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Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states
Andrea Esposito, Simona Bianco, Andrea M. Chiariello, Alex Abraham, Luca Fiorillo, Mattia Conte, Raffaele Campanile, Mario Nicodemi
The mammalian genome has a complex, functional 3D organization. However, it remains largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we infer from only Hi-C the cell-type-specific arrangement of DNA binding…
Stripenn detects architectural stripes from chromatin conformation data using computer vision
Sora Yoon, Aditi Chandra, Golnaz Vahedi.
Architectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer…
Systematic reconstruction of cellular trajectories across mouse embryogenesis
Chengxiang Qiu, Junyue Cao, Beth K. Martin, Tony Li, Ian C. Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M. Disteche, Stephen A. Murray, Malte Spielmann, Cecilia B. Moens, Cole Trapnell, Jay Shendure.
Mammalian embryogenesis is characterized by rapid cellular proliferation and diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells expressing a panoply of molecular…
A spatial genome aligner for multiplexed DNA-FISH
Jia, B. B., Jussila, A. P., Kern, J. C., Zhu, Q., Ren, B....
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....
Keystone Symposia: Higher-Order Chromatin Architecture in Time and Space
November 15-17, 2021. 10AM EST. Registration required....
4DN 2021 Annual Meeting
The 2021 4D Nucleome Annual Meeting will be held virtually on Zoom on December 8-10, 2021. Additional information and registration will come soon, stay tuned on the Web Portal!...
A spatial genome aligner for multiplexed DNA-FISH
Jia, B. B., Jussila, A. P., Kern, J. C., Zhu, Q., Ren, B....
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....
Keystone Symposia: Higher-Order Chromatin Architecture in Time and Space
November 15-17, 2021. 10AM EST. Registration required....
