nucleated transcriptional condensates amplify gene expression | Wei, M.-T., Chang, Y.-C., Shimobayashi, S. F., Shin, Y., Brangwynne, C. P. | 10.1101/737387 | 2019-08-21 |
| A supervised learning framework for chromatin loop detection in genome-wide contact maps | Salameh, T. J., Wang, X., Song, F., Zhang, B., Wright, S. M., Khunsriraksakul, C., Yue, F. | 10.1101/739698 | 2019-08-20 |
| Distinct features of nucleolus-associated domains in mouse embryonic stem cells | Bizhanova, A., Yan, A., Yu, J., Zhu, L. J., Kaufman, P. D. | 10.1101/740480 | 2019-08-20 |
| Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living Cells | Wang, H., Nakamura, M., Zhao, D., Nguyen, C. M., Yu, C., Lo, A., Daley, T., La Russa, M., Liu, Y., Qi, L. S. | 10.1101/734483 | 2019-08-14 |
| Measuring significant changes in chromatin conformation with ACCOST | Cook, K. B., Le Roch, K. G., Vert, J.-P., Noble, W. | 10.1101/727768 | 2019-08-06 |
| Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable Insets | Lekschas, F., Behrisch, M., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H. | 10.1101/301036 | 2019-07-25 |
| Dynamic changes in RNA-chromatin interactome promote endothelial dysfunction | Calandrelli, R., Xu, L., Luo, Y., Wu, W., Fan, X., Nguyen, T., Chen, C., Sriram, K., Natarajan, R., Chen, Z., Zhong, S. | 10.1101/712950 | 2019-07-24 |
| Zhao, B., Chaturvedi, P., Zimmerman, D. L., Belmont, A. S. | 10.1101/708024 | 2019-07-23 | |
| pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracks | Zhang, H. B., Kim, M., Chuang, J. H., Ruan, Y. | 10.1101/709683 | 2019-07-20 |
| Schuh, L., Saint-Antoine, M., Sanford, E., Emert, B., Singh, A., Marr, C., Goyal, Y., Raj, A. | 10.1101/704247 | 2019-07-18 | |
| Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C | Belaghzal, H., Borrman, T., Stephens, A. D., Lafontaine, D. L., Venev, S. V., Marko, J. F., Weng, Z., Dekker, J. | 10.1101/704957 | 2019-07-16 |
FANG, H., Bonora, G., Lewandowski, J., Thakur, J., Filippova, G. N., Henikoff, S., Shendure, J., Duan, Z., Rinn, J., Deng, X., Noble, W. S., Disteche, C. M. | 10.1101/687236 | 2019-06-30 | |
| Chemogenetic control of nanobodies | Farrants, H., Tarnawski, M., Müller, T. G., Otsuka, S., Hiblot, J., Koch, B., Kueblbeck, M., Kräusslich, H.-G., Ellenberg, J., Johnsson, K. | 10.1101/683557 | 2019-06-27 |
| Local rewiring of genome - nuclear lamina interactions by transcription. | Brueckner, L., Zhao, P. A., van Schaik, T., Leemans, C., Sima, J., Peric-Hupkes, D., Gilbert, D. M., van Steensel, B. | 10.1101/685255 | 2019-06-27 |
| A chromosome folding intermediate at the condensin-to-cohesin transition during telophase | Abramo, K., Valton, A.-L., Venev, S. V., Ozadam, H., Fox, A. N., Dekker, J. | 10.1101/678474 | 2019-06-21 |
| Multiplex chromatin interaction analysis by signal processing and statistical algorithms | Kim, M., Zheng, M., Tian, S. Z., Capurso, D., Lee, B., Chuang, J. H., Ruan, Y. | 10.1101/665232 | 2019-06-10 |
| Wang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J. | 10.1101/657080 | 2019-06-03 | |
| Marko, J. F., De Los Rios, P., Barducci, A., Gruber, S. | 10.1101/325373 | 2019-05-23 | |
| Inferring diploid 3D chromatin structures from Hi-C data | Cauer, A., Yardimci, G. G., Vert, J.-P., Varoquaux, N., Noble, W. | 10.1101/644294 | 2019-05-21 |
| Jointly embedding multiple single-cell omics measurements | Liu, J., Huang, Y., Singh, R., Vert, J.-P., Noble, W. | 10.1101/644310 | 2019-05-21 |
| Spring Model - chromatin modeling tool based on OpenMM | Kadlof, M., Rozycka, J., Plewczynski, D. | 10.1101/642322 | 2019-05-20 |
| Ultrastructural details of mammalian chromosome architecture | Krietenstein, N., Abraham, S., Venev, S., Abdennur, N., Gibcus, J., Hsieh, T.-H., Parsi, K. M., Yang, L., Maehr, R., Mirny, L., Dekker, J., Rando, O. | 10.1101/639922 | 2019-05-17 |
| Resolving the 3D landscape of transcription-linked mammalian chromatin folding | Hsieh, T.-H. S., Slobodyanyuk, E., Hansen, A. S., Cattoglio, C., Rando, O. J., Tjian, R., Darzacq, X. | 10.1101/638775 | 2019-05-17 |
| Improved CUT&RUN chromatin profiling and analysis tools | Meers, M. P., Bryson, T. D., Henikoff, S. | 10.1101/569129 | 2019-05-16 |
| Concerted localization resets precede YAP-dependent transcription | Franklin, J. M., Ghosh, R. P., Shi, Q., Liphardt, J. T. | 10.1101/539049 | 2019-05-06 |
| Spatial genome re-organization between fetal and adult hematopoietic stem cells | Chen, C., Yu, W., Tober, J., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G., Speck, N., Tan, K. | 10.1101/628214 | 2019-05-05 |
| Photoactivation of silicon rhodamines via a light-induced protonation | Frei, M. S., Hoess, P., Lampe, M., Nijmeijer, B., Kueblbeck, M., Ellenberg, J., Ries, J., Pitsch, S., Reymond, L., Johnsson, K. | 10.1101/626853 | 2019-05-04 |
| Tibanna: software for scalable execution of portable pipelines on the cloud | Lee, S., Johnson, J., Vitzthum, C., Kırlı, K., Alver, B. H., Park, P. J. | 10.1101/440974 | 2019-04-29 |
| Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells | Ruan, Y., Plewczynski, D., Zhu, J. J., Parteka, Z., Lee, B., Szalaj, P., Wang, P., Jodkowska, K., Arron, J., Chew, T. L. | 10.1101/621920 | 2019-04-29 |
| FIREcaller: an R package for detecting frequently interacting regions from Hi-C data | Crowley, C., Yang, Y., Qiu, Y., Hu, B., Won, H., Ren, B., Hu, M., Li, Y. | 10.1101/619288 | 2019-04-29 |
| Mapping RNA-chromatin interactions by sequencing with iMARGI V.2 | Wu, W., Yan, Z., Nguyen, T. C., Chen, Z., Chien, S., Zhong, S. | - | 2019-04-18 |
| ChIA-DropBox: a novel analysis and visualization pipeline for multiplex chromatin interactions | Tian, S. Z., Capurso, D., Kim, M., Lee, B., Zheng, M., Ruan, Y. | 10.1101/613034 | 2019-04-18 |
| Multi-scale deep tensor factorization learns a latent representation of the human epigenome | Schreiber, J., Durham, T. J., Bilmes, J., Noble, W. S. | 10.1101/364976 | 2019-04-11 |
| Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition | Zhang, H., Emerson, D., Gilgenast, T., Titus, K., Lan, Y., Huang, P., Zhang, D., Wang, H., Keller, C., Giardine, B., Hardison, R., Phillips-Cremins, J., Blobel, G. | 10.1101/604355 | 2019-04-11 |
| RNA polymerases as moving barriers to condensin loop extrusion | Brandao, H. B., Wang, X., Paul, P., van den Berg, A., Rudner, D. Z., Mirny, L. A. | 10.1101/604280 | 2019-04-10 |
| Transcription amplification by nuclear speckle association | Kim, J., Khanna, N., Belmont, A. S. | 10.1101/604298 | 2019-04-09 |
| Common DNA sequence variation influences 3-dimensional conformation of the human genome | Gorkin, D., Qiu, Y., Hu, M., Fletez-Brant, K., Liu, T., Schmitt, A., Noor, A., Chiou, J., Gaulton, K., Sebat, J., Li, Y., Hansen, K., Ren, B. | 10.1101/592741 | 2019-03-30 |
Schlichthaerle, T., Strauss, M. T., Schueder, F., Auer, A., Nijmeijer, B., Kueblbeck, M., Jimenez Sabinina, V., Thevatasan, J. V., Ries, J., Ellenberg, J., Jungmann, R. | 10.1101/579961 | 2019-03-23 | |
| Nuclear pores as versatile reference standards for quantitative superresolution microscopy | Thevathasan, J. V., Kahnwald, M., Cieslinski, K., Hoess, P., Peneti, S. K., Reitberger, M., Heid, D., Kasuba, K. C., Hoerner, S. J., Li, Y., Wu, Y.-L., Mund, M., Matti, U., Pereira, P. M., Henriques, R., Nijmeijer-Winter, B., Kueblbeck, M., Jimenez Sabinina, V., Ellenberg, J., Ries, J. | 10.1101/582668 | 2019-03-20 |
| Ramani, V., Deng, X., Qiu, R., Lee, C., Disteche, C. M., Noble, W. S., Duan, Z., Shendure, J. | 10.1101/579573 | 2019-03-15 | |
| CUT&Tag for efficient epigenomic profiling of small samples and single cells | Kaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., Henikoff, S. | 10.1101/568915 | 2019-03-06 |
| Absolute quantification of cohesin, CTCF and their regulators in human cells | Holzmann, J., Politi, A. Z., Nagasaka, K., Hantsche-Grininger, M., Walther, N., Koch, B., Fuchs, J., Dürnberger, G., Tang, W., Ladurner, R., Stocsits, R. R., Busslinger, G. A., Novak, B., Mechtler, K., Davidson, I. F., Ellenberg, J., Peters, J.-M. | 10.1101/560425 | 2019-02-27 |
| EpiAlignment: alignment with both DNA sequence and epigenomic data | Lu, J., Cao, X., Zhong, S. | 10.1101/562199 | 2019-02-27 |
| Supervised classification enables rapid annotation of cell atlases | Pliner, H. A., Shendure, J., Trapnell, C. | 10.1101/538652 | 2019-02-25 |
| Determining cellular CTCF and cohesin abundances to constrain 3D genome models | Cattoglio, C., Pustova, I., Walther, N., Ho, J. J., Hantsche-Grininger, M., Inouye, C. J., Hossain, M. J., Dailey, G. M., Ellenberg, J., Darzacq, X., Tjian, R., Hansen, A. S. | 10.1101/370650 | 2019-02-24 |
| Cooler: scalable storage for Hi-C data andother genomically-labeled arrays | Abdennur, N., Mirny, L. | 10.1101/557660 | 2019-02-22 |
| Localization microscopy at doubled precision with patterned illumination | Cnossen, J., Hinsdale, T., Thorsen, R., Schueder, F., Jungmann, R., Smith, C. S., Rieger, B., Stallinga, S. | 10.1101/554337 | 2019-02-20 |
| Comparing 3D genome organization in multiple species using Phylo-HMRF | Yang, Y., Zhang, Y., Ren, B., Dixon, J., Ma, J. | 10.1101/552505 | 2019-02-19 |
| Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy | Bertero, A., Fields, P. A., Smith, A. S., Leonard, A., Beussman, K., Sniadecki, N. J., Kim, D.-H., Tse, H.-F., Pabon, L., Shendure, J., Noble, W. S., Murry, C. E. | 10.1101/555250 | 2019-02-19 |
| Dynamics of gene expression in single root cells of A. thaliana | Jean-Baptiste, K., McFaline-Figueroa, J. L., Alexandre, C. M., Dorrity, M. W., Saunders, L., Bubb, K. L., Trapnell, C., Fields, S., Queitsch, C., Cuperus, J. T. | 10.1101/448514 | 2019-02-11 |
| MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome | Tian, D., Zhang, R., Zhang, Y., Zhu, X., Ma, J. | 10.1101/542092 | 2019-02-07 |
| Giusti-Rodriguez, P. M., Sullivan, P. F. | 10.1101/406330 | 2019-01-30 | |
| Schreiber, J., Bilmes, J., Noble, W. | 10.1101/533273 | 2019-01-29 | |
Paliou, C., Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A., Chiariello, A. M. M., Bianco, S., Annunziatella, C., Helmuth, J., Haas, S., Jerkovic, I., Brieske, N., Wittler, L., Timmermann, B., Nicodemi, M., Vingron, M., Mundlos, S., Andrey, G. | 10.1101/528877 | 2019-01-23 | |
| Biggs, R., Stephens, A. D., Liu, P., Marko, J. F. | 10.1101/423541 | 2019-01-04 | |
| ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization | Capurso, D., Wang, J., Tian, S. Z., Cai, L., Namburi, S., Lee, B., Tjong, H., Tang, Z., Wang, P., Wei, C.-L., Ruan, Y., Li, S. | 10.1101/506683 | 2018-12-27 |
| Xiong, K., Ma, J. | 10.1101/505503 | 2018-12-23 | |
| An RNA-binding region regulates CTCF clustering and chromatin looping | Hansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Darzacq, X., Tjian, R. | 10.1101/495432 | 2018-12-16 |
| Guided nuclear exploration increases CTCF target search efficiency | Hansen, A. S., Amitai, A., Cattoglio, C., Tjian, R., Darzacq, X. | 10.1101/495457 | 2018-12-13 |
Cheng, L.-C., Baboo, S., Lindsay, C., Brusman, L. E., Martinez-Bartolome, S., Tapia, O., Zhang, X., Yates, J. R., Gerace, L. | 10.1101/486415 | 2018-12-03 | |
| Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin | Vertii, A., Ou, J., Yu, J., Yan, A., Pages, H., Liu, H., Zhu, L. J., Kaufman, P. D. | 10.1101/484568 | 2018-12-03 |
| Limits of chromosome compaction by loop-extruding motors | Banigan, E. J., Mirny, L. A. | 10.1101/476424 | 2018-11-21 |
| Genome-wide co-localization of RNA-DNA interactions and fusion RNA pairs | Yan, Z., Huang, N., Wu, W., Chen, W., Jiang, Y., Chen, J., Huang, X., Wen, X., Xu, J., Jin, Q., Zhang, K., Chen, Z., Chien, S., Zhong, S. | 10.1101/472019 | 2018-11-20 |
| Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum | Dudchenko, O., Pham, M., Lui, C., Batra, S. S., Hoeger, M., Nyquist, S. K., Durand, N. C., Shamim, M. S., Machol, I., Erskine, W., Aiden, E. L., Kaur, P. | 10.1101/473553 | 2018-11-20 |
| Li, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., Ren, B. | 10.1101/470963 | 2018-11-15 | |
Leemans, C., van der Zwalm, M., Brueckner, L., Comoglio, F., van Schaik, T., Pagie, L., van Arensbergen, J., van Steensel, B. | 10.1101/464081 | 2018-11-06 | |
GHOSH, R. P., SHI, Q., YANG, L., REDDICK, M. P., NIKITINA, T., ZHURKIN, V. B., FORDYCE, P., STASEVICH, T. J., CHANG, H. Y., GREENLEAF, W. J., LIPHARDT, J. T. | 10.1101/450262 | 2018-10-26 | |
| Highly Structured Homolog Pairing Reflects Functional Organization of the Drosophila Genome | AlHaj Abed, J., Erceg, J., Goloborodko, A., Nguyen, S. C., McCole, R. B., Saylor, W., Fudenberg, G., Lajoie, B. R., Dekker, J., Mirny, L. A., Wu, T. | 10.1101/443887 | 2018-10-17 |
| The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos | Erceg, J., AlHaj Abed, J., Goloborodko, A., Lajoie, B. R., Fudenberg, G., Abdennur, N., Imakaev, M., McCole, R. B., Nguyen, S. C., Saylor, W., Joyce, E. F., Senaratne, T. N., Hannan, M. A., Nir, G., Dekker, J., Mirny, L. A., Wu, C.-t. | 10.1101/443028 | 2018-10-17 |
| Khanna, N., Zhang, J., Dudko, O., Murre, C. | 10.1101/441444 | 2018-10-12 | |
| Condensin II inactivation in interphase does not affect chromatin folding or gene expression | Abdennur, N., Schwarzer, W., Pekowska, A., Shaltiel, I. A., Huber, W., Haering, C. H., Mirny, L., Spitz, F. | 10.1101/437459 | 2018-10-07 |
Stephens, A. D., Liu, P. Z., Kandula, V., Chen, H., Almassalha, L. M., Backman, V., O'Halloran, T., Adam, S. A., Goldman, R. D., Banigan, E. J., Marko, J. F. | 10.1101/423442 | 2018-09-21 | |
| Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond | Nomidis, S. K., Skoruppa, E., Carlon, E., Marko, J. F. | 10.1101/422683 | 2018-09-20 |
| Sadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D. | 10.1101/266981 | 2018-09-14 | |
| Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Yang, Y., Li, Y., Ren, B., Hu, M. | 10.1101/411835 | 2018-09-08 | |
| The accessible chromatin landscape of the hippocampus at single-cell resolution | Sinnamon, J. R., Torkenczy, K. A., Linhoff, M. W., Vitak, S. A., Pliner, H. A., Trapnell, C., Steemers, F. J., Mandel, G., Adey, A. C. | 10.1101/407668 | 2018-09-04 |
Lawlor, N., Marquez, E. J., Orchard, P., Narisu, N., Shamim, M. S., Thibodeau, A., Varshney, A., Kursawe, R., Erdos, M. R., Kanke, M., Gu, H., Pak, E., Dutra, A., Russell, S., Li, X., Piecuch, E., Luo, O., Chines, P. S., Fuchbserger, C., Sethupathy, P., Aiden, A. P., Ruan, Y., Aiden, E. L., Collins, F. S., Ucar, D., Parker, S. C. J., Stitzel, M. L. | 10.1101/399139 | 2018-08-23 | |
| Photon count estimation in single-molecule localization microscopy | Rieger, B., Stallinga, S., Hulleman, C. N., Thorsen, R. O., Grunwald, D., Hammer, M. | 10.1101/396424 | 2018-08-20 |
Sun, Z., Chen, L., Xin, H., Huang, Q., Cillo, A., Tabib, T., Ding, Y., Kolls, J., Bruno, T., Lafyatis, R., Vignali, D., Chen, K., Hu, M., Chen, W. | 10.1101/392662 | 2018-08-16 | |
| Symmons, O., Chang, M., Mellis, I., Kalish, J. M., Bartolomei, M. S., Raj, A. | 10.1101/386359 | 2018-08-07 | |
| A combination of transcription factors mediates inducible interchromosomal pairing | Kim, S., Dunham, M., Shendure, J. | 10.1101/385047 | 2018-08-05 |
| Marko, J., Biggs, R., Sun, M., Hornick, J. | 10.1101/384982 | 2018-08-04 | |
McSwiggen, D. T., Hansen, A. S., Marie-Nelly, H., Teves, S., Heckert, A., Dugast-Darzacq, C., Hao, Y., Umemoto, K. K., Tjian, R., Darzacq, X. | 10.1101/375071 | 2018-07-30 | |
Nir, G., Farabella, I., Perez Estrada, C., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. H., Nguyen, S. C., McCole, R. B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N. M. C., Nguyen, H. Q., Hannan, M. A., Russell, S., Durand, N. C., Rao, S. S. P., Kishi, J. Y., Soler-Vila, P., Di Pierro, M., Onuchic, J. N., Callahan, S., Schreiner, J., Stuckey, J., Yin, P., Lieberman Aiden, E., Marti-Renom, M. A., Wu, C.- t. | 10.1101/374058 | 2018-07-28 | |
| Mir, M., Stadler, M. R., Ortiz, S. A., Harrison, M. M., Darzacq, X., Eisen, M. B. | 10.1101/377812 | 2018-07-26 | |
| Receptor-ligand rebinding kinetics in confinement | Erbas, A., Olvera de la Cruz, M., Marko, J. | 10.1101/370395 | 2018-07-16 |
| Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture | Schreiber, J., Libbrecht, M., Bilmes, J., Noble, W. | 10.1101/103614 | 2018-07-15 |
| CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning | Oomen, M. E., Hansen, A., Liu, Y., Darzacq, X., Dekker, J. | 10.1101/365866 | 2018-07-11 |
| LADL: Light-activated dynamic looping for endogenous gene expression control | Rege, M., Kim, J. H., Valeri, J., Dunagin, M., Metzger, A., Gong, W., Beagan, J., Raj, A., Phillips-Cremins, J. E. | 10.1101/349340 | 2018-06-18 |
| Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritis | Jarvis, J. N., Zhu, L., Jiang, K., Wong, L., Buck, M. J., Chen, Y., Moncrief, H., Macintosh, L. A., Liu, T., Sing, X., Li, D., Wang, T., O'Neil, K. M. | 10.1101/349811 | 2018-06-18 |
| Kim, J., Han, K. Y., Khanna, N., Ha, T., Belmont, A. S. | 10.1101/347955 | 2018-06-15 | |
| RNA polymerase II clustering through CTD phase separation | Boehning, M., Dugast-Darzacq, C., Rankovic, M., Hansen, A. S., Yu, T.-K., Marie-Nelly, H., McSwiggen, D. T., Kokic, G., Dailey, G. M., Cramer, P., Darzacq, X., Zweckstetter, M. | 10.1101/316372 | 2018-06-15 |
| Yin, Y., Jiang, Y., Berletch, J. B., Disteche, C. M., Noble, W. S., Steemers, F. J., Adey, A. C., Shendure, J. A. | 10.1101/338053 | 2018-06-12 | |
| HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps | Kerpedjiev, P., Abdennur, N., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S. B., Azhir, A., Kumar, N., Hwang, J., Lee, S., Alver, B. H., Pfister, H., Mirny, L. A., Park, P. J., Gehlenborg, N. | 10.1101/121889 | 2018-06-04 |
Kim, J.-S., He, X., Liu, J., Duan, Z., Kim, T., Gerard, J., Kim, B., Lane, W. S., Noble, W. S., Budnik, B., Waldman, T. | 10.1101/325209 | 2018-05-17 | |
Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G., Cattoglio, C., Banala, S., Lavis, L., Darzacq, X., Tjian, R. | 10.1101/208710 | 2018-05-16 | |
| GITAR: an Open Source Tool for Analysis and Visualization of Hi-C Data | Calandrelli, R., Wu, Q., Guan, J., Zhong, S. | 10.1101/259515 | 2018-05-08 |
| Exponential fluorescent amplification of individual RNAs using clampFISH probes | Rouhanifard, S. H., Mellis, I. A., Dunagin, M., Bayatpour, S., Symmons, O., Cote, A., Raj, A. | 10.1101/222794 | 2018-05-07 |
| TSA-Seq Mapping of Nuclear Genome Organization | Chen, Y., Zhang, Y., Wang, Y., Zhang, L., Brinkman, E. K., Adam, S. A., Goldman, R., van Steensel, B., Ma, J., Belmont, A. S. | 10.1101/307892 | 2018-04-25 |
| Complementary chromosome folding by transcription factors and cohesin | Pereira, M. C. F., Brackley, C. A., Michieletto, D., Annunziatella, C., Bianco, S., Chiariello, A. M., Nicodemi, M., Marenduzzo, D. | 10.1101/305359 | 2018-04-23 |
| Quantitative imaging of chromatin decompaction in living cells | Dultz, E., Mancini, R., Polles, G., Vallotton, P., Alber, F., Weis, K. | 10.1101/219253 | 2018-04-22 |
| Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays | Gibcus, J. H., Samejima, K., Goloborodko, A., Samejima, I., Naumova, N., Kanemaki, M., Xie, L., Paulson, J. R., Earnshaw, W. C., Mirny, L. A., Dekker, J. | 10.1101/174649 | 2018-04-20 |
| RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome | Chen, W., Yan, Z., Li, S., Huang, N., Huang, X., Zhang, J., Zhong, S. | 10.1101/300483 | 2018-04-12 |
| An inter-chromosomal transcription hub activates the unfolded protein response in plasma cells | Bortnick, A., He, Z., Aubrey, M., Chandra, V., Denholtz, M., Chen, K., Lin, Y. C., Murre, C. | 10.1101/295915 | 2018-04-07 |
Walther, N., Hossain, M. J., Politi, A. Z., Koch, B., Kueblbeck, M., Oedegaard-Fougner, O., Lampe, M., Ellenberg, J. | 10.1101/237834 | 2018-03-22 | |
| Identification of cis elements for spatio-temporal control of DNA replication | Sima, J., Chakraborty, A., Dileep, V., Michalski, M., Rivera-Mulia, J. C., Trevilla-Garcia, C., Klein, K. N., Bartlett, D., Washburn, B. K., Paulsen, M. T., Vera, D., Nora, E. P., Kraft, K., Mundlos, S., Bruneau, B. G., Ljungman, M., Fraser, P., Ay, F., Gilbert, D. M. | 10.1101/285650 | 2018-03-21 |
| Bracha, D., Walls, M. T., Wei, M.-T., Zhu, L., Kurian, M., Toettcher, J. E., Brangwynne, C. P. | 10.1101/283655 | 2018-03-16 | |
| Continuous-trait probabilistic model for comparing multi-species functional genomic data | Yang, Y., Gu, Q., Zhang, Y., Sasaki, T., Crivello, J., O'Neill, R. J., Gilbert, D. M., Ma, J. | 10.1101/283093 | 2018-03-16 |
| GIVE: toward portable genome browsers for personal websites | Cao, X., Yan, Z., Wu, Q., Zheng, A., Zhong, S. | 10.1101/177832 | 2018-03-15 |
| SAVER: Gene expression recovery for UMI-based single cell RNA sequencing | Huang, M., Wang, J., Torre, E., Dueck, H., Shaffer, S., Bonasio, R., Murray, J., Raj, A., Li, M., Zhang, N. R. | 10.1101/138677 | 2018-03-08 |
| Bartman, C. R., Keller, C. A., Giardine, B., Hardison, R. C., Blobel, G. A., Raj, A. | 10.1101/275354 | 2018-03-02 | |
| Barton, C., Morganella, S., Oedegaard, O., Alexander, S., Ries, J., Fitzgerald, T., Ellenberg, J., Birney, E. | 10.1101/115436 | 2018-02-22 | |
| Emerging Evidence of Chromosome Folding by Loop Extrusion | Fudenberg, G., Abdennur, N., Imakaev, M., Goloborodko, A., Mirny, L. | 10.1101/264648 | 2018-02-16 |
| Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks | Singh, S., Yang, Y., Poczos, B., Ma, J. | 10.1101/085241 | 2018-02-05 |
| Measuring the reproducibility and quality of Hi-C data | Yardımcı, G. G., Ozadam, H., Sauria, M. E. G., Ursu, O., Yan, K.-K., Yang, T., Chakraborty, A., Kaul, A., Lajoie, B. R., Song, F., Zhan, Y., Ay, F., Gerstein, M., Kundaje, A., Li, Q., Taylor, J., Yue, F., Dekker, J., Noble, W. S. | 10.1101/188755 | 2018-02-05 |
| Defect-Facilitated Buckling in Supercoiled Double-Helix DNA | Brahmachari, S., Dittmore, A., Takagi, Y., Neuman, K. C., Marko, J. F. | 10.1101/259689 | 2018-02-04 |
| Predicting CTCF-mediated chromatin loops using CTCF-MP | Zhang, R., Wang, Y., Yang, Y., Zhang, Y., Ma, J. | 10.1101/259416 | 2018-02-02 |
| C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2 | Gao, X. D., Tu, L.-C., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., Sontheimer, E. J. | 10.1101/171819 | 2018-01-31 |
| Bend-Induced Twist Waves and the Structure of Nucleosomal DNA | Skoruppa, E., Nomidis, S. K., Marko, J. F., Carlon, E. | 10.1101/256818 | 2018-01-30 |
Dudchenko, O., Shamim, M. S., Batra, S., Durand, N. C., Musial, N. T., Mostofa, R., Pham, M., Glenn St Hilaire, B., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S. K., Korchina, V., Pletch, K., Flanagan, J. P., Tomaszewicz, A., McAloose, D., Perez Estrada, C., Novak, B. J., Omer, A. D., Aiden, E. L. | 10.1101/254797 | 2018-01-28 | |
| Multiplex Chromatin Interaction Analysis with Single-Molecule Precision | Zheng, M., Tian, S. Z., Maurya, R., Lee, B., Kim, M., Capurso, D., Piecuch, E., Gong, L., Zhu, J. J., Wong, C. H., Ngan, C. Y., Wang, P., Ruan, X., Wei, C.-L., Ruan, Y. | 10.1101/252049 | 2018-01-25 |
| Correlative live and super-resolution imaging reveals the dynamic structure of replication domains | Xiang, W., Roberti, M. J., Heriche, J.-K., Huet, S., Alexander, S., Ellenberg, J. | 10.1101/189373 | 2018-01-24 |
| Heterochromatin drives organization of conventional and inverted nuclei | Falk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B. R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I., Mirny, L. | 10.1101/244038 | 2018-01-09 |
Matthews, B. J., Dudchenko, O., Kingan, S., Koren, S., Antoshechkin, I., Crawford, J. E., Glassford, W. J., Herre, M., Redmond, S. N., Rose, N. H., Weedall, G. D., Wu, Y., Batra, S. S., Brito-Sierra, C. A., Buckingham, S. D., Campbell, C. L., Chan, S., Cox, E., Evans, B. R., Fansiri, T., Filipovic, I., Fontaine, A., Gloria-Soria, A., Hall, R., Joardar, V. S., Jones, A. K., Kay, R. G. G., Kodali, V., Lee, J., Lycett, G. J., Mitchell, S. N., Muehling, J., Murphy, M. R., Omer, A., Partridge, F. A., Peluso, P., Aiden, A. P., Ramasamy, V., Rasic, G., Roy, S., Saavedra-Rodriguez, K., Sharan, S., Sha | 10.1101/240747 | 2017-12-29 | |
| Chromatin interaction data visualization in the WashU Epigenome Browser | Li, D., Hsu, S., Purushotham, D., Wang, T. | 10.1101/239368 | 2017-12-24 |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome | Bonora, G., Deng, X., Fang, H., Ramani, V., Qui, R., Berletch, J., Filippova, G. N., Duan, Z., Schendure, J., Noble, W. S., Disteche, C. M. | 10.1101/165340 | 2017-12-15 |
| Allele-specific control of replication timing and genome organization during development | Rivera-Mulia, J. C., Dimond, A., Vera, D., Trevilla-Garcia, C., Sasaki, T., Zimmerman, J., Dupont, C., Gribnau, J., Fraser, P., Gilbert, D. M. | 10.1101/221762 | 2017-11-21 |
| Dynamic reorganization of nuclear architecture during human cardiogenesis | Fields, P. A., Ramani, V., Bonora, G., Yardimci, G. G., Bertero, A., Reinecke, H., Pabon, L., Noble, W. S., Shendure, J., Murry, C. | 10.1101/222877 | 2017-11-21 |
| Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus | Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M., Shishkin, A., Bhat, P., Trinh, V., Aznauryan, E., Russell, P., Cheng, C., Jovanovic, M., Chow, A., McDonel, P., Garber, M., Guttman, M. | 10.1101/219683 | 2017-11-18 |
| CHRAC/ACF Contribute to the Repressive Ground State of Chromatin | Scacchetti, A., Brueckner, L., Jain, D., Schauer, T., Zhang, X., Schnorrer, F., van Steensel, B., Straub, T., Becker, P. B. | 10.1101/218768 | 2017-11-13 |
| A Cell Type-Specific Class of Chromatin Loops Anchored at Large DNA Methylation Nadirs | Jeong, M., Huang, X., Zhang, X., Su, J., Shamim, M., Bochkov, I., Reyes, J., Jung, H., Heikamp, E., Presser Aiden, A., Li, W., Aiden, E., Goodell, M. A. | 10.1101/212928 | 2017-11-09 |
| Removing unwanted variation between samples in Hi-C experiments | Fletez-Brant, K., Qiu, Y., Gorkin, D. U., Hu, M., Hansen, K. D. | 10.1101/214361 | 2017-11-06 |
| Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins | Stephens, A. D., Liu, P. Z., Banigan, E. J., Almassalha, L. M., Backman, V., Adam, S. A., Goldman, R., Marko, J. | 10.1101/206367 | 2017-10-29 |
| Spot-On: robust model-based analysis of single-particle tracking experiments | Hansen, A. S., Woringer, M., Grimm, J. B., Lavis, L. D., Tjian, R., Darzacq, X. | 10.1101/171983 | 2017-10-26 |
Allahyar, A., Vermeulen, C., Bouwman, B., Krijger, P., Verstegen, M., Geeven, G., van Kranenburg, M., Pieterse, M., Straver, R., Haarhuis, J., Teunissen, H., Renkens, I., Kloosterman, W., Rowland, B., de Wit, E., de Ridder, J., de Laat, W. | 10.1101/206094 | 2017-10-20 | |
| Juicebox.js provides a cloud-based visualization system for Hi-C data | Robinson, J., Turner, D., Durand, N. C., Thorvaldsdottir, H., Mesirov, J. P., Aiden, E. L. | 10.1101/205740 | 2017-10-19 |
| Hulleman, C., Huisman, M., Moerland, R., Grunwald, D., Stallinga, S., Rieger, B. | 10.1101/204776 | 2017-10-17 | |
| Chromatin Organization by an Interplay of Loop Extrusion and Compartmental Segregation | Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N., Mirny, L. | 10.1101/196261 | 2017-10-03 |
| Mechanics and buckling of biopolymeric shells and cell nuclei | Banigan, E. J., Stephens, A. D., Marko, J. F. | 10.1101/197566 | 2017-10-02 |
| Nucleation of multiple buckled structures in intertwined DNA double helices | Brahmachari, S., Gunn, K. H., Giuntoli, R. D., Mondragon, A., Marko, J. F. | 10.1101/196345 | 2017-09-30 |
| CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics | Ma, H., Tu, L.-C., Naseri, A., Chung, Y.-C., Grunwald, D., Zhang, S., Pederson, T. | 10.1101/195966 | 2017-09-29 |
| Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundaries | Sun, J., Zhou, L., Emerson, D. J., Gilgenast, T. G., Titus, K., Beagan, J. A., Phillips-Cremins, J. E. | 10.1101/191213 | 2017-09-20 |
| High-throughput identification of RNA nuclear enrichment sequences | Shukla, C. J., McCorkindale, A. L., Gerhardinger, C., Korthauer, K. D., Cabili, M. N., Shechner, D. M., Irizarry, R. A., Maass, P. G., Rinn, J. L. | 10.1101/189654 | 2017-09-15 |
| SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices | Cohen, N. M., Olivares-Chauvet, P., Lubling, Y., Baran, Y., Lifshitz, A., Hoichman, M., Tanay, A. | 10.1101/187203 | 2017-09-12 |
Ma, W., Ay, F., Lee, C., Gulsoy, G., Deng, X., Cook, S., Hesson, J., Cavanaugh, C., Ware, C. B., Krumm, A., Shendure, J., Blau, C. A., Disteche, C. M., Noble, W. S., Duan, Z. | 10.1101/184846 | 2017-09-05 | |
| A Mechanism of Cohesin-Dependent Loop Extrusion Organizes Zygotic Genome Architecture | Gassler, J., Brandao, H. B., Imakaev, M., Flyamer, I. M., Ladstatter, S., Bickmore, W. A., Peters, J.-M., Mirny, L. A., Tachibana-Konwalski, K. | 10.1101/177766 | 2017-08-17 |
| 3D Single-Molecule Super-Resolution Microscopy With A Tilted Light Sheet | Gustavsson, A.-K., Petrov, P. N., Lee, M. Y., Shechtman, Y., Moerner, W. E. | 10.1101/135699 | 2017-08-14 |
| Fast, robust and precise 3D localization for arbitrary point spread functions | Li, Y., Mund, M., Hoess, P., Matti, U., Nijmeijer, B., Jimenez Sabinina, V., Ellenberg, J., Schoen, I., Ries, J. | 10.1101/172643 | 2017-08-10 |
| Yang, T., Zhang, F., Yardimci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., Li, Q. | 10.1101/101386 | 2017-08-04 | |
| Heterogeneity and Intrinsic Variation in Spatial Genome Organization | Finn, E., Pegoraro, G., Brandao, H. B., Valton, A.-L., Oomen, M. E., Dekker, J., Mirny, L., Misteli, T. | 10.1101/171801 | 2017-08-03 |
| Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells | Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A. | 10.1101/083212 | 2017-07-16 |
| Dileep, V., Gilbert, D. M. | 10.1101/158352 | 2017-07-14 | |
Tasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., Wang, Y., Genova, J., Ma, J., Belmont, A. S., Zhao, H. | 10.1101/162156 | 2017-07-12 | |
| HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small Multiples | Lekschas, F., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H. | 10.1101/123588 | 2017-07-09 |
| A Fluorogenic Array Tag for Temporally Unlimited Single Molecule Tracking | Ghosh, R. P., Franklin, M. J., Draper, W. E., Shi, Q., Liphardt, J. T. | 10.1101/159004 | 2017-07-03 |
| Noma, A., Smith, C. S., Huisman, M., Martin, R. M., Moore, M. J., Grunwald, D. | 10.1101/156091 | 2017-06-26 | |
| Chromatin accessibility dynamics of myogenesis at single cell resolution | Pliner, H., Packer, J., McFaline-Figueroa, J., Cusanovich, D., Daza, R., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., Adey, A., Steemers, F., Shendure, J., Trapnell, C. | 10.1101/155473 | 2017-06-26 |
| Kaewsapsak, P., Shechner, D. M., Mallard, W., Rinn, J. L., Ting, A. Y. | 10.1101/153098 | 2017-06-21 | |
| Dense Bicoid Hubs Accentuate Binding along the Morphogen Gradient | Mir, M., Reimer, A., Haines, J. E., Li, X.-Y., Stadler, M., Garcia, H., Eisen, M. B., Darzacq, X. | 10.1101/133124 | 2017-06-08 |
| qSR: A software for quantitative analysis of single molecule and super-resolution data | Andrews, J. O., Narayanan, A., Spille, J.-H., Cho, W.-K., Thaler, J. D., Cisse, I. I. | 10.1101/146241 | 2017-06-05 |
| Tu, L.-C., Huisman, M., Chung, Y.-C., Smith, C., Grunwald, D. | 10.1101/145110 | 2017-06-02 | |
| Li, H., Kalhor, R., Li, B., Su, T., Berk, A., Kurdistani, S., Alber, F., Chen, L. | 10.1101/142604 | 2017-05-26 | |
Phanstiel, D. H., Van Bortle, K., Spacek, D. V., Hess, G. T., Saad Shamim, M., Machol, I., Love, M. I., Lieberman Aiden, E., Bassik, M. C., Snyder, M. P. | 10.1101/142026 | 2017-05-25 | |
| Torre, E. A., Dueck, H., Shaffer, S., Gospocic, J., Gupte, R., Bonasio, R., Kim, J., Murray, J., Raj, A. | 10.1101/138289 | 2017-05-18 | |
Rao, S., Huang, S.-C., Glenn St. Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bochkov, I. D., Huang, X., Shamim, M. S., Omer, A. D., Bernstein, B. E., Casellas, R., Lander, E. S., Lieberman Aiden, E. | 10.1101/139782 | 2017-05-18 | |
| Torque and buckling in stretched intertwined double-helix DNAs | Marko, J., Brahmachari, S. | 10.1101/135905 | 2017-05-09 |
| Facilitated Dissociation Of Transcription Factors From Single DNA Binding Sites | Kamar, R. I., Banigan, E. J., Erbas, A., Giuntoli, R. D., Olvera de la Cruz, M., Johnson, R. C., Marko, J. F. | 10.1101/135947 | 2017-05-09 |
| Sun, X., Bizhanova, A., Matheson, T. D., Yu, J., Zhu, L. J., Kaufman, P. D. | 10.1101/134767 | 2017-05-08 | |
| Supercoiling DNA locates mismatches | Dittmore, A., Brahmachari, S., Takagi, Y., Marko, J. F., Neuman, K. C. | 10.1101/130567 | 2017-04-25 |
| Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers | Crocker, J., Tsai, A., Muthusamy, A. K., Lavis, L. D., Singer, R. H., Stern, D. L. | 10.1101/128280 | 2017-04-18 |
| Woringer, M., Darzacq, X., Zimmer, C., Mir, M. | 10.1101/125815 | 2017-04-10 | |
| An Integrative Framework For Detecting Structural Variations In Cancer Genomes | Dixon, J., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardimci, 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., Mulia, J. C. R., 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., Ay, F., Noble, W. S., Dekker, J., Gilbert, D. M., Yue, F. | 10.1101/119651 | 2017-03-28 |
Kubo, N., Ishii, H., Gorkin, D., Meitinger, F., Xiong, X., Fang, R., Liu, T., Ye, Z., Li, B., Dixon, J., Desai, A., Zhao, H., Ren, B. | 10.1101/118737 | 2017-03-20 | |
| HUGIn: Hi-C Unifying Genomic Interrogator | Martin, J. S., Xu, Z., Reiner, A. P., Mohlke, K. L., Sullivan, P., Ren, B., Hu, M., Li, Y. | 10.1101/117531 | 2017-03-16 |
| Dawson, W., Plewczynski, D. | 10.1101/105676 | 2017-03-08 | |
| Repli-seq: genome-wide analysis of replication timing by next-generation sequencing | Marchal, C., Sasaki, T., Vera, D., Wilson, K., Sima, J., Rivera-Mulia, J.-C., Trevilla Garcia, C., Nogues, C., Nafie, E., Gilbert, D. M. | 10.1101/104653 | 2017-03-01 |
| HiCPlus: Resolution Enhancement of Hi-C interaction heatmap | Zhang, Y., An, L., Hu, M., Tang, J., Yue, F. | 10.1101/112631 | 2017-03-01 |
Wang, Y., Zhang, B., Zhang, L., An, L., Xu, J., Li, D., Choudhary, M. N., Li, Y., Hu, M., Hardison, R., Wang, T., Yue, F. | 10.1101/112268 | 2017-02-27 | |
| A fluorogenic nanobody array tag for prolonged single molecule imaging in live cells | Ghosh, R., Draper, W., Franklin, J. M., Shi, Q., Liphardt, J. | 10.1101/111690 | 2017-02-27 |
| p53 dynamically directs TFIID assembly on target gene promoters | Coleman, R. A., Qiao, Z., Singh, S. K., Peng, C. S., Cianfrocco, M., Zhang, Z., Piasecka, A., Aldeborgh, H., Basishvili, G., Liu, W.-L. | 10.1101/083014 | 2017-02-24 |
| Real-time chromatin dynamics at the single gene levelduring transcription activation | Germier, T., Kocanova, S., Walther, N., Bancaud, A., Shaban, H. A., Sellou, H., Politi, A., Ellenberg, J., Gallardo, F., Bystricky, K. | 10.1101/111179 | 2017-02-23 |
Yan, J., Chen, S.-A. A., Local, A., Liu, T., Qiu, Y., Lee, A.-Y., Jung, I., Preissl, S., Rivera, C. M., Wang, C., Ishii, H., Fang, R., Ye, Z., Ge, K., Hu, M., Ren, B. | 10.1101/110239 | 2017-02-21 | |
| Reversed graph embedding resolves complex single-cell developmental trajectories | Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H., Trapnell, C. | 10.1101/110668 | 2017-02-21 |
Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., Adey, A., Waterston, R. H., Trapnell, C., Shendure, J. | 10.1101/104844 | 2017-02-02 | |
| Direct visualization of transcriptional activation by physical enhancer-promoter proximity | Chen, H., Fujioka, M., Jaynes, J. B., Gregor, T. | 10.1101/099523 | 2017-01-31 |
| The 4D Nucleome Project | Dekker, J., Belmont, A. S., Guttman, M., Leshyk, V. O., Lis, J. T., Lomvardas, S., Mirny, L. A., O'Shea, C. C., Park, P. J., Ren, B., Ritland, J. C., Shendure, J., Zhong, S., The 4D Nucleome Network | 10.1101/103499 | 2017-01-26 |
| PGS: a dynamic and automated population-based genome structure software | Hua, N., Tjong, H., Shin, H., Gong, K., Zhou, X. J., Alber, F. | 10.1101/103358 | 2017-01-26 |
| Takei, Y., Shah, S., Harvey, S., Qi, L. S., Cai, L. | 10.1101/101477 | 2017-01-18 | |
| The 3D genome organization of Drosophila melanogaster through data integration | Li, Q., Tjong, H., Li, X., Gong, K., Zhou, X. J., Chiolo, I., Alber, F. | 10.1101/099911 | 2017-01-15 |
| Comprehensive characterization of neutrophil genome topology | Zhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M. P., Alber, F., Murre, C. | 10.1101/100198 | 2017-01-15 |
| Eagen, K. P., Lieberman Aiden, E., Kornberg, R. D. | 10.1101/099804 | 2017-01-12 | |
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L., Bruneau, B. | 10.1101/095802 | 2017-01-09 | |
| Cohesin dependent compaction of mitotic chromosomes | Schalbetter, S. A., Goloborodko, A., Fudenberg, G., Belton, J. M., Miles, C., Yu, M., Dekker, J., Mirny, L., Baxter, J. | 10.1101/094946 | 2016-12-17 |
| Two independent modes of chromosome organization are revealed by cohesin removal | Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C., Mirny, L., Spitz, F. | 10.1101/094185 | 2016-12-15 |
| Cell cycle dynamics of chromosomal organisation at single-cell resolution | Nagano, T., Lubling, Y., Varnai, C., Dudley, C., Leung, W., Baran, Y., Mandelson Cohen, N., Wingett, S., Fraser, P., Tanay, A. | 10.1101/094466 | 2016-12-15 |
| CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct Dynamics | Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., Darzacq, X. | 10.1101/093476 | 2016-12-13 |
| The dynamic three-dimensional organization of the diploid yeast genome | Kim, S., Liachko, I., Brickner, D. G., Cook, K., Noble, W. S., Brickner, J. H., Shendure, J., Dunham, M. | 10.1101/091827 | 2016-12-05 |
| Belaghzal, H., Dekker, J., Gibcus, J. H. | 10.1101/090001 | 2016-11-27 | |
| Detecting hierarchical 3-D genome domain reconfiguration with network modularity | Norton, H. K., Huang, H., Emerson, D. J., Kim, J., Gu, S., Bassett, D. S., Phillips-Cremins, J. E. | 10.1101/089011 | 2016-11-22 |
| Calibrating photon counts from a single image | Heintzmann, R., Relich, P. K., Nieuwenhuizen, R. P. J., Lidke, K. A., Rieger, B. | - | 2016-11-17 |
| Visualizing adenosine to inosine RNA editing in single mammalian cells | Mellis, I. A., Gupte, R. K., Raj, A., Rouhanifard, S. H. | 10.1101/088146 | 2016-11-16 |
| Software tools for visualizing Hi-C data | Yardimci, G. G., Noble, W. S. | 10.1101/086017 | 2016-11-07 |
| Matheson, T., Kaufman, P. | 10.1101/082339 | 2016-10-21 | |
| FISH-ing for captured contacts: towards reconciling FISH and 3C | Fudenberg, G., Imakaev, M. | 10.1101/081448 | 2016-10-17 |
| Comparative analysis of 2D and 3D distance measurements to study spatial genome organization | Elizabeth Finn, Gianluca Pegoraro, Sigal Shachar, Tom Misteli | 10.1101/076893 | 2016-09-23 |
| Rongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony Schmitt, Bing Ren | 10.1101/074294 | 2016-09-09 | |
| Tsung-Han Hsieh, Geoffrey Fudenberg, Anton Goloborodko, Oliver Rando | 10.1101/071357 | 2016-08-24 | |
| A Dynamic Mode of Mitotic Bookmarking by Transcription Factors | Sheila S Teves, Luye An, Anders S Hansen, Liangqi Xie, Xavier Darzacq, Robert Tjian | 10.1101/066464 | 2016-08-01 |
| Massively multiplex single-cell Hi-C | Vijay Ramani, Xinxian Deng, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure | 10.1101/065052 | 2016-07-23 |
| Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar | 10.1101/054031 | 2016-05-18 | |
| Formation of Chromosomal Domains by Loop Extrusion | Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny | 10.1101/024620 | 2016-03-15 |
| Compaction and segregation of sister chromatids via active loop extrusion | Anton Goloborodko, Maxim V. Imakaev, John F. Marko, Leonid A. Mirny | 10.1101/038281 | 2016-01-30 |
| RTFBSDB: an integrated framework for transcription factor binding site analysis | Zhong Wang, Andre L Martins, Charles G Danko | 10.1101/036053 | 2016-01-06 |