4DN Pre-Prints

Pre-print PublicationsFunded by NIH 4DN program

Pre-prints

TitleAuthorsDOIDate
Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes
Karolina Jodkowska, Zofia Parteka-Tojek, Abhishek Agarwal, Michał Denkiewicz, Sevastianos Korsak, Mateusz Chiliński, Krzysztof Banecki, Dariusz Plewczynski
10.1101/2024.05.16.594268
2024-05-20
Super-enhancer interactomes from single cells link clustering and transcriptionDerek J. Le, Antonina Hafner, Sadhana Gaddam, Kevin C. Wang, Alistair N. Boettiger10.1101/2024.05.08.5932512024-05-10
MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing
Chuanbin Su, Keerthivasan Raanin Chandradoss, Thomas Malachowski, Ravi Boya, Han-Seul Ryu, Kristen J. Brennand, Jennifer E. Phillips-Cremins
10.1101/2024.04.29.591790
2024-05-02
CRISPR Screening Uncovers a Long-Range Enhancer for ONECUT1 in Pancreatic Differentiation and Links a Diabetes Risk Variant
Samuel Joseph Kaplan, Wilfred Wong, Jielin Yan, Julian Pulecio, Hyein S. Cho, Qianzi Li, Jiahui Zhao, Jayanti Leslie-Iyer, Jonathan Kazakov, Dylan Murphy, Renhe Luo, Kushal K. Dey, Effie Apostolou, Christina S. Leslie, Danwei Huangfu
10.1101/2024.04.26.591412
2024-04-29
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
Omid Gholamalamdari, Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang, Gabriela A. Hernandez Gonzalez, Athanasios E. Vouzas, Peiyao A. Zhao, David M. Gilbert, Jian Ma, Bas van Steensel, Andrew S. Belmont
10.1101/2024.04.23.5908092024-04-23
Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organellesAndronov, L.; Han, M.; Zhu, Y.; Balaji, A.; Roy, A. R.; Barentine, A. E. S.; Patel, P.; Garhyan, J.; Qi, L. S.; Moerner, W. E.10.1101/2023.11.07.5661102024-04-01
Daniel, B., Chen, A. Y., Sandor, K., Zhang, W., Miao, Z., Lareau, C. A., Yost, K. E., Chang, H., Satpathy, A.10.1101/2024.02.29.5828722024-03-04
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.
10.1101/2024.02.29.5828132024-02-29
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 dataLi, 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 ChromatinKorsak, S., Plewczynski, D.
10.1101/2024.01.10.574968
2024-01-12
Machine learning reveals the diversity of human 3D chromatin contact patternsGilbertson, 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 differentiationTitus, 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 organellesAndronov, 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 LearningKuang, S., Pollard, K. S.0.1101/2023.10.22.5634982023-10-24
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 ProfilingFoyt, 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 cellsChiariello, 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 CerebellumZhao, 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 statesReffsin, 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 subcompartmentsXiong, K., Zhang, R., Ma, J.
10.1101/2023.05.24.542032
2023-05-25
High-resolution spatial multi-omics reveals cell-type specific nuclear compartmentsTakei, 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 metastasisMcGinnis, 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 insightsGunsalus, 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 organizationWang, 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 microscopyEbrahimi, 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 TherapeuticsFinn, 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 efficiencyBhat, 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 locusChen, 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 transcriptionYang, 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 foldingGunsalus, 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 chromosomesHafner, 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 cellsHasenson, 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 timingYang, 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-HigashiZhang, 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 learningDincer, 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-FISHJia, 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 networksKarbalayghareh, 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 cellsTang, 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 pairsLee, 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 barriersSpracklin, 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 scaleYildirim, 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 infectionWang, 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/dCas9Gao, 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:1910.113702021-04-26
Stripenn detects architectural stripes from chromatin conformation data using computer visionYoon, S., Vahedi, G.
10.1101/2021.04.16.440239
2021-04-18
Quantification of durable CRISPR-based gene silencing activityNakamura, 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 chromatinZhang, 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 HiCARWei, 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 dataYu, 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 HigashiZhang, R., Zhou, T., Ma, J.
10.1101/2020.12.13.422537
2020-12-15
SPICEMIX: Integrative single-cell spatial modeling for inferring cell identityChidester, 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 interactionsZhang, 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 PythonLin, 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 vivoBrandão, 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 leukemiaJanssens, 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 MismatchesDesai, 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 dataMarin, 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 condensatesCourchaine, 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 separationEeftens, 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 DNAZaichuk, 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 dataDemetci, 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 processesMoudgil, 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
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Chen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C.
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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.
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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.
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Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell LinesCheng, R. R., Contessoto, V., Aiden, E. L., Wolynes, P. G., Di Pierro, M., Onuchic, J. N.
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Accurate 4Pi single-molecule localization using an experimental PSF modelLi, Y., Buglakova, E., Zhang, Y., Thevathasan, J. V., Bewersdorf, J., Ries, J.
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EMU: reconfigurable graphical user interfaces for Micro-ManagerDeschamps, J., Ries, J.
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Emert, B., Cote, C., Torre, E. A., Dardani, I. P., Jiang, C., Jain, N., Shaffer, S. M., Raj, A.
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Detecting chromatin interactions along and between sister chromatids with SisterCOomen, M. E., Hedger, A. K., Watts, J. K., Dekker, J.
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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.
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Regulation of gene expression by repression condensates during developmentTreen, N., Shimobayashi, S. F., Eeftens, J., Brangwynne, C. P., Levine, M.
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An Improved 4’-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNAWielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J. T., Lin, H.
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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
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Wang, J., Singh, A., Ozer, A., Zipfel, W. R.
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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.
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CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome ReorganizationFeng, Y., Wang, Y., Yang, C., Naseri, A., Pederson, T., Zheng, J., Xiao, X., Zhang, S., Xie, W., Ma, H.
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Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture MappingWelch, L. R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W. F., Welch, J. D., Pombo, A.
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Exploring the coronavirus epidemic using the new WashU Virus Genome BrowserFlynn, J., Purushotham, D., Choudhary, M. N., Zhuo, X., Fan, C., Matt, G., Li, D., Wang, T.
10.1101/2020.02.07.939124
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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
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GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping dataMarkowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Pombo, A., Schwarz, R. F.
10.1101/2020.01.30.927061
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Probing multi-way chromatin interaction with hypergraph representation learningZhang, R., Ma, J.
10.1101/2020.01.22.916171
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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
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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.
10.1101/3790162019-12-21
Cell cycle dynamics of lamina associated DNAvan Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B.
10.1101/2019.12.19.881979
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Lekschas, F., Peterson, B., Haehn, D., Ma, E., Gehlenborg, N., Pfister, H.10.1101/5975182019-12-12
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.
10.1101/8673412019-12-08
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.
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High-Resolution 3D Fluorescent Imaging of Intact TissuesEl-Nachef, D., Martinson, A. M., Yang, X., Murry, C. E., MacLellan, W. R.10.1101/8552542019-11-26
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.
10.1101/5348002019-11-18
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.
10.1101/6388092019-11-10
Hyper-SAGNN: a self-attention based graph neural network for hypergraphsZhang, R., Zou, Y., Ma, J.-2019-11-06
Biswas, J., Rahman, R., Gupta, V., Rosbash, M., Singer, R.10.1101/8296062019-11-04
TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear specklesZhang, L., Zhang, Y., Chen, Y., Gholamalamdari, O., Ma, J., Belmont, A. S.10.1101/8244332019-10-30
Chromosome disentanglement driven via optimal compaction of loop-extruded brush structuresBrahmachari, S., Marko, J. F.10.1101/6161022019-10-25
Huisman, M., Hammer, M., Rigano, A., Farzam, F., Gopinathan, R., Smith, C., Grunwald, D., Strambio-De-Castillia, C.
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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.
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Chromosome organization by one-sided and two-sided loop extrusionBanigan, E. J., van den Berg, A. A., Brandao, H. B., Marko, J. F., Mirny, L. A.10.1101/8153402019-10-22
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.
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A cost-efficient open source laser engine for microscopySchroeder, D., Deschamps, J., Dasgupta, A., Matti, U., Ries, J.10.1101/7964822019-10-15
Co-opted transposons help perpetuate conserved higher-order chromosomal structuresChoudhary, M. N., Friedman, R. Z., Wang, J. T., Jang, H. S., Zhuo, X., Wang, T.10.1101/4853422019-10-14
Architectural RNA is required for heterochromatin organizationThakur, J., Fang, H., Llagas, T., Disteche, C. M., Henikoff, S.10.1101/7848352019-09-27
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.
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Kordon, M., Zarebski, M., Solarczyk, K., Ma, H., Pederson, T., Dobrucki, J. W.10.1101/7722692019-09-18
Chromatin is frequently unknotted at the megabase scaleGoundaroulis, D., Aiden, E. L., Stasiak, A.10.1101/7628722019-09-09
Zhao, P.A., Sasaki, T., Gilbert, D. M.10.1101/7556292019-09-05
NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded CellsYang, L., Ghosh, R. P., Franklin, J. M., You, C., Liphardt, J.10.1101/7497542019-08-28
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.
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Nucleated transcriptional condensates amplify gene expressionWei, M.-T., Chang, Y.-C., Shimobayashi, S. F., Shin, Y., Brangwynne, C. P.10.1101/7373872019-08-21
A supervised learning framework for chromatin loop detection in genome-wide contact mapsSalameh, T. J., Wang, X., Song, F., Zhang, B., Wright, S. M., Khunsriraksakul, C., Yue, F.10.1101/7396982019-08-20
Distinct features of nucleolus-associated domains in mouse embryonic stem cellsBizhanova, A., Yan, A., Yu, J., Zhu, L. J., Kaufman, P. D.10.1101/7404802019-08-20
Temporal-Spatial Visualization of Endogenous Chromosome Rearrangements in Living CellsWang, H., Nakamura, M., Zhao, D., Nguyen, C. M., Yu, C., Lo, A., Daley, T., La Russa, M., Liu, Y., Qi, L. S.10.1101/7344832019-08-14
Measuring significant changes in chromatin conformation with ACCOSTCook, K. B., Le Roch, K. G., Vert, J.-P., Noble, W.10.1101/7277682019-08-06
Pattern-Driven Navigation in 2D Multiscale Visualizations with Scalable InsetsLekschas, F., Behrisch, M., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H.10.1101/3010362019-07-25
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.
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Zhao, B., Chaturvedi, P., Zimmerman, D. L., Belmont, A. S.10.1101/7080242019-07-23
pyBedGraph: a Python package for fast operations on 1-dimensional genomic signal tracksZhang, H. B., Kim, M., Chuang, J. H., Ruan, Y.10.1101/7096832019-07-20
Schuh, L., Saint-Antoine, M., Sanford, E., Emert, B., Singh, A., Marr, C., Goyal, Y., Raj, A.10.1101/7042472019-07-18
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.
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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.
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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.
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Local rewiring of genome - nuclear lamina interactions by transcription.
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A chromosome folding intermediate at the condensin-to-cohesin transition during telophaseAbramo, K., Valton, A.-L., Venev, S. V., Ozadam, H., Fox, A. N., Dekker, J.10.1101/6784742019-06-21
Multiplex chromatin interaction analysis by signal processing and statistical algorithmsKim, M., Zheng, M., Tian, S. Z., Capurso, D., Lee, B., Chuang, J. H., Ruan, Y.10.1101/6652322019-06-10
Wang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J.10.1101/6570802019-06-03
Marko, J. F., De Los Rios, P., Barducci, A., Gruber, S.10.1101/3253732019-05-23
Inferring diploid 3D chromatin structures from Hi-C dataCauer, A., Yardimci, G. G., Vert, J.-P., Varoquaux, N., Noble, W.10.1101/6442942019-05-21
Jointly embedding multiple single-cell omics measurementsLiu, J., Huang, Y., Singh, R., Vert, J.-P., Noble, W.10.1101/6443102019-05-21
Spring Model - chromatin modeling tool based on OpenMMKadlof, M., Rozycka, J., Plewczynski, D.10.1101/6423222019-05-20
Ultrastructural details of mammalian chromosome architecture
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Resolving the 3D landscape of transcription-linked mammalian chromatin foldingHsieh, T.-H. S., Slobodyanyuk, E., Hansen, A. S., Cattoglio, C., Rando, O. J., Tjian, R., Darzacq, X.10.1101/6387752019-05-17
Improved CUT&RUN chromatin profiling and analysis toolsMeers, M. P., Bryson, T. D., Henikoff, S.10.1101/5691292019-05-16
Concerted localization resets precede YAP-dependent transcriptionFranklin, J. M., Ghosh, R. P., Shi, Q., Liphardt, J. T.10.1101/5390492019-05-06
Spatial genome re-organization between fetal and adult hematopoietic stem cellsChen, C., Yu, W., Tober, J., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G., Speck, N., Tan, K.10.1101/6282142019-05-05
Photoactivation of silicon rhodamines via a light-induced protonation
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Tibanna: software for scalable execution of portable pipelines on the cloudLee, S., Johnson, J., Vitzthum, C., Kırlı, K., Alver, B. H., Park, P. J.10.1101/4409742019-04-29
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.
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FIREcaller: an R package for detecting frequently interacting regions from Hi-C dataCrowley, C., Yang, Y., Qiu, Y., Hu, B., Won, H., Ren, B., Hu, M., Li, Y.10.1101/6192882019-04-29
Mapping RNA-chromatin interactions by sequencing with iMARGI V.2Wu, 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 interactionsTian, S. Z., Capurso, D., Kim, M., Lee, B., Zheng, M., Ruan, Y.10.1101/6130342019-04-18
Multi-scale deep tensor factorization learns a latent representation of the human epigenomeSchreiber, J., Durham, T. J., Bilmes, J., Noble, W. S.10.1101/3649762019-04-11
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.
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RNA polymerases as moving barriers to condensin loop extrusionBrandao, H. B., Wang, X., Paul, P., van den Berg, A., Rudner, D. Z., Mirny, L. A.10.1101/6042802019-04-10
Transcription amplification by nuclear speckle associationKim, J., Khanna, N., Belmont, A. S.10.1101/6042982019-04-09
Common DNA sequence variation influences 3-dimensional conformation of the human genome
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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.
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Nuclear pores as versatile reference standards for quantitative superresolution microscopy
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Ramani, V., Deng, X., Qiu, R., Lee, C., Disteche, C. M., Noble, W. S., Duan, Z., Shendure, J.10.1101/5795732019-03-15
CUT&Tag for efficient epigenomic profiling of small samples and single cells
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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.
10.1101/5604252019-02-27
EpiAlignment: alignment with both DNA sequence and epigenomic dataLu, J., Cao, X., Zhong, S.10.1101/5621992019-02-27
Supervised classification enables rapid annotation of cell atlasesPliner, H. A., Shendure, J., Trapnell, C.10.1101/5386522019-02-25
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.
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Cooler: scalable storage for Hi-C data andother genomically-labeled arraysAbdennur, N., Mirny, L.10.1101/5576602019-02-22
Localization microscopy at doubled precision with patterned illuminationCnossen, J., Hinsdale, T., Thorsen, R., Schueder, F., Jungmann, R., Smith, C. S., Rieger, B., Stallinga, S.10.1101/5543372019-02-20
Comparing 3D genome organization in multiple species using Phylo-HMRFYang, Y., Zhang, Y., Ren, B., Dixon, J., Ma, J.10.1101/5525052019-02-19
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.
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Dynamics of gene expression in single root cells of A. thaliana
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MOCHI enables discovery of heterogeneous interactome modules in 3D nucleomeTian, D., Zhang, R., Zhang, Y., Zhu, X., Ma, J.10.1101/5420922019-02-07
Giusti-Rodriguez, P. M., Sullivan, P. F.10.1101/4063302019-01-30
Schreiber, J., Bilmes, J., Noble, W.10.1101/5332732019-01-29
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.
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Biggs, R., Stephens, A. D., Liu, P., Marko, J. F.10.1101/4235412019-01-04
ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization
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An RNA-binding region regulates CTCF clustering and chromatin loopingHansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Darzacq, X., Tjian, R.10.1101/4954322018-12-16
Guided nuclear exploration increases CTCF target search efficiencyHansen, A. S., Amitai, A., Cattoglio, C., Tjian, R., Darzacq, X.10.1101/4954572018-12-13
Cheng, L.-C., Baboo, S., Lindsay, C., Brusman, L. E., Martinez-Bartolome, S., Tapia, O., Zhang, X., Yates, J. R., Gerace, L.
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Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast HeterochromatinVertii, A., Ou, J., Yu, J., Yan, A., Pages, H., Liu, H., Zhu, L. J., Kaufman, P. D.10.1101/4845682018-12-03
Limits of chromosome compaction by loop-extruding motorsBanigan, E. J., Mirny, L. A.10.1101/4764242018-11-21
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.
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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.
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Li, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., Ren, B.10.1101/4709632018-11-15
Leemans, C., van der Zwalm, M., Brueckner, L., Comoglio, F., van Schaik, T., Pagie, L., van Arensbergen, J., van Steensel, B.
10.1101/4640812018-11-06
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.
10.1101/4502622018-10-26
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.
10.1101/4438872018-10-17
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.
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Khanna, N., Zhang, J., Dudko, O., Murre, C.10.1101/4414442018-10-12
Condensin II inactivation in interphase does not affect chromatin folding or gene expressionAbdennur, N., Schwarzer, W., Pekowska, A., Shaltiel, I. A., Huber, W., Haering, C. H., Mirny, L., Spitz, F.10.1101/4374592018-10-07
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.
10.1101/4234422018-09-21
Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyondNomidis, S. K., Skoruppa, E., Carlon, E., Marko, J. F.10.1101/4226832018-09-20
Sadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D.10.1101/2669812018-09-14
Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Yang, Y., Li, Y., Ren, B., Hu, M.10.1101/4118352018-09-08
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.
10.1101/4076682018-09-04
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.
10.1101/3991392018-08-23
Photon count estimation in single-molecule localization microscopyRieger, B., Stallinga, S., Hulleman, C. N., Thorsen, R. O., Grunwald, D., Hammer, M.10.1101/3964242018-08-20
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.
10.1101/3926622018-08-16
Symmons, O., Chang, M., Mellis, I., Kalish, J. M., Bartolomei, M. S., Raj, A.10.1101/3863592018-08-07
A combination of transcription factors mediates inducible interchromosomal pairingKim, S., Dunham, M., Shendure, J.10.1101/3850472018-08-05
Marko, J., Biggs, R., Sun, M., Hornick, J.10.1101/3849822018-08-04
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.
10.1101/3750712018-07-30
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.
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Mir, M., Stadler, M. R., Ortiz, S. A., Harrison, M. M., Darzacq, X., Eisen, M. B.10.1101/3778122018-07-26
Receptor-ligand rebinding kinetics in confinementErbas, A., Olvera de la Cruz, M., Marko, J.10.1101/3703952018-07-16
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architectureSchreiber, J., Libbrecht, M., Bilmes, J., Noble, W.10.1101/1036142018-07-15
CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioningOomen, M. E., Hansen, A., Liu, Y., Darzacq, X., Dekker, J.10.1101/3658662018-07-11
LADL: Light-activated dynamic looping for endogenous gene expression controlRege, M., Kim, J. H., Valeri, J., Dunagin, M., Metzger, A., Gong, W., Beagan, J., Raj, A., Phillips-Cremins, J. E.10.1101/3493402018-06-18
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.
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Kim, J., Han, K. Y., Khanna, N., Ha, T., Belmont, A. S.10.1101/3479552018-06-15
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.
10.1101/3163722018-06-15
Yin, Y., Jiang, Y., Berletch, J. B., Disteche, C. M., Noble, W. S., Steemers, F. J., Adey, A. C., Shendure, J. A.10.1101/3380532018-06-12
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.
10.1101/1218892018-06-04
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.
10.1101/3252092018-05-17
Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G., Cattoglio, C., Banala, S., Lavis, L., Darzacq, X., Tjian, R.
10.1101/2087102018-05-16
GITAR: an Open Source Tool for Analysis and Visualization of Hi-C DataCalandrelli, R., Wu, Q., Guan, J., Zhong, S.10.1101/2595152018-05-08
Exponential fluorescent amplification of individual RNAs using clampFISH probesRouhanifard, S. H., Mellis, I. A., Dunagin, M., Bayatpour, S., Symmons, O., Cote, A., Raj, A.10.1101/2227942018-05-07
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.
10.1101/3078922018-04-25
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.
10.1101/3053592018-04-23
Quantitative imaging of chromatin decompaction in living cellsDultz, E., Mancini, R., Polles, G., Vallotton, P., Alber, F., Weis, K.10.1101/2192532018-04-22
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.
10.1101/1746492018-04-20
RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genomeChen, W., Yan, Z., Li, S., Huang, N., Huang, X., Zhang, J., Zhong, S.10.1101/3004832018-04-12
An inter-chromosomal transcription hub activates the unfolded protein response in plasma cellsBortnick, A., He, Z., Aubrey, M., Chandra, V., Denholtz, M., Chen, K., Lin, Y. C., Murre, C.10.1101/2959152018-04-07
Walther, N., Hossain, M. J., Politi, A. Z., Koch, B., Kueblbeck, M., Oedegaard-Fougner, O., Lampe, M., Ellenberg, J.
10.1101/2378342018-03-22
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.
10.1101/2856502018-03-21
Bracha, D., Walls, M. T., Wei, M.-T., Zhu, L., Kurian, M., Toettcher, J. E., Brangwynne, C. P.10.1101/2836552018-03-16
Continuous-trait probabilistic model for comparing multi-species functional genomic dataYang, Y., Gu, Q., Zhang, Y., Sasaki, T., Crivello, J., O'Neill, R. J., Gilbert, D. M., Ma, J.10.1101/2830932018-03-16
GIVE: toward portable genome browsers for personal websitesCao, X., Yan, Z., Wu, Q., Zheng, A., Zhong, S.10.1101/1778322018-03-15
SAVER: Gene expression recovery for UMI-based single cell RNA sequencingHuang, M., Wang, J., Torre, E., Dueck, H., Shaffer, S., Bonasio, R., Murray, J., Raj, A., Li, M., Zhang, N. R.10.1101/1386772018-03-08
Bartman, C. R., Keller, C. A., Giardine, B., Hardison, R. C., Blobel, G. A., Raj, A.10.1101/2753542018-03-02
Barton, C., Morganella, S., Oedegaard, O., Alexander, S., Ries, J., Fitzgerald, T., Ellenberg, J., Birney, E.10.1101/1154362018-02-22
Emerging Evidence of Chromosome Folding by Loop ExtrusionFudenberg, G., Abdennur, N., Imakaev, M., Goloborodko, A., Mirny, L.10.1101/2646482018-02-16
Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural NetworksSingh, S., Yang, Y., Poczos, B., Ma, J.10.1101/0852412018-02-05
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.
10.1101/1887552018-02-05
Defect-Facilitated Buckling in Supercoiled Double-Helix DNABrahmachari, S., Dittmore, A., Takagi, Y., Neuman, K. C., Marko, J. F.10.1101/2596892018-02-04
Predicting CTCF-mediated chromatin loops using CTCF-MPZhang, R., Wang, Y., Yang, Y., Zhang, Y., Ma, J.10.1101/2594162018-02-02
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.
10.1101/1718192018-01-31
Bend-Induced Twist Waves and the Structure of Nucleosomal DNASkoruppa, E., Nomidis, S. K., Marko, J. F., Carlon, E.10.1101/2568182018-01-30
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.
10.1101/2547972018-01-28
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.
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Correlative live and super-resolution imaging reveals the dynamic structure of replication domainsXiang, W., Roberti, M. J., Heriche, J.-K., Huet, S., Alexander, S., Ellenberg, J.10.1101/1893732018-01-24
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.
10.1101/2440382018-01-09
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
10.1101/2407472017-12-29
Chromatin interaction data visualization in the WashU Epigenome BrowserLi, D., Hsu, S., Purushotham, D., Wang, T.10.1101/2393682017-12-24
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.
10.1101/1653402017-12-15
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.
10.1101/2217622017-11-21
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.
10.1101/2228772017-11-21
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.
10.1101/2196832017-11-18
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.
10.1101/2187682017-11-13
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.
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Removing unwanted variation between samples in Hi-C experimentsFletez-Brant, K., Qiu, Y., Gorkin, D. U., Hu, M., Hansen, K. D.10.1101/2143612017-11-06
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.
10.1101/2063672017-10-29
Spot-On: robust model-based analysis of single-particle tracking experimentsHansen, A. S., Woringer, M., Grimm, J. B., Lavis, L. D., Tjian, R., Darzacq, X.10.1101/1719832017-10-26
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.
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Juicebox.js provides a cloud-based visualization system for Hi-C dataRobinson, J., Turner, D., Durand, N. C., Thorvaldsdottir, H., Mesirov, J. P., Aiden, E. L.10.1101/2057402017-10-19
Hulleman, C., Huisman, M., Moerland, R., Grunwald, D., Stallinga, S., Rieger, B.10.1101/2047762017-10-17
Chromatin Organization by an Interplay of Loop Extrusion and Compartmental SegregationNuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N., Mirny, L.10.1101/1962612017-10-03
Mechanics and buckling of biopolymeric shells and cell nucleiBanigan, E. J., Stephens, A. D., Marko, J. F.10.1101/1975662017-10-02
Nucleation of multiple buckled structures in intertwined DNA double helicesBrahmachari, S., Gunn, K. H., Giuntoli, R. D., Mondragon, A., Marko, J. F.10.1101/1963452017-09-30
CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome DynamicsMa, H., Tu, L.-C., Naseri, A., Chung, Y.-C., Grunwald, D., Zhang, S., Pederson, T.10.1101/1959662017-09-29
Genetic drivers of repeat expansion disorders localize to 3-D chromatin domain boundariesSun, J., Zhou, L., Emerson, D. J., Gilgenast, T. G., Titus, K., Beagan, J. A., Phillips-Cremins, J. E.10.1101/1912132017-09-20
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.
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SHAMAN: bin-free randomization, normalization and screening of Hi-C matricesCohen, N. M., Olivares-Chauvet, P., Lubling, Y., Baran, Y., Lifshitz, A., Hoichman, M., Tanay, A.10.1101/1872032017-09-12
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.
10.1101/1848462017-09-05
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.
10.1101/1777662017-08-17
3D Single-Molecule Super-Resolution Microscopy With A Tilted Light SheetGustavsson, A.-K., Petrov, P. N., Lee, M. Y., Shechtman, Y., Moerner, W. E.10.1101/1356992017-08-14
Fast, robust and precise 3D localization for arbitrary point spread functionsLi, Y., Mund, M., Hoess, P., Matti, U., Nijmeijer, B., Jimenez Sabinina, V., Ellenberg, J., Schoen, I., Ries, J.10.1101/1726432017-08-10
Yang, T., Zhang, F., Yardimci, G. G., Song, F., Hardison, R. C., Noble, W. S., Yue, F., Li, Q.10.1101/1013862017-08-04
Heterogeneity and Intrinsic Variation in Spatial Genome OrganizationFinn, E., Pegoraro, G., Brandao, H. B., Valton, A.-L., Oomen, M. E., Dekker, J., Mirny, L., Misteli, T.10.1101/1718012017-08-03
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.
10.1101/0832122017-07-16
Dileep, V., Gilbert, D. M.10.1101/1583522017-07-14
Tasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., Wang, Y., Genova, J., Ma, J., Belmont, A. S., Zhao, H.
10.1101/1621562017-07-12
HiPiler: Visual Exploration Of Large Genome Interaction Matrices With Interactive Small MultiplesLekschas, F., Bach, B., Kerpedjiev, P., Gehlenborg, N., Pfister, H.10.1101/1235882017-07-09
A Fluorogenic Array Tag for Temporally Unlimited Single Molecule TrackingGhosh, R. P., Franklin, M. J., Draper, W. E., Shi, Q., Liphardt, J. T.10.1101/1590042017-07-03
Noma, A., Smith, C. S., Huisman, M., Martin, R. M., Moore, M. J., Grunwald, D.10.1101/1560912017-06-26
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.
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Kaewsapsak, P., Shechner, D. M., Mallard, W., Rinn, J. L., Ting, A. Y.10.1101/1530982017-06-21
Dense Bicoid Hubs Accentuate Binding along the Morphogen GradientMir, M., Reimer, A., Haines, J. E., Li, X.-Y., Stadler, M., Garcia, H., Eisen, M. B., Darzacq, X.10.1101/1331242017-06-08
qSR: A software for quantitative analysis of single molecule and super-resolution dataAndrews, J. O., Narayanan, A., Spille, J.-H., Cho, W.-K., Thaler, J. D., Cisse, I. I.10.1101/1462412017-06-05
Tu, L.-C., Huisman, M., Chung, Y.-C., Smith, C., Grunwald, D.10.1101/1451102017-06-02
Li, H., Kalhor, R., Li, B., Su, T., Berk, A., Kurdistani, S., Alber, F., Chen, L.10.1101/1426042017-05-26
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.
10.1101/1420262017-05-25
Torre, E. A., Dueck, H., Shaffer, S., Gospocic, J., Gupte, R., Bonasio, R., Kim, J., Murray, J., Raj, A.10.1101/1382892017-05-18
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.
10.1101/1397822017-05-18
Torque and buckling in stretched intertwined double-helix DNAsMarko, J., Brahmachari, S.10.1101/1359052017-05-09
Facilitated Dissociation Of Transcription Factors From Single DNA Binding SitesKamar, R. I., Banigan, E. J., Erbas, A., Giuntoli, R. D., Olvera de la Cruz, M., Johnson, R. C., Marko, J. F.10.1101/1359472017-05-09
Sun, X., Bizhanova, A., Matheson, T. D., Yu, J., Zhu, L. J., Kaufman, P. D.10.1101/1347672017-05-08
Supercoiling DNA locates mismatchesDittmore, A., Brahmachari, S., Takagi, Y., Marko, J. F., Neuman, K. C.10.1101/1305672017-04-25
Nuclear Microenvironments Modulate Transcription From Low-Affinity EnhancersCrocker, J., Tsai, A., Muthusamy, A. K., Lavis, L. D., Singer, R. H., Stern, D. L.10.1101/1282802017-04-18
Woringer, M., Darzacq, X., Zimmer, C., Mir, M.10.1101/1258152017-04-10
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.
10.1101/1196512017-03-28
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.
10.1101/1187372017-03-20
HUGIn: Hi-C Unifying Genomic InterrogatorMartin, J. S., Xu, Z., Reiner, A. P., Mohlke, K. L., Sullivan, P., Ren, B., Hu, M., Li, Y.10.1101/1175312017-03-16
Dawson, W., Plewczynski, D.10.1101/1056762017-03-08
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.
10.1101/1046532017-03-01
HiCPlus: Resolution Enhancement of Hi-C interaction heatmapZhang, Y., An, L., Hu, M., Tang, J., Yue, F.10.1101/1126312017-03-01
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.
10.1101/1122682017-02-27
A fluorogenic nanobody array tag for prolonged single molecule imaging in live cellsGhosh, R., Draper, W., Franklin, J. M., Shi, Q., Liphardt, J.10.1101/1116902017-02-27
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.
10.1101/0830142017-02-24
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.
10.1101/1111792017-02-23
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.
10.1101/1102392017-02-21
Reversed graph embedding resolves complex single-cell developmental trajectoriesQiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H., Trapnell, C.10.1101/1106682017-02-21
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.
10.1101/1048442017-02-02
Direct visualization of transcriptional activation by physical enhancer-promoter proximityChen, H., Fujioka, M., Jaynes, J. B., Gregor, T.10.1101/0995232017-01-31
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
10.1101/1034992017-01-26
PGS: a dynamic and automated population-based genome structure softwareHua, N., Tjong, H., Shin, H., Gong, K., Zhou, X. J., Alber, F.10.1101/1033582017-01-26
Takei, Y., Shah, S., Harvey, S., Qi, L. S., Cai, L.10.1101/1014772017-01-18
The 3D genome organization of Drosophila melanogaster through data integrationLi, Q., Tjong, H., Li, X., Gong, K., Zhou, X. J., Chiolo, I., Alber, F.10.1101/0999112017-01-15
Comprehensive characterization of neutrophil genome topologyZhu, Y., Gong, K., Denholtz, M., Chandra, V., Kamps, M. P., Alber, F., Murre, C.10.1101/1001982017-01-15
Eagen, K. P., Lieberman Aiden, E., Kornberg, R. D.10.1101/0998042017-01-12
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L., Bruneau, B.
10.1101/0958022017-01-09
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.
10.1101/0949462016-12-17
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.
10.1101/0941852016-12-15
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.
10.1101/0944662016-12-15
CTCF and Cohesin Regulate Chromatin Loop Stability with Distinct DynamicsHansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., Darzacq, X.10.1101/0934762016-12-13
The dynamic three-dimensional organization of the diploid yeast genomeKim, S., Liachko, I., Brickner, D. G., Cook, K., Noble, W. S., Brickner, J. H., Shendure, J., Dunham, M.10.1101/0918272016-12-05
Belaghzal, H., Dekker, J., Gibcus, J. H.10.1101/0900012016-11-27
Detecting hierarchical 3-D genome domain reconfiguration with network modularityNorton, H. K., Huang, H., Emerson, D. J., Kim, J., Gu, S., Bassett, D. S., Phillips-Cremins, J. E.10.1101/0890112016-11-22
Calibrating photon counts from a single imageHeintzmann, 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 cellsMellis, I. A., Gupte, R. K., Raj, A., Rouhanifard, S. H.10.1101/0881462016-11-16
Software tools for visualizing Hi-C dataYardimci, G. G., Noble, W. S.10.1101/0860172016-11-07
Matheson, T., Kaufman, P.10.1101/0823392016-10-21
FISH-ing for captured contacts: towards reconciling FISH and 3CFudenberg, G., Imakaev, M.10.1101/0814482016-10-17
Comparative analysis of 2D and 3D distance measurements to study spatial genome organizationElizabeth Finn, Gianluca Pegoraro, Sigal Shachar, Tom Misteli10.1101/0768932016-09-23
Rongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony Schmitt, Bing Ren10.1101/0742942016-09-09
Tsung-Han Hsieh, Geoffrey Fudenberg, Anton Goloborodko, Oliver Rando10.1101/0713572016-08-24
A Dynamic Mode of Mitotic Bookmarking by Transcription FactorsSheila S Teves, Luye An, Anders S Hansen, Liangqi Xie, Xavier Darzacq, Robert Tjian10.1101/0664642016-08-01
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
10.1101/0650522016-07-23
Amit Blumberg, Edward J. Rice, Anshul Kundaje, Charles G. Danko, Dan Mishmar10.1101/0540312016-05-18
Formation of Chromosomal Domains by Loop ExtrusionGeoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, Anton Goloborodko, Nezar Abdennur, Leonid A Mirny10.1101/0246202016-03-15
Compaction and segregation of sister chromatids via active loop extrusionAnton Goloborodko, Maxim V. Imakaev, John F. Marko, Leonid A. Mirny10.1101/0382812016-01-30
RTFBSDB: an integrated framework for transcription factor binding site analysisZhong Wang, Andre L Martins, Charles G Danko10.1101/0360532016-01-06

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