A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian L., Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman
Published in Cell (18.12.2014)
Published in Cell (18.12.2014)
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Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
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.
Published in Nature genetics (01.12.2019)
Published in Nature genetics (01.12.2019)
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De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
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
Published in Science (American Association for the Advancement of Science) (07.04.2017)
Published in Science (American Association for the Advancement of Science) (07.04.2017)
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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
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
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (24.11.2015)
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Durand, Neva C., Shamim, Muhammad S., Machol, Ido, Rao, Suhas S.P., Huntley, Miriam H., Lander, Eric S., Aiden, Erez Lieberman
Published in Cell systems (01.07.2016)
Published in Cell systems (01.07.2016)
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Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data
Robinson, James T., Turner, Douglass, Durand, Neva C., Thorvaldsdóttir, Helga, Mesirov, Jill P., Aiden, Erez Lieberman
Published in Cell systems (28.02.2018)
Published in Cell systems (28.02.2018)
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
Durand, Neva C., Robinson, James T., Shamim, Muhammad S., Machol, Ido, Mesirov, Jill P., Lander, Eric S., Aiden, Erez Lieberman
Published in Cell systems (01.07.2016)
Published in Cell systems (01.07.2016)
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The Energetics and Physiological Impact of Cohesin Extrusion
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
Published in Cell (17.05.2018)
Published in Cell (17.05.2018)
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Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
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
Published in PLoS genetics (26.12.2018)
Published in PLoS genetics (26.12.2018)
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Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
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
Published in Proceedings of the National Academy of Sciences - PNAS (02.08.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (02.08.2016)
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CTCF looping is established during gastrulation in medaka embryos
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Published in Genome research (01.06.2021)
Published in Genome research (01.06.2021)
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Chromatin architecture transitions from zebrafish sperm through early embryogenesis
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
Published in Genome research (01.06.2021)
Published in Genome research (01.06.2021)
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The Energetics and Physiological Impact of Cohesin Extrusion
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
Published in Cell (20.09.2018)
Published in Cell (20.09.2018)
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Genetic determinants of co-accessible chromatin regions in activated T cells across humans
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
Published in Nature genetics (01.08.2018)
Published in Nature genetics (01.08.2018)
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A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing
Adastra, Per A, Durand, Neva C, Mitra, Namita, Pulido, Saul Godinez, Mahajan, Ragini, Blackburn, Alyssa, Colaric, Zane L, Theisen, Joshua W. M, Weisz, David, Dudchenko, Olga, Gnirke, Andreas, Rao, Suhas S. P, Kaur, Parwinder, Aiden, Erez Lieberman, Aiden, Aviva Presser
Published in PloS one (30.11.2023)
Published in PloS one (30.11.2023)
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus)
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
Published in BMC biology (16.11.2017)
Published in BMC biology (16.11.2017)
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Journal Article
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, Suhas S.P., Huntley, Miriam H., Durand, Neva C., Stamenova, Elena K., Bochkov, Ivan D., Robinson, James T., Sanborn, Adrian L., Machol, Ido, Omer, Arina D., Lander, Eric S., Aiden, Erez Lieberman
Published in Cell (30.07.2015)
Published in Cell (30.07.2015)
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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement
Garg, Vanika, Dudchenko, Olga, Wang, Jinpeng, Khan, Aamir W., Gupta, Saurabh, Kaur, Parwinder, Han, Kai, Saxena, Rachit K., Kale, Sandip M., Pham, Melanie, Yu, Jigao, Chitikineni, Annapurna, Zhang, Zhikang, Fan, Guangyi, Lui, Christopher, Valluri, Vinodkumar, Meng, Fanbo, Bhandari, Aditi, Liu, Xiaochuan, Yang, Tao, Chen, Hua, Valliyodan, Babu, Roorkiwal, Manish, Shi, Chengcheng, Yang, Hong Bin, Durand, Neva C., Pandey, Manish K., Li, Guowei, Barmukh, Rutwik, Wang, Xingjun, Chen, Xiaoping, Lam, Hon-Ming, Jiang, Huifang, Zong, Xuxiao, Liang, Xuanqiang, Liu, Xin, Liao, Boshou, Guo, Baozhu, Jackson, Scott, Nguyen, Henry T., Zhuang, Weijian, Shubo, Wan, Wang, Xiyin, Aiden, Erez Lieberman, Bennetzen, Jeffrey L., Varshney, Rajeev K.
Published in Journal of advanced research (01.12.2022)
Published in Journal of advanced research (01.12.2022)
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The ENCODE Uniform Analysis Pipelines
Hitz, Benjamin C, Jin-Wook, Lee, Jolanki, Otto, Kagda, Meenakshi S, Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J Seth, Sloan, Cricket A, Dreszer, Timothy, Rowe, Laurence D, Podduturi, Nikhil R, Malladi, Venkat S, Chan, Esther T, Davidson, Jean M, Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie L, Lee, Brian T, Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel S, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva C, Dudchenko, Olga, Weisz, David, Rao, Suhas S P, Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad Saad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, Kent, W James, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J Michael
Published in bioRxiv (06.04.2023)
Published in bioRxiv (06.04.2023)
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Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
Sandoval-Velasco, Marcela, Dudchenko, Olga, Rodríguez, Juan Antonio, Pérez Estrada, Cynthia, Dehasque, Marianne, Fontsere, Claudia, Mak, Sarah S.T., Khan, Ruqayya, Contessoto, Vinícius G., Oliveira Junior, Antonio B., Kalluchi, Achyuth, Zubillaga Herrera, Bernardo J., Jeong, Jiyun, Roy, Renata P., Christopher, Ishawnia, Weisz, David, Omer, Arina D., Batra, Sanjit S., Shamim, Muhammad S., Durand, Neva C., O’Connell, Brendan, Roca, Alfred L., Plikus, Maksim V., Kusliy, Mariya A., Romanenko, Svetlana A., Lemskaya, Natalya A., Serdyukova, Natalya A., Modina, Svetlana A., Perelman, Polina L., Kizilova, Elena A., Baiborodin, Sergei I., Rubtsov, Nikolai B., Machol, Gur, Rath, Krisha, Mahajan, Ragini, Kaur, Parwinder, Gnirke, Andreas, Garcia-Treviño, Isabel, Coke, Rob, Flanagan, Joseph P., Pletch, Kelcie, Ruiz-Herrera, Aurora, Plotnikov, Valerii, Pavlov, Innokentiy S., Pavlova, Naryya I., Protopopov, Albert V., Di Pierro, Michele, Graphodatsky, Alexander S., Lander, Eric S., Rowley, M. Jordan, Wolynes, Peter G., Onuchic, José N., Dalén, Love, Marti-Renom, Marc A., Gilbert, M. Thomas P., Aiden, Erez Lieberman
Published in Cell (11.07.2024)
Published in Cell (11.07.2024)
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