Nguyen, Huy Q., Chattoraj, Shyamtanu, Castillo, David, Nguyen, Son C., Nir, Guy, Lioutas, Antonios, Hershberg, Elliot A., Martins, Nuno M. C., Reginato, Paul L., Hannan, Mohammed, Beliveau, Brian J., Church, George M., Daugharthy, Evan R., Marti-Renom, Marc A., Wu, C.-ting (2020) 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nature Methods, 17 (8) 822-832 doi:10.1038/s41592-020-0890-0

See Also

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	Wernersson, Erik, Gelali, Eleni, Girelli, Gabriele, Wang, Su, Castillo, David, Mattsson Langseth, Christoffer, Verron, Quentin, Nguyen, Huy Q., Chattoraj, Shyamtanu, Martinez Casals, Anna, Blom, Hans, Lundberg, Emma, Nilsson, Mats, Marti-Renom, Marc A., Wu, Chao-ting, Crosetto, Nicola, Bienko, Magda (2024) Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images. Nature Methods, 21 (7) 1245-1256 doi:10.1038/s41592-024-02294-7
	Beliveau, Brian J., Kishi, Jocelyn Y., Nir, Guy, Sasaki, Hiroshi M., Saka, Sinem K., Nguyen, Son C., Wu, Chao-ting, Yin, Peng (2018) OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. Proceedings of the National Academy of Sciences, 115 (10) doi:10.1073/pnas.1714530115
	Erceg, Jelena, AlHaj Abed, Jumana, Goloborodko, Anton, Lajoie, Bryan R., Fudenberg, Geoffrey, Abdennur, Nezar, Imakaev, Maxim, McCole, Ruth B., Nguyen, Son C., Saylor, Wren, Joyce, Eric F., Senaratne, T. Niroshini, Hannan, Mohammed A., Nir, Guy, Dekker, Job, Mirny, Leonid A., Wu, C.-ting (2019) The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nature Communications, 10. doi:10.1038/s41467-019-12211-8
	Hershberg, Elliot A., Camplisson, Conor K., Close, Jennie L., Attar, Sahar, Chern, Ryan, Liu, Yuzhen, Akilesh, Shreeram, Nicovich, Philip R., Beliveau, Brian J. (2021) PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments. Nature Methods, 18 (8) 937-944 doi:10.1038/s41592-021-01187-3
	Beliveau, Brian J., Boettiger, Alistair N., Avendaño, Maier S., Jungmann, Ralf, McCole, Ruth B., Joyce, Eric F., Kim-Kiselak, Caroline, Bantignies, Frédéric, Fonseka, Chamith Y., Erceg, Jelena, Hannan, Mohammed A., Hoang, Hien G., Colognori, David, Lee, Jeannie T., Shih, William M., Yin, Peng, Zhuang, Xiaowei, Wu, Chao-ting (2015) Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nature Communications, 6. doi:10.1038/ncomms8147
	Hershberg, Elliot A., Camplisson, Conor K., Close, Jennie L., Attar, Sahar, Chern, Ryan, Liu, Yuzhen, Akilesh, Shreeram, Nicovich, Philip R., Beliveau, Brian J. (2021) Author Correction: PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments. Nature Methods, 18 (10) 1265 doi:10.1038/s41592-021-01273-6
	Zhang, Nan, Mendieta-Esteban, Julen, Magli, Alessandro, Lilja, Karin C., Perlingeiro, Rita C. R., Marti-Renom, Marc A., Tsirigos, Aristotelis, Dynlacht, Brian David (2020) Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology. Nature Communications, 11 (1) doi:10.1038/s41467-020-19999-w
	Spill, Yannick G., Castillo, David, Vidal, Enrique, Marti-Renom, Marc A. (2019) Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution. Nature Communications, 10. doi:10.1038/s41467-019-09907-2
	Payne, Andrew C., Chiang, Zachary D., Reginato, Paul L., Mangiameli, Sarah M., Murray, Evan M., Yao, Chun-Chen, Markoulaki, Styliani, Earl, Andrew S., Labade, Ajay S., Jaenisch, Rudolf, Church, George M., Boyden, Edward S., Buenrostro, Jason D., Chen, Fei (2021) In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science, 371 (6532). doi:10.1126/science.aay3446
	Marti-Renom, Marc A. (2021) Benchmarking experiments with polymer modeling. Nature Methods, 18 (5) 456-457 doi:10.1038/s41592-021-01134-2
	Culley, Siân, Albrecht, David, Jacobs, Caron, Pereira, Pedro Matos, Leterrier, Christophe, Mercer, Jason, Henriques, Ricardo (2020) Author Correction: Quantitative mapping and minimization of super-resolution optical imaging artifacts. Nature Methods, 17 (11) 1167 doi:10.1038/s41592-020-00983-7