4DN Pre-Prints

Pre-print PublicationsFunded by NIH 4DN program


Identification of a self-renewing muscle satellite cell state by single-cell chromatin accessibility profilingOkafor, A. E., Lin, X., Situ, C., Wei, X., Wei, X., Wu, Z., Diao, Y.10.1101/2022.09.16.5083392022-09-17
Sun, T., Xu, Y., Xiang, Y., Soderblom, E. J., Diao, Y.10.1101/2022.09.08.5071722022-09-12
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.
In silico discovery of repetitive elements as key sequence determinants of 3D genome foldingGunsalus, L. M., Keiser, M. J., Pollard, K. S.10.1101/2022.08.11.5034102022-08-12
Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal GutBara, A. M., Chen, L., Ma, C., Underwood, J., Moreci, R. S., Sumigray, K., Sun, T., Diao, Y., Verzi, M., Lechler, T.10.1101/2022.07.26.5016242022-07-28
Beyond TADs: microscopy reveals 2 axes of chromosome organization by CTCF and cohesinHafner, A., Park, M., Berger, S. E., Nora, E., Boettiger, A. N.10.1101/2022.07.13.4999822022-
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.10.1101/2022.06.28.4980432022-0
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.
Nucleoli and the nucleoli-centromere association are dynamic during normal development and in cancer
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.
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.10.1101/2022.05.11.4914512022-05-11
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.
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.
CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timingYang, Y., Wang, Y., Zhang, Y., Ma, J.10.1101/2022.04.21.4886842022-04-22
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.
Ultrafast and interpretable single-cell 3D genome analysis with Fast-HigashiZhang, R., Zhou, T., Ma, J.10.1101/2022.04.18.4886832022-04-19
NIPBL and WAPL balance cohesin activity to regulate chromatin folding and gene expressionLuppino, J. M., Field, A., Nguyen, S. C., Park, D. S., Shah, P. P., Lan, Y., Yunker, R., Jain, R., Adelman, K., Joyce, E. F.10.1101/2022.04.19.4887852022-04-19
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation
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.
Reducing peptide sequence bias in quantitative mass spectrometry data with machine learningDincer, A. B., Lu, Y., Schweppe, D., Oh, S., Noble, W. S.10.1101/2022.04.11.4879452022-04-12
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.
A spatial genome aligner for multiplexed DNA-FISHJia, B. B., Jussila, A. P., Kern, J. C., Zhu, Q., Ren, B.10.1101/2022.03.25.4858452022-03-27
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.
Cas9-Mediated Knockout of Ndrg2 Enhances the Regenerative Potential of Dendritic Cells for Wound Healing
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.
Quantitative fate mapping: Reconstructing progenitor field dynamics via retrospective lineage barcodingFang, W., Bell, C. M., Sapirstein, A., Asami, S., Leeper, K., Zack, D. J., Ji, H., Kalhor, R.10.1101/2022.02.13.4802152022-02-14
Widespread contribution of transposable elements to the rewiring of mammalian 3D genomes and gene regulationChoudhary, M. N., Quaid, K., Xing, X., Schmidt, H., Wang, T.10.1101/2022.02.01.4752392022-02-03
Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome BrowserLi, D., Purushotham, D., Harrison, J. K., Wang, T.10.1101/2022.01.18.4768492022-01-21
Zou, R. S., Marin-Gonzalez, A., Liu, Y., Liu, H. B., Shen, L., Dveirin, R., Luo, J. X. J., Kalhor, R., Ha, T.10.1101/2022.01.18.4768362022-01-20
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.
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.
Single-fiber nucleosome density shapes the regulatory output of a mammalian chromatin remodeling enzyme
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.
Chromatin interaction aware gene regulatory modeling with graph attention networksKarbalayghareh, A., Sahin, M., Leslie, C. S.10.1101/2021.03.31.4379782021-12-10
CRISPR Cas13-based tools to track and manipulate endogenous telomeric repeat-containing RNAs in living cellsXu, M., Chigumira, T., Chen, Z., Tones, J., Zhao, R., Dahl, K. N., Chenoweth, D. M., Zhang, H.10.1101/2021.12.03.4711092021-12-04
Boe, R. H., Ayyappan, V., Schuh, L., Raj, A.10.1101/2021.11.26.4701342021-11-26
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.
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin foldingConte, M., Irani, E., Chiariello, A. M., Abraham, A., Bianco, S., Esposito, A., Nicodemi, M.10.1101/2021.11.02.4665892021-11-02
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.
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.10.1101/2021.10.21.4653512021-10-23
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.
Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulationSingh, A. P., Wu, P., Ryabichko, S., Raimundo, J., Swan, M., Wieschaus, E., Gregor, T., Toettcher, J. E.10.1101/2021.10.13.4642802021-10-14
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.
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.
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.10.1101/2021.08.24.4575522021-08-26
Liu, Y., Dekker, J.10.1101/2021.08.24.4575552021-08-26
BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen
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.
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.
Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriersSpracklin, G., Abdennur, N. A., Imakaev, M., Chowdhury, N., Pradhan, S., Mirny, L., Dekker, J.10.1101/2021.08.05.4553402021-08-06
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.
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.10.1101/2021.07.11.4519762021-07-12
Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state
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.
Sharma, A., Akshay, A., Rogne, M., Eskeland, R.10.1101/2021.06.21.4493162021-06-22
Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells
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.
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.10.1101/2021.06.09.4477602021-06-09
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.
Interrogation of the Dynamic Properties of Higher-Order Heterochromatin Using CRISPR/dCas9Gao, Y., Han, M., Shang, S., Wang, H., Qi, L. S.10.1101/2021.06.06.4473002021-06-07
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.
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.
Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architectureTakei, Y., Zheng, S., Yun, J., Shah, S., Pierson, N., White, J., Schindler, S., Tischbirek, C., Yuan, G.-C., Cai, L.10.1101/2021.04.26.4415472021-04-27
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..
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
Stripenn detects architectural stripes from chromatin conformation data using computer visionYoon, S., Vahedi, G.10.1101/2021.04.16.4402392021-04-18
Quantification of durable CRISPR-based gene silencing activityNakamura, M., Ivec, A., Gao, Y., Qi, L. S.10.1101/2021.03.31.4363552021-03-31
Esposito, A., Bianco, S., Chiariello, A. M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R., Nicodemi, M.10.1101/2021.03.01.4334162021-03-01
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.
Genome-wide variability in recombination activity is associated with meiotic chromatin organizationJin, X., Fudenberg, G., Pollard, K. S.10.1101/2021.01.06.4255992021-01-07
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.
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.
Mechanical frustration of phase separation in the cell nucleus by chromatinZhang, Y., Lee, D. S. W., Meir, Y., Brangwynne, C. P., Wingreen, N. S.10.1101/2020.12.24.4242222020-12-24
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.10.1101/2020.11.02.3660622020-12-19
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.10.1101/2020.12.18.4235512020-12-18
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.10.1101/2020.12.13.4225432020-12-15
Multiscale and integrative single-cell Hi-C analysis with HigashiZhang, R., Zhou, T., Ma, J.10.1101/2020.12.13.4225372020-12-15
SPICEMIX: Integrative single-cell spatial modeling for inferring cell identityChidester, B., Zhou, T., Ma, J.10.1101/2020.11.29.3830672020-11-30
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.
DANGO: Predicting higher-order genetic interactionsZhang, R., Ma, J., Ma, J.10.1101/2020.11.26.4007392020-11-27
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent CellsSwygert, S. G., Lin, D., Portillo-Ledesma, S., Lin, P.-Y., Hunt, D. R., Kao, C.-F., Schlick, T., Noble, W. S., Tsukiyama, T.10.1101/2020.11.24.3967132020-11-24
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.
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.
HiC-ACT: Improved Detection of Chromatin Interactions from Hi-C Data via Aggregated Cauchy TestLagler, T. M., Yang, Y., Abnousi, A., Hu, M., Li, Y.10.1101/2020.10.28.3598692020-10-29
HiCRep.py: Fast comparison of Hi-C contact matrices in PythonLin, D., Sanders, J., Noble, W. S.10.1101/2020.10.27.3577562020-10-28
DNA-loop extruding SMC complexes can traverse one another in vivoBrandão, H. B., Ren, Z., Karaboja, X., Mirny, L. A., Wang, X.10.1101/2020.10.26.3563292020-10-27
Deep learning enables fast and dense single-molecule localization with high accuracySpeiser, A., Müller, L.-R., Matti, U., Obara, C. J., Legant, W. R., Kreshuk, A., Macke, J. H., Ries, J., Turaga, S. C.10.1101/2020.10.26.3551642020-10-26
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.
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.
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.10.1101/2020.10.06.3289482020-10-08
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.10.1101/2019.12.20.8855332020-10-04
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.10.1101/2020.09.29.3156712020-09-30
DMA-tudor interaction modules control the specificity of in vivo condensatesCourchaine, E. M., Barentine, A. E. S., Straube, K., Bewersdorf, J., Neugebauer, K. M.10.1101/2020.09.15.2979942020-09-16
Marko, J. F., Qiao, H., Liu, N., Biggs, R. J., Peng, Y.10.1101/2020.08.31.2764022020-09-01
Bashkirova, E., Monahan, K., Campbell, C. E., Osinski, J. M., Tan, L., Schieren, I., Barnea, G., Xie, S., Gronostajski, R. M., Lomvardas, S.
A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates
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.
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.
Epigenetic memory as a time integral over prior history of Polycomb phase separationEeftens, J. M., Kapoor, M., Brangwynne, C. P.10.1101/2020.08.19.2547062020-08-19
Arrastia, M. V., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S., Selck, D. A., Guttman, M., Ismagilov, R. F.
Transcript assembly improves expression quantification of transposable elements in single cell RNA-seq dataShao, W., Wang, T.10.1101/2020.07.31.2310272020-07-31
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C
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.
Single-Molecule Micromanipulation Studies Of Methylated DNAZaichuk, T., Marko, J.10.1101/2020.07.29.2271992020-07-30
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.
Feng, Y., Wang, Y., Wang, X., He, X., Yang, C., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., Xie, W., Ma, H.10.1101/2020.07.15.2047192020-07-16
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.
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.
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.
Chromatin Mechanics Dictates Subdiffusion and Coarsening Dynamics of Embedded CondensatesLee, D. S. W., Wingreen, N. S., Brangwynne, C. P.10.1101/2020.06.03.1285612020-06-04
Gene regulation gravitates towards either addition or multiplication when combining the effects of two signalsSanford, E. M., Emert, B. L., Cote, A., Raj, A.10.1101/2020.05.26.1169622020-05-27
Chromatin folding variability across single-cells results from state degeneracy in phase-separationConte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., Nicodemi, M.10.1101/2020.05.16.0992752020-05-16
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.
Gromov-Wasserstein optimal transport to align single-cell multi-omics dataDemetci, P., Santorella, R., Sandstede, B., Noble, W. S., Singh, R.10.1101/2020.04.28.0667872020-04-29
The qBED track: a novel genome browser visualization for point processesMoudgil, A., Li, D., Hsu, S., Purushotham, D., Wang, T., Mitra, R. D.10.1101/2020.04.27.0600612020-04-29
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C dataJain, D., Chu, C., Alver, B. H., Lee, S., Lee, E. A., Park, P. J.10.1101/2020.04.27.0601452020-04-28
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.
Chen, Z., Shaw, A., Wilson, H., Woringer, M., Darzacq, X., Marqusee, S., Wang, Q., Bustamante, C.10.1101/2020.04.10.0364422020-04-11
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.
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.
Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell LinesCheng, R. R., Contessoto, V., Aiden, E. L., Wolynes, P. G., Di Pierro, M., Onuchic, J. N.10.1101/2020.03.21.0019172020-03-22
Accurate 4Pi single-molecule localization using an experimental PSF modelLi, Y., Buglakova, E., Zhang, Y., Thevathasan, J. V., Bewersdorf, J., Ries, J.10.1101/2020.03.18.9971632020-03-19
EMU: reconfigurable graphical user interfaces for Micro-ManagerDeschamps, J., Ries, J.10.1101/2020.03.18.9974942020-03-19
Emert, B., Cote, C., Torre, E. A., Dardani, I. P., Jiang, C., Jain, N., Shaffer, S. M., Raj, A.10.1101/2020.03.18.9966602020-03-19
Detecting chromatin interactions along and between sister chromatids with SisterCOomen, M. E., Hedger, A. K., Watts, J. K., Dekker, J.10.1101/2020.03.10.9862082020-03-11
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.
Chromatin Topology Reorganization and Transcription Repression by PML/RARα in Acute Promyeloid LeukemiaRuan, Y.10.1101/2020.03.05.9790702020-03-06
Regulation of gene expression by repression condensates during developmentTreen, N., Shimobayashi, S. F., Eeftens, J., Brangwynne, C. P., Levine, M.10.1101/2020.03.03.9756802020-03-04
An Improved 4’-Aminomethyltroxsalen-Based DNA Crosslinker for Biotinylation of DNAWielenberg, K., Wang, M., Yang, M., Ozer, A., Lis, J. T., Lin, H.10.1101/2020.02.29.9713172020-02-29
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.
Fluorophore-labelled RNA aptamers to common protein tags as super-resolution imaging reagents.Wang, J., Singh, A., Ozer, A., Zipfel, W. R.10.1101/2020.02.27.9685782020-02-28
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.
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.10.1101/2020.02.18.9546102020-02-19
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.10.1101/2020.02.10.9410472020-02-13
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.10.1101/2020.02.07.9391242020-02-11
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.
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.10.1101/2020.01.30.9270612020-01-31
Probing multi-way chromatin interaction with hypergraph representation learningZhang, R., Ma, J.10.1101/2020.01.22.9161712020-01-23
Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleusMa, J., Do, M., Le Gros, M. A., Peskin, C. S., Larabell, C. A., Mori, Y., Isaacson, S. A.10.1101/2020.01.16.9093332020-01-17
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.
Cell cycle dynamics of lamina associated DNAvan Schaik, T., Vos, M., Peric-Hupkes, D., van Steensel, B.10.1101/2019.12.19.8819792019-12-19
Peax: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation LearningLekschas, 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.
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.
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
Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data
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.
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.
Hyper-SAGNN: a self-attention based graph neural network for hypergraphsZhang, R., Zou, Y., Ma, J.-2019-11-06
MS2-TRIBE evaluates protein-RNA interactions and nuclear organization of transcription by RNA editingBiswas, 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.-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.
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.
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
ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL
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.
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 hubsKenworthy, C. A., Liou, S.-H., Chandris, P., Wong, V., Dziuba, P., Lavis, L. D., Liu, W.-L., Singer, R. H., Coleman, R. A.10.1101/1116742019-08-22
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 dysfunctionCalandrelli, R., Xu, L., Luo, Y., Wu, W., Fan, X., Nguyen, T., Chen, C., Sriram, K., Natarajan, R., Chen, Z., Zhong, S.10.1101/7129502019-07-24
Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGICZhao, 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
Gene networks with transcriptional bursting recapitulate rare transient coordinated expression states in cancerSchuh, 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-CBelaghzal, H., Borrman, T., Stephens, A. D., Lafontaine, D. L., Venev, S. V., Marko, J. F., Weng, Z., Dekker, J.10.1101/7049572019-07-16
Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome
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.
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.
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.10.1101/6852552019-06-27
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
HiNT: a computational method for detecting copy number variations and translocations from Hi-C dataWang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J.10.1101/6570802019-06-03
DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexesMarko, 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
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.
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
Frei, M. S., Hoess, P., Lampe, M., Nijmeijer, B., Kueblbeck, M., Ellenberg, J., Ries, J., Pitsch, S., Reymond, L., Johnsson, K.
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 cellsRuan, Y., Plewczynski, D., Zhu, J. J., Parteka, Z., Lee, B., Szalaj, P., Wang, P., Jodkowska, K., Arron, J., Chew, T. L.10.1101/6219202019-04-29
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.
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
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.
Direct visualization of single nuclear pore complex proteins using genetically-encoded probes for DNA-PAINT
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.
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.
Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cellsRamani, 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 cellsKaya-Okur, H. S., Wu, S. J., Codomo, C. A., Pledger, E. S., Bryson, T. D., Henikoff, J. G., Ahmad, K., Henikoff, S.10.1101/5689152019-03-06
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.
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.
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.
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.
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
Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development
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.
Effects of altering histone post-translational modifications on mitotic chromosome structure and mechanicsBiggs, 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
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.
Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactionsXiong, K., Ma, J.10.1101/5055032018-12-23
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.
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.
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.
Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cellsLi, G., Liu, Y., Zhang, Y., Fang, R., Kellis, M., Ren, B.10.1101/4709632018-11-15
Promoter-intrinsic and local chromatin features determine gene repression in lamina-associated domains
Leemans, C., van der Zwalm, M., Brueckner, L., Comoglio, F., van Schaik, T., Pagie, L., van Arensbergen, J., van Steensel, B.
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.
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.
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
Physicochemical mechanotransduction alters nuclear shape and mechanics via heterochromatin formation
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.
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
Spatial Chromatin Architecture Alteration by Structural Variations in Human Genomes at Population ScaleSadowski, M., Kraft, A., Szalaj, P., Wlasnowolski, M., Tang, Z., Ruan, Y., Plewczynski, D.10.1101/2669812018-09-14
MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experimentsJuric, 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.
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.
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.
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional burstingSymmons, 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
Condensin controls mitotic chromosome stiffness and stability without forming a structurally contiguous scaffoldMarko, 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.
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
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.
Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryosMir, 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.
Nuclear speckle fusion via long-range directional motion regulates the number and size of specklesKim, 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.
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.
Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organizationKim, 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
Dynamic and Selective Low-Complexity Domain Interactions Revealed by Live-Cell Single-Molecule ImagingChong, 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.
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.
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.
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
A quantitative map of human Condensins provides new insights into mitotic chromosome architectureWalther, 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.
Mapping local and global liquid-liquid phase behavior in living cells using light-activated multivalent seedsBracha, 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
Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulationBartman, C. R., Keller, C. A., Giardine, B., Hardison, R. C., Blobel, G. A., Raj, A.10.1101/2753542018-03-02
ChromoTrace: Reconstruction of 3D Chromosome Configurations by Super-Resolution MicroscopyBarton, 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.
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.
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.
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.
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.
Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control
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
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.
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.
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.
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.
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.
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.
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 laminsStephens, 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
Locus-Specific Enhancer Hubs And Architectural Loop Collisions Uncovered From Single Allele DNA Topologies
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.
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
Fluorescence polarization control for on-off switching of single molecules at cryogenic temperaturesHulleman, 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.
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
Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
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.
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.
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
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficientYang, 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.
Single-cell replication profiling reveals stochastic regulation of the mammalian replication-timing program.Dileep, V., Gilbert, D. M.10.1101/1583522017-07-14
CRISPR/Cas9-mediated Knock-in of an Optimized TetO Repeat for Live Cell Imaging of Endogenous Loci
Tasan, I., Sustackova, G., Zhang, L., Kim, J., Sivaguru, M., HamediRad, M., Wang, Y., Genova, J., Ma, J., Belmont, A. S., Zhao, H.
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
Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPsNoma, 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.
Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinkingKaewsapsak, 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
Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It?Tu, L.-C., Huisman, M., Chung, Y.-C., Smith, C., Grunwald, D.10.1101/1451102017-06-02
Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation CaptureLi, H., Kalhor, R., Li, B., Su, T., Berk, A., Kurdistani, S., Alber, F., Chen, L.10.1101/1426042017-05-26
Static And Dynamic DNA Loops Form AP-1 Bound Activation Hubs During Macrophage Development
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.
A Comparison Between Single Cell RNA Sequencing And Single Molecule RNA FISH For Rare Cell AnalysisTorre, 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.
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
A Versatile Compressed Sensing Scheme For Faster And Less Phototoxic 3D Fluorescence MicroscopyWoringer, 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.
Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells
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.
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
Free energy based high-resolution modeling of CTCF-mediated chromatin loops for human genomeDawson, 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.
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.
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.
Histone H3 Lysine 4 methyltransferases MLL3 and MLL4 Modulate Long-range Chromatin Interactions at Enhancers
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.
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
Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing
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.
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
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
Multiplexed dynamic imaging of genomic loci in single cells by combined CRISPR imaging and DNA sequential FISHTakei, 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
Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction MapEagen, 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.
Cohesin dependent compaction of mitotic chromosomesSchalbetter, 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.
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.
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
MAPPING OF LONG-RANGE CHROMATIN INTERACTIONS BY PROXIMITY LIGATION ASSISTED CHIP-SEQRongxin Fang, Miao Yu, Guoqiang Li, Sora Chee, Tristin Liu, Anthony Schmitt, Bing Ren10.1101/0742942016-09-09
Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genomeTsung-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
Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolutionAmit 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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