Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

par Robinson, James T., Turner, Douglass, Durand, Neva C., Thorvaldsdóttir, Helga, Mesirov, Jill P., Aiden, Erez Lieberman
Publié dans Cell Syst (2018)

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

par Durand, Neva C., Robinson, James T., Shamim, Muhammad S., Machol, Ido, Mesirov, Jill P., Lander, Eric S., Aiden, Erez Lieberman
Publié dans Cell Syst (2016)

Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments

par Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Rao, Suhas S. P., Huntley, Miriam H., Lander, Eric S., Aiden, Erez Lieberman
Publié dans Cell Syst (2016)

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

par Dudchenko, Olga, Batra, Sanjit S., Omer, Arina D., Nyquist, Sarah K., Hoeger, Marie, Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Lander, Eric S., Aiden, Aviva Presser, Aiden, Erez Lieberman
Publié dans Science (2017)

A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping

par Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian, Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman
Publié dans Cell (2014)

CTCF looping is established during gastrulation in medaka embryos

par Nakamura, Ryohei, Motai, Yuichi, Kumagai, Masahiko, Wike, Candice L., Nishiyama, Haruyo, Nakatani, Yoichiro, Durand, Neva C., Kondo, Kaori, Kondo, Takashi, Tsukahara, Tatsuya, Shimada, Atsuko, Cairns, Bradley R., Aiden, Erez Lieberman, Morishita, Shinichi, Takeda, Hiroyuki
Publié dans Genome Res (2021)

Chromatin architecture transitions from zebrafish sperm through early embryogenesis

par Wike, Candice L., Guo, Yixuan, Tan, Mengyao, Nakamura, Ryohei, Shaw, Dana Klatt, Díaz, Noelia, Whittaker-Tademy, Aneasha F., Durand, Neva C., Aiden, Erez Lieberman, Vaquerizas, Juan M., Grunwald, David, Takeda, Hiroyuki, Cairns, Bradley R.
Publié dans Genome Res (2021)

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

par Darrow, Emily M., Huntley, Miriam H., Dudchenko, Olga, Stamenova, Elena K., Durand, Neva C., Sun, Zhuo, Huang, Su-Chen, Sanborn, Adrian L., Machol, Ido, Shamim, Muhammad, Seberg, Andrew P., Lander, Eric S., Chadwick, Brian P., Aiden, Erez Lieberman
Publié dans Proc Natl Acad Sci U S A (2016)

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

par Sanborn, Adrian L., Rao, Suhas S. P., Huang, Su-Chen, Durand, Neva C., Huntley, Miriam H., Jewett, Andrew I., Bochkov, Ivan D., Chinnappan, Dharmaraj, Cutkosky, Ashok, Li, Jian, Geeting, Kristopher P., Gnirke, Andreas, Melnikov, Alexandre, McKenna, Doug, Stamenova, Elena K., Lander, Eric S., Aiden, Erez Lieberman
Publié dans Proc Natl Acad Sci U S A (2015)

Activity-by-Contact model of enhancer-promoter regulation from thousands of CRISPR perturbations

par Fulco, Charles P., Nasser, Joseph, Jones, Thouis R., Munson, Glen, Bergman, Drew T., Subramanian, Vidya, Grossman, Sharon R., Anyoha, Rockwell, Doughty, Benjamin R., Patwardhan, Tejal A., Nguyen, Tung H., Kane, Michael, Perez, Elizabeth M., Durand, Neva C., Lareau, Caleb A., Stamenova, Elena K., Aiden, Erez Lieberman, Lander, Eric S., Engreitz, Jesse M.
Publié dans Nat Genet (2019)

Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)

par Larsen, Peter A., Harris, R. Alan, Liu, Yue, Murali, Shwetha C., Campbell, C. Ryan, Brown, Adam D., Sullivan, Beth A., Shelton, Jennifer, Brown, Susan J., Raveendran, Muthuswamy, Dudchenko, Olga, Machol, Ido, Durand, Neva C., Shamim, Muhammad S., Aiden, Erez Lieberman, Muzny, Donna M., Gibbs, Richard A., Yoder, Anne D., Rogers, Jeffrey, Worley, Kim C.
Publié dans BMC Biol (2017)

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

par Gate, Rachel E., Cheng, Christine S., Aiden, Aviva P., Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M. Grace, Subramaniam, Meena, Shamim, Muhammad, Hougen, Kendrick L., Wortman, Ivo, Huang, Su-Chen, Durand, Neva C., Feng, Ting, De Jager, Philip L., Chang, Howard Y., Aiden, Erez Lieberman, Benoist, Christophe, Beer, Michael A., Ye, Chun J., Regev, Aviv
Publié dans Nat Genet (2018)

The energetics and physiological impact of cohesin extrusion

par Vian, Laura, Pękowska, Aleksandra P, Rao, Suhas S.P., Kieffer-Kwon, Kyong-Rim, Jung, Seolkyoung, Baranello, Laura, Huang, Su-Chen, El Khattabi, Laila, Dose, Marei, Pruett, Nathanael, Sanborn, Adrian L., Canela, Andres, Maman, Yaakov, Oksanen, Anna, Resch, Wolfgang, Li, Xingwang, Lee, Byoungkoo, Kovalchuk, Alexander L., Tang, Zhonghui, Nelson, Steevenson, Pierro, Michele Di, Cheng, Ryan R., Machol, Ido, St Hilaire, Brian Glenn, Durand, Neva C., Shamim, Muhammad S., Stamenova, Elena K., Onuchic, José N., Ruan, Yijun, Nussenzweig, Andre, Levens, David, Aiden, Erez Lieberman, Casellas, Rafael
Publié dans Cell (2018)

The Energetics and Physiological Impact of Cohesin Extrusion

par Vian, Laura, Pękowska, Aleksandra, Rao, Suhas S.P., Kieffer-Kwon, Kyong-Rim, Jung, Seolkyoung, Baranello, Laura, Huang, Su-Chen, El Khattabi, Laila, Dose, Marei, Pruett, Nathanael, Sanborn, Adrian L., Canela, Andres, Maman, Yaakov, Oksanen, Anna, Resch, Wolfgang, Li, Xingwang, Lee, Byoungkoo, Kovalchuk, Alexander L., Tang, Zhonghui, Nelson, Steevenson, Di Pierro, Michele, Cheng, Ryan R., Machol, Ido, St Hilaire, Brian Glenn, Durand, Neva C., Shamim, Muhammad S., Stamenova, Elena K., Onuchic, José N., Ruan, Yijun, Nussenzweig, Andre, Levens, David, Aiden, Erez Lieberman, Casellas, Rafael
Publié dans Cell (2018)

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

par Nir, Guy, Farabella, Irene, Pérez Estrada, Cynthia, Ebeling, Carl G., Beliveau, Brian J., Sasaki, Hiroshi M., Lee, S. Dean, Nguyen, Son C., McCole, Ruth B., Chattoraj, Shyamtanu, Erceg, Jelena, AlHaj Abed, Jumana, Martins, Nuno M. C., Nguyen, Huy Q., Hannan, Mohammed A., Russell, Sheikh, Durand, Neva C., Rao, Suhas S. P., Kishi, Jocelyn Y., Soler-Vila, Paula, Di Pierro, Michele, Onuchic, José N., Callahan, Steven P., Schreiner, John M., Stuckey, Jeff A., Yin, Peng, Aiden, Erez Lieberman, Marti-Renom, Marc A., Wu, C.-ting
Publié dans PLoS Genet (2018)