Search Results - "Durand, Neva C"

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping by 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

“…We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid…”
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Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations by 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.

“…Enhancer elements in the human genome control how genes are expressed in specific cell types and harbor thousands of genetic variants that influence risk for…”
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Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes by 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

“…We recently used in situ Hi-C to create kilobase-resolution 3D maps of mammalian genomes. Here, we combine these maps with new Hi-C, microscopy, and…”
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The Energetics and Physiological Impact of Cohesin Extrusion by 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

“…Cohesin extrusion is thought to play a central role in establishing the architecture of mammalian genomes. However, extrusion has not been visualized in vivo,…”
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CTCF looping is established during gastrulation in medaka embryos by 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

“…Chromatin looping plays an important role in genome regulation. However, because ChIP-seq and loop-resolution Hi-C (DNA-DNA proximity ligation) are extremely…”
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Chromatin architecture transitions from zebrafish sperm through early embryogenesis by 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

“…Chromatin architecture mapping in 3D formats has increased our understanding of how regulatory sequences and gene expression are connected and regulated in a…”
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The Energetics and Physiological Impact of Cohesin Extrusion by 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

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A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing by 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

“…Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom…”
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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus) by 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

“…The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome…”
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De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds by 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

“…The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective…”
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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments by Durand, Neva C, Shamim, Muhammad S, Machol, Ido, Rao, Suhas S P, Huntley, Miriam H, Lander, Eric S, Aiden, Erez Lieberman

“…Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an…”
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Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data by Robinson, James T, Turner, Douglass, Durand, Neva C, Thorvaldsdóttir, Helga, Mesirov, Jill P, Aiden, Erez Lieberman

“…Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the…”
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom by Durand, Neva C, Robinson, James T, Shamim, Muhammad S, Machol, Ido, Mesirov, Jill P, Lander, Eric S, Aiden, Erez Lieberman

“…Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce…”
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Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture by 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

“…During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite…”
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Genetic determinants of co-accessible chromatin regions in activated T cells across humans by 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

“…Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation…”
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Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling by 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

“…Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C…”
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping by 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

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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement by 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.

“…[Display omitted] •The study presents chromosome-length genome assemblies of six legume species.•Evolutionary events that shaped the present day legumes are…”
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Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample by 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

“…Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here,…”
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A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping by 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

“…We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human…”
Get full text