Publications
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2026
esBAF and INO8°C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.
Bonilla, Braulio, Patty, Benjamin J, Sambare, Snehal V, Dekker, Job, Fazzio, Thomas G, Hainer, Sarah J
UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.
Liu, Jiangyuan, Gibcus, Johan H, Dekker, Job
Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasm.
Schooley, Allana, Venev, Sergey V, Aksenova, Vasilisa, Lehman, Jesse W, Navarrete, Emily, Pai, Athma A, Dasso, Mary, Dekker, Job
An integrated view of the structure and function of the human 4D nucleome.
Dekker, Job, Oksuz, Betul Akgol, Zhang, Yang, Wang, Ye, Minsk, Miriam K, Kuang, Shuzhen, Yang, Liyan, Gibcus, Johan H, Krietenstein, Nils, Rando, Oliver J
... , Xu, Jie, Janssens, Derek H, Henikoff, Steven, Kukalev, Alexander, Andréa, Willemin, Winick-Ng, Warren, Kempfer, Rieke, Pombo, Ana, Yu, Miao, Kumar, Pradeep, Zhang, Liguo, Belmont, Andrew S, Sasaki, Takayo, van Schaik, Tom, Brueckner, Laura, Peric-Hupkes, Daan, van Steensel, Bas, Wang, Ping, Chai, Haoxi, Kim, Minji, Ruan, Yijun, Zhang, Ran, Quinodoz, Sofia A, Bhat, Prashant, Guttman, Mitchell, Zhao, Wenxin, Chien, Shu, Liu, Yuan, Venev, Sergey V, Plewczynski, Dariusz, Azcarate, Ibai Irastorza, Szabó, Dominik, Thieme, Christoph J, Szczepińska, Teresa, Chiliński, Mateusz, Sengupta, Kaustav, Conte, Mattia, Esposito, Andrea, Abraham, Alex, Zhang, Ruochi, Wang, Yuchuan, Wen, Xingzhao, Wu, Qiuyang, Yang, Yang, Liu, Jie, Boninsegna, Lorenzo, Yildirim, Asli, Zhan, Yuxiang, Chiariello, Andrea Maria, Bianco, Simona, Lee, Lindsay, Hu, Ming, Li, Yun, Barnett, R Jordan, Cook, Ashley L, Emerson, Daniel J, Marchal, Claire, Zhao, Peiyao, Park, Peter J, Alver, Burak H, Schroeder, Andrew J, Navelkar, Rahi, Bakker, Clara, Ronchetti, William, Ehmsen, Shannon, Veit, Alexander D, Gehlenborg, Nils, Wang, Ting, Li, Daofeng, Wang, Xiaotao, Nicodemi, Mario, Ren, Bing, Zhong, Sheng, Phillips-Cremins, Jennifer E, Gilbert, David M, Pollard, Katherine S, Alber, Frank, Ma, Jian, Noble, William S, Yue, Feng Show all
2025
mRNA initiation and termination are spatially coordinated.
Calvo-Roitberg, Ezequiel, Carroll, Christine L, Kim, GyeungYun, Sanabria, Valeria, Venev, Sergey V, Mick, Steven T, Paquette, Joseph D, Uriostegui-Arcos, Maritere, Dekker, Job, Fiszbein, Ana
... , Pai, Athma A Show all
Dynamic changes in chromosome and nuclear architecture during maturation of normal and ALS C9orf72 motor neurons.
Uyan, Özgün, Sambare, Snehal, Oomen, Marlies E, Wightman, Nicholas, Schooley, Allana, Klim, Joseph R, Belaghzal, Houda, Aydemir, Özkan, Akgol-Oksuz, Betul, Uslu, Zeynep Sena Agim
... , Eggan, Kevin, Brown, Robert H Jr, Dekker, Job Show all
esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions.
Bonilla, Braulio, Patty, Benjamin J, Sambare, Snehal V, Dekker, Job, Fazzio, Thomas G, Hainer, Sarah J
Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions.
Smith, Rebecca G, Fu, Yu, Schiela, Kathleen L, Dautle, Madison, Williams, Ryan, Wilson, Hannah M, Azadegan, Chloe, Whetstine, Johnathan R, Dekker, Job, Liu, Yu
Mitotic chromosomes harbor cell type- and species-specific structural features within a universal loop array conformation.
Oomen, Marlies E, Fox, A Nicole, Gonzalez, Inma, Molliex, Amandine, Papadopoulou, Thaleia, Navarro, Pablo, Dekker, Job
Rules of engagement for condensins and cohesins guide mitotic chromosome formation.
Samejima, Kumiko, Gibcus, Johan H, Abraham, Sameer, Cisneros-Soberanis, Fernanda, Samejima, Itaru, Beckett, Alison J, Pučeková, Nina, Abad, Maria Alba, Spanos, Christos, Medina-Pritchard, Bethan
... , Paulson, James R, Xie, Linfeng, Jeyaprakash, A Arockia, Prior, Ian A, Mirny, Leonid A, Dekker, Job, Goloborodko, Anton, Earnshaw, William C Show all
TOP2B is required for compartment strength changes upon retinoic acid treatment in SH-SY5Y cells.
Hildebrand, Erica M, Cowell, Ian G, Khazeem, Mushtaq M, Sambare, Snehal, Uyan, Ozgun, Dekker, Job, Austin, Caroline A
2024
The chromosome folding problem and how cells solve it.
Dekker, Job, Mirny, Leonid A
An integrated view of the structure and function of the human 4D nucleome.
Dekker, Job, Oksuz, Betul Akgol, Zhang, Yang, Wang, Ye, Minsk, Miriam K, Kuang, Shuzhen, Yang, Liyan, Gibcus, Johan H, Krietenstein, Nils, Rando, Oliver J
... , Xu, Jie, Janssens, Derek H, Henikoff, Steven, Kukalev, Alexander, Willemin, Andréa, Winick-Ng, Warren, Kempfer, Rieke, Pombo, Ana, Yu, Miao, Kumar, Pradeep, Zhang, Liguo, Belmont, Andrew S, Sasaki, Takayo, van Schaik, Tom, Brueckner, Laura, Peric-Hupkes, Daan, van Steensel, Bas, Wang, Ping, Chai, Haoxi, Kim, Minji, Ruan, Yijun, Zhang, Ran, Quinodoz, Sofia A, Bhat, Prashant, Guttman, Mitchell, Zhao, Wenxin, Chien, Shu, Liu, Yuan, Venev, Sergey V, Plewczynski, Dariusz, Azcarate, Ibai Irastorza, Szabó, Dominik, Thieme, Christoph J, Szczepińska, Teresa, Chiliński, Mateusz, Sengupta, Kaustav, Conte, Mattia, Esposito, Andrea, Abraham, Alex, Zhang, Ruochi, Wang, Yuchuan, Wen, Xingzhao, Wu, Qiuyang, Yang, Yang, Liu, Jie, Boninsegna, Lorenzo, Yildirim, Asli, Zhan, Yuxiang, Chiariello, Andrea Maria, Bianco, Simona, Lee, Lindsay, Hu, Ming, Li, Yun, Barnett, R Jordan, Cook, Ashley L, Emerson, Daniel J, Marchal, Claire, Zhao, Peiyao, Park, Peter, Alver, Burak H, Schroeder, Andrew, Navelkar, Rahi, Bakker, Clara, Ronchetti, William, Ehmsen, Shannon, Veit, Alexander, Gehlenborg, Nils, Wang, Ting, Li, Daofeng, Wang, Xiaotao, Nicodemi, Mario, Ren, Bing, Zhong, Sheng, Phillips-Cremins, Jennifer E, Gilbert, David M, Pollard, Katherine S, Alber, Frank, Ma, Jian, Noble, William S, Yue, Feng Show all
Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.
Conte, Mattia, Abraham, Alex, Esposito, Andrea, Yang, Liyan, Gibcus, Johan H, Parsi, Krishna M, Vercellone, Francesca, Fontana, Andrea, Di Pierno, Florinda, Dekker, Job
... , Nicodemi, Mario Show all
Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm.
Schooley, Allana, Venev, Sergey V, Aksenova, Vasilisa, Navarrete, Emily, Dasso, Mary, Dekker, Job
Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.
Conte, Mattia, Abraham, Alex, Esposito, Andrea, Yang, Liyan, Gibcus, Johan H, Parsi, Krishna M, Vercellone, Francesca, Fontana, Andrea, Pierno, Florinda Di, Dekker, Job
... , Nicodemi, Mario Show all
Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns.
Watson, Emma V, Lee, Jake June-Koo, Gulhan, Doga C, Melloni, Giorgio E M, Venev, Sergey V, Magesh, Rayna Y, Frederick, Abdulrazak, Chiba, Kunitoshi, Wooten, Eric C, Naxerova, Kamila
... , Dekker, Job, Park, Peter J, Elledge, Stephen J Show all
Rules of engagement for condensins and cohesins guide mitotic chromosome formation.
Samejima, Kumiko, Gibcus, Johan H, Abraham, Sameer, Cisneros-Soberanis, Fernanda, Samejima, Itaru, Beckett, Alison J, Pučeková, Nina, Abad, Maria Alba, Medina-Pritchard, Bethan, Paulson, James R
... , Xie, Linfeng, Jeyaprakash, A Arockia, Prior, Ian A, Mirny, Leonid A, Dekker, Job, Goloborodko, Anton, Earnshaw, William C Show all
Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.
Hildebrand, Erica M, Polovnikov, Kirill, Dekker, Bastiaan, Liu, Yu, Lafontaine, Denis L, Fox, A Nicole, Li, Ying, Venev, Sergey V, Mirny, Leonid A, Dekker, Job
Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells.
Kocanova, Silvia, Raynal, Flavien, Goiffon, Isabelle, Oksuz, Betul Akgol, Baú, Davide, Kamgoué, Alain, Cantaloube, Sylvain, Zhan, Ye, Lajoie, Bryan, Marti-Renom, Marc A
... , Dekker, Job, Bystricky, Kerstin Show all
mRNA initiation and termination are spatially coordinated.
Calvo-Roitberg, Ezequiel, Carroll, Christine L, Venev, Sergey V, Kim, GyeungYun, Mick, Steven T, Dekker, Job, Fiszbein, Ana, Pai, Athma A
RNA-mediated symmetry breaking enables singular olfactory receptor choice.
Pourmorady, Ariel D, Bashkirova, Elizaveta V, Chiariello, Andrea M, Belagzhal, Houda, Kodra, Albana, Duffié, Rachel, Kahiapo, Jerome, Monahan, Kevin, Pulupa, Joan, Schieren, Ira
... , Osterhoudt, Alexa, Dekker, Job, Nicodemi, Mario, Lomvardas, Stavros Show all
2023
Revisiting chromatin packaging in mouse sperm.
Yin, Qiangzong, Yang, Chih-Hsiang, Strelkova, Olga S, Wu, Jingyi, Sun, Yu, Gopalan, Sneha, Yang, Liyan, Dekker, Job, Fazzio, Thomas G, Li, Xin Zhiguo
... , Gibcus, Johan, Rando, Oliver J Show all
Editorial overview: Multiscale regulation of genome folding in space, time, and across the tree of life.
Cavalli, Giacomo, Dekker, Job
Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma.
Gentien, David, Saberi-Ansari, Elnaz, Servant, Nicolas, Jolly, Ariane, de la Grange, Pierre, Némati, Fariba, Liot, Géraldine, Saule, Simon, Teissandier, Aurélie, Bourc'his, Deborah
... , Girard, Elodie, Wong, Jennifer, Masliah-Planchon, Julien, Narmanli, Erkan, Liu, Yuanlong, Torun, Emma, Goulancourt, Rebecca, Rodrigues, Manuel, Gaudé, Laure Villoing, Reyes, Cécile, Bazire, Matéo, Chenegros, Thomas, Henry, Emilie, Rapinat, Audrey, Bohec, Mylene, Baulande, Sylvain, M'kacher, Radhia, Jeandidier, Eric, Nicolas, André, Ciriello, Giovanni, Margueron, Raphael, Decaudin, Didier, Cassoux, Nathalie, Piperno-Neumann, Sophie, Stern, Marc-Henri, Gibcus, Johan Harmen, Dekker, Job, Heard, Edith, Roman-Roman, Sergio, Waterfall, Joshua J Show all
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
Dekker, Job, Alber, Frank, Aufmkolk, Sarah, Beliveau, Brian J, Bruneau, Benoit G, Belmont, Andrew S, Bintu, Lacramioara, Boettiger, Alistair, Calandrelli, Riccardo, Disteche, Christine M
... , Gilbert, David M, Gregor, Thomas, Hansen, Anders S, Huang, Bo, Huangfu, Danwei, Kalhor, Reza, Leslie, Christina S, Li, Wenbo, Li, Yun, Ma, Jian, Noble, William S, Park, Peter J, Phillips-Cremins, Jennifer E, Pollard, Katherine S, Rafelski, Susanne M, Ren, Bing, Ruan, Yijun, Shav-Tal, Yaron, Shen, Yin, Shendure, Jay, Shu, Xiaokun, Strambio-De-Castillia, Caterina, Vertii, Anastassiia, Zhang, Huaiying, Zhong, Sheng Show all
Mechanisms of insertions at a DNA double-strand break.
Min, Jaewon, Zhao, Junfei, Zagelbaum, Jennifer, Lee, Jina, Takahashi, Sho, Cummings, Portia, Schooley, Allana, Dekker, Job, Gottesman, Max E, Rabadan, Raul
... , Gautier, Jean Show all
Author Correction: Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Zagelbaum, Jennifer, Schooley, Allana, Zhao, Junfei, Schrank, Benjamin R, Callen, Elsa, Zha, Shan, Gottesman, Max E, Nussenzweig, André, Rabadan, Raul, Dekker, Job
... , Gautier, Jean Show all
Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis.
Syed, Sabriya A, Shqillo, Kristina, Nand, Ankita, Zhan, Ye, Dekker, Job, Imbalzano, Anthony N
Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus.
Zhou, Coral Y, Dekker, Bastiaan, Liu, Ziyuan, Cabrera, Hilda, Ryan, Joel, Dekker, Job, Heald, Rebecca
The little skate genome and the evolutionary emergence of wing-like fins.
Marlétaz, Ferdinand, de la Calle-Mustienes, Elisa, Acemel, Rafael D, Paliou, Christina, Naranjo, Silvia, Martínez-García, Pedro Manuel, Cases, Ildefonso, Sleight, Victoria A, Hirschberger, Christine, Marcet-Houben, Marina
... , Navon, Dina, Andrescavage, Ali, Skvortsova, Ksenia, Duckett, Paul Edward, González-Rajal, Álvaro, Bogdanovic, Ozren, Gibcus, Johan H, Yang, Liyan, Gallardo-Fuentes, Lourdes, Sospedra, Ismael, Lopez-Rios, Javier, Darbellay, Fabrice, Visel, Axel, Dekker, Job, Shubin, Neil, Gabaldón, Toni, Nakamura, Tetsuya, Tena, Juan J, Lupiáñez, Darío G, Rokhsar, Daniel S, Gómez-Skarmeta, José Luis Show all
Capturing Chromosome Conformation Across Length Scales.
Yang, Liyan, Akgol Oksuz, Betul, Dekker, Job, Gibcus, Johan Harmen
Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq.
Spracklin, George, Yang, Liyan, Pradhan, Sriharsa, Dekker, Job
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization.
Zagelbaum, Jennifer, Schooley, Allana, Zhao, Junfei, Schrank, Benjamin R, Callen, Elsa, Zha, Shan, Gottesman, Max E, Nussenzweig, André, Rabadan, Raul, Dekker, Job
... , Gautier, Jean Show all
Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
Spracklin, George, Abdennur, Nezar, Imakaev, Maxim, Chowdhury, Neil, Pradhan, Sriharsa, Mirny, Leonid A, Dekker, Job
2022
A cohesin traffic pattern genetically linked to gene regulation.
Valton, Anne-Laure, Venev, Sergey V, Mair, Barbara, Khokhar, Eraj Shafiq, Tong, Amy H Y, Usaj, Matej, Chan, Katherine, Pai, Athma A, Moffat, Jason, Dekker, Job
Regulation of the mitotic chromosome folding machines.
Dekker, Bastiaan, Dekker, Job
CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity.
Liu, Yu, Dekker, Job
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions.
Mirny, Leonid, Dekker, Job
Cohesin-mediated loop anchors confine the locations of human replication origins.
Emerson, Daniel J, Zhao, Peiyao A, Cook, Ashley L, Barnett, R Jordan, Klein, Kyle N, Saulebekova, Dalila, Ge, Chunmin, Zhou, Linda, Simandi, Zoltan, Minsk, Miriam K
... , Titus, Katelyn R, Wang, Weitao, Gong, Wanfeng, Zhang, Di, Yang, Liyan, Venev, Sergey V, Gibcus, Johan H, Yang, Hongbo, Sasaki, Takayo, Kanemaki, Masato T, Yue, Feng, Dekker, Job, Chen, Chun-Long, Gilbert, David M, Phillips-Cremins, Jennifer E Show all
Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis.
Cui, Guoxin, Liew, Yi Jin, Konciute, Migle K, Zhan, Ye, Hung, Shiou-Han, Thistle, Jana, Gastoldi, Lucia, Schmidt-Roach, Sebastian, Dekker, Job, Aranda, Manuel
Author Correction: Perspectives on ENCODE.
Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A
... , Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, Myers, Richard M Show all
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder
... , Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, Weng, Zhiping Show all
Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.
Stevens, Lewis, Moya, Nicolas D, Tanny, Robyn E, Gibson, Sophia B, Tracey, Alan, Na, Huimin, Chitrakar, Rojin, Dekker, Job, Walhout, Albertha J M, Baugh, L Ryan
... , Andersen, Erik C Show all
Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling.
Sanders, Jacob T, Golloshi, Rosela, Das, Priyojit, Xu, Yang, Terry, Peyton H, Nash, Darrian G, Dekker, Job, McCord, Rachel Patton
Spatial organization of transcribed eukaryotic genes.
Leidescher, Susanne, Ribisel, Johannes, Ullrich, Simon, Feodorova, Yana, Hildebrand, Erica, Galitsyna, Alexandra, Bultmann, Sebastian, Link, Stephanie, Thanisch, Katharina, Mulholland, Christopher
... , Dekker, Job, Leonhardt, Heinrich, Mirny, Leonid, Solovei, Irina Show all
2021
Symbiodinium microadriaticum (coral microalgal endosymbiont).
Voolstra, Christian R, Aranda, Manuel, Zhan, Ye, Dekker, Job
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.
Cha, Hye Ji, Uyan, Özgün, Kai, Yan, Liu, Tianxin, Zhu, Qian, Tothova, Zuzana, Botten, Giovanni A, Xu, Jian, Yuan, Guo-Cheng, Dekker, Job
... , Orkin, Stuart H Show all
Systematic evaluation of chromosome conformation capture assays.
Akgol Oksuz, Betul, Yang, Liyan, Abraham, Sameer, Venev, Sergey V, Krietenstein, Nils, Parsi, Krishna Mohan, Ozadam, Hakan, Oomen, Marlies E, Nand, Ankita, Mao, Hui
... , Genga, Ryan M J, Maehr, Rene, Rando, Oliver J, Mirny, Leonid A, Gibcus, Johan H, Dekker, Job Show all
Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization.
Choppakatla, Pavan, Dekker, Bastiaan, Cutts, Erin E, Vannini, Alessandro, Dekker, Job, Funabiki, Hironori
Erratum to: Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
Tigano, Anna, Jacobs, Arne, Wilder, Aryn P, Nand, Ankita, Zhan, Ye, Dekker, Job, Therkildsen, Nina Overgaard
Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture.
Lafontaine, Denis L, Yang, Liyan, Dekker, Job, Gibcus, Johan H
Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation.
Tigano, Anna, Jacobs, Arne, Wilder, Aryn P, Nand, Ankita, Zhan, Ye, Dekker, Job, Therkildsen, Nina Overgaard
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.
Nand, Ankita, Zhan, Ye, Salazar, Octavio R, Aranda, Manuel, Voolstra, Christian R, Dekker, Job
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
Belaghzal, Houda, Borrman, Tyler, Stephens, Andrew D, Lafontaine, Denis L, Venev, Sergey V, Weng, Zhiping, Marko, John F, Dekker, Job
Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.
Tothova, Zuzana, Valton, Anne-Laure, Gorelov, Rebecca A, Vallurupalli, Mounica, Krill-Burger, John M, Holmes, Amie, Landers, Catherine C, Haydu, J Erika, Malolepsza, Edyta, Hartigan, Christina
... , Donahue, Melanie, Popova, Katerina D, Koochaki, Sebastian, Venev, Sergey V, Rivera, Jeanne, Chen, Edwin, Lage, Kasper, Schenone, Monica, D'Andrea, Alan D, Carr, Steven A, Morgan, Elizabeth A, Dekker, Job, Ebert, Benjamin L Show all
2020
Multi-contact 3C reveals that the human genome during interphase is largely not entangled.
Tavares-Cadete, Filipe, Norouzi, Davood, Dekker, Bastiaan, Liu, Yu, Dekker, Job
Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain.
Brossas, Caroline, Valton, Anne-Laure, Venev, Sergey V, Chilaka, Sabarinadh, Counillon, Antonin, Laurent, Marc, Goncalves, Coralie, Duriez, Bénédicte, Picard, Franck, Dekker, Job
... , Prioleau, Marie-Noëlle Show all
rad21 Is Involved in Corneal Stroma Development by Regulating Neural Crest Migration.
Zhang, Bi Ning, Liu, Yu, Yang, Qichen, Leung, Pui Ying, Wang, Chengdong, Wong, Thomas Chi Bun, Tham, Clement C, Chan, Sun On, Pang, Chi Pui, Chen, Li Jia
... , Dekker, Job, Zhao, Hui, Chu, Wai Kit Show all
Detecting chromatin interactions between and along sister chromatids with SisterC.
Oomen, Marlies E, Hedger, Adam K, Watts, Jonathan K, Dekker, Job
Large domains of heterochromatin direct the formation of short mitotic chromosome loops.
Fitz-James, Maximilian H, Tong, Pin, Pidoux, Alison L, Ozadam, Hakan, Yang, Liyan, White, Sharon A, Dekker, Job, Allshire, Robin C
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder
... , Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, Weng, Zhiping Show all
Perspectives on ENCODE.
Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A
... , Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, Myers, Richard M Show all
Ultrastructural Details of Mammalian Chromosome Architecture.
Krietenstein, Nils, Abraham, Sameer, Venev, Sergey V, Abdennur, Nezar, Gibcus, Johan, Hsieh, Tsung-Han S, Parsi, Krishna Mohan, Yang, Liyan, Maehr, René, Mirny, Leonid A
... , Dekker, Job, Rando, Oliver J Show all
Mechanisms and Functions of Chromosome Compartmentalization.
Hildebrand, Erica M, Dekker, Job
SPEN integrates transcriptional and epigenetic control of X-inactivation.
Dossin, François, Pinheiro, Inês, Żylicz, Jan J, Roensch, Julia, Collombet, Samuel, Le Saux, Agnès, Chelmicki, Tomasz, Attia, Mikaël, Kapoor, Varun, Zhan, Ye
... , Dingli, Florent, Loew, Damarys, Mercher, Thomas, Dekker, Job, Heard, Edith Show all
Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.
Gisselbrecht, Stephen S, Palagi, Alexandre, Kurland, Jesse V, Rogers, Julia M, Ozadam, Hakan, Zhan, Ye, Dekker, Job, Bulyk, Martha L
2019
Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation.
Viny, Aaron D, Bowman, Robert L, Liu, Yu, Lavallée, Vincent-Philippe, Eisman, Shira E, Xiao, Wenbin, Durham, Benjamin H, Navitski, Anastasia, Park, Jane, Braunstein, Stephanie
... , Alija, Besmira, Karzai, Abdul, Csete, Isabelle S, Witkin, Matthew, Azizi, Elham, Baslan, Timour, Ott, Christopher J, Pe'er, Dana, Dekker, Job, Koche, Richard, Levine, Ross L Show all
A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.
Abramo, Kristin, Valton, Anne-Laure, Venev, Sergey V, Ozadam, Hakan, Fox, A Nicole, Dekker, Job
Highly structured homolog pairing reflects functional organization of the Drosophila genome.
AlHaj Abed, Jumana, Erceg, Jelena, Goloborodko, Anton, Nguyen, Son C, McCole, Ruth B, Saylor, Wren, Fudenberg, Geoffrey, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A
... , Wu, C-Ting Show all
The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos.
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 Show all
Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei.
Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R, Leonhardt, Heinrich, Joffe, Boris, Dekker, Job, Fudenberg, Geoffrey, Solovei, Irina
... , Mirny, Leonid A Show all
Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.
Dileep, Vishnu, Wilson, Korey A, Marchal, Claire, Lyu, Xiaowen, Zhao, Peiyao A, Li, Ben, Poulet, Axel, Bartlett, Daniel A, Rivera-Mulia, Juan Carlos, Qin, Zhaohui S
... , Robins, Allan J, Schulz, Thomas C, Kulik, Michael J, McCord, Rachel Patton, Dekker, Job, Dalton, Stephen, Corces, Victor G, Gilbert, David M Show all
Heterochromatin drives compartmentalization of inverted and conventional nuclei.
Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R, Leonhardt, Heinrich, Joffe, Boris, Dekker, Job, Fudenberg, Geoffrey, Solovei, Irina
... , Mirny, Leonid A Show all
Measuring the reproducibility and quality of Hi-C data.
Yardımcı, Galip Gürkan, Ozadam, Hakan, Sauria, Michael E G, Ursu, Oana, Yan, Koon-Kiu, Yang, Tao, Chakraborty, Abhijit, Kaul, Arya, Lajoie, Bryan R, Song, Fan
... , Zhan, Ye, Ay, Ferhat, Gerstein, Mark, Kundaje, Anshul, Li, Qunhua, Taylor, James, Yue, Feng, Dekker, Job, Noble, William S Show all
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
Finn, Elizabeth H, Pegoraro, Gianluca, Brandão, Hugo B, Valton, Anne-Laure, Oomen, Marlies E, Dekker, Job, Mirny, Leonid, Misteli, Tom
CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.
Oomen, Marlies E, Hansen, Anders S, Liu, Yu, Darzacq, Xavier, Dekker, Job
The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome.
Gdula, Michal R, Nesterova, Tatyana B, Pintacuda, Greta, Godwin, Jonathan, Zhan, Ye, Ozadam, Hakan, McClellan, Michael, Moralli, Daniella, Krueger, Felix, Green, Catherine M
... , Reik, Wolf, Kriaucionis, Skirmantas, Heard, Edith, Dekker, Job, Brockdorff, Neil Show all
2018
Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.
Oudelaar, A Marieke, Davies, James O J, Hanssen, Lars L P, Telenius, Jelena M, Schwessinger, Ron, Liu, Yu, Brown, Jill M, Downes, Damien J, Chiariello, Andrea M, Bianco, Simona
... , Nicodemi, Mario, Buckle, Veronica J, Dekker, Job, Higgs, Douglas R, Hughes, Jim R Show all
Higher-Order Organization Principles of Pre-translational mRNPs.
Metkar, Mihir, Ozadam, Hakan, Lajoie, Bryan R, Imakaev, Maxim, Mirny, Leonid A, Dekker, Job, Moore, Melissa J
Integrative detection and analysis of structural variation in cancer genomes.
Dixon, Jesse R, Xu, Jie, Dileep, Vishnu, Zhan, Ye, Song, Fan, Le, Victoria T, Yardımcı, Galip Gürkan, Chakraborty, Abhijit, Bann, Darrin V, Wang, Yanli
... , Clark, Royden, Zhang, Lijun, Yang, Hongbo, Liu, Tingting, Iyyanki, Sriranga, An, Lin, Pool, Christopher, Sasaki, Takayo, Rivera-Mulia, Juan Carlos, Ozadam, Hakan, Lajoie, Bryan R, Kaul, Rajinder, Buckley, Michael, Lee, Kristen, Diegel, Morgan, Pezic, Dubravka, Ernst, Christina, Hadjur, Suzana, Odom, Duncan T, Stamatoyannopoulos, John A, Broach, James R, Hardison, Ross C, Ay, Ferhat, Noble, William Stafford, Dekker, Job, Gilbert, David M, Yue, Feng Show all
3C-Based Chromatin Interaction Analyses.
Kim, Tae Hoon, Dekker, Job
5C Analysis of 3C, ChIP-Loop, and Control Libraries.
Kim, Tae Hoon, Dekker, Job
4C Analysis of 3C, ChIP-Loop, and Control Libraries.
Kim, Tae Hoon, Dekker, Job
Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis.
Kim, Tae Hoon, Dekker, Job
CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.
Pulikkan, John Anto, Hegde, Mahesh, Ahmad, Hafiz Mohd, Belaghzal, Houda, Illendula, Anuradha, Yu, Jun, O'Hagan, Kelsey, Ou, Jianhong, Muller-Tidow, Carsten, Wolfe, Scot A
... , Zhu, Lihua Julie, Dekker, Job, Bushweller, John Hackett, Castilla, Lucio Hernán Show all
Generation of Control Ligation Product Libraries for 3C Analyses.
Kim, Tae Hoon, Dekker, Job
Generation of ChIP-Loop Libraries.
Kim, Tae Hoon, Dekker, Job
Generation of 3C Libraries from Cross-Linked Cells.
Kim, Tae Hoon, Dekker, Job
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.
Kundu, Sharmistha, Ji, Fei, Sunwoo, Hongjae, Jain, Gaurav, Lee, Jeannie T, Sadreyev, Ruslan I, Dekker, Job, Kingston, Robert E
CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia.
Pulikkan, John Anto, Hegde, Mahesh, Ahmad, Hafiz Mohd, Belaghzal, Houda, Illendula, Anuradha, Yu, Jun, O'Hagan, Kelsey, Ou, Jianhong, Muller-Tidow, Carsten, Wolfe, Scot A
... , Zhu, Lihua Julie, Dekker, Job, Bushweller, John Hackett, Castilla, Lucio Hernán Show all
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.
Gao, Xin D, Tu, Li-Chun, Mir, Aamir, Rodriguez, Tomás, Ding, Yuehe, Leszyk, John, Dekker, Job, Shaffer, Scott A, Zhu, Lihua Julie, Wolfe, Scot A
... , Sontheimer, Erik J Show all
Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions.
Kim, Tae Hoon, Dekker, Job
ChIP-seq.
Kim, Tae Hoon, Dekker, Job
ChIP-chip.
Kim, Tae Hoon, Dekker, Job
ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR).
Kim, Tae Hoon, Dekker, Job
ChIP.
Kim, Tae Hoon, Dekker, Job
Preparation of Cross-Linked Chromatin for ChIP.
Kim, Tae Hoon, Dekker, Job
Formaldehyde Cross-Linking.
Kim, Tae Hoon, Dekker, Job
A pathway for mitotic chromosome formation.
Gibcus, Johan H, Samejima, Kumiko, Goloborodko, Anton, Samejima, Itaru, Naumova, Natalia, Nuebler, Johannes, Kanemaki, Masato T, Xie, Linfeng, Paulson, James R, Earnshaw, William C
... , Mirny, Leonid A, Dekker, Job Show all
2017
Corrigendum: The 4D nucleome project.
Dekker, Job, Belmont, Andrew S, Guttman, Mitchell, Leshyk, Victor O, Lis, John T, Lomvardas, Stavros, Mirny, Leonid A, O'Shea, Clodagh C, Park, Peter J, Ren, Bing
... , Politz, Joan C Ritland, Shendure, Jay, Zhong, Sheng Show all
The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes.
Rodríguez-Carballo, Eddie, Lopez-Delisle, Lucille, Zhan, Ye, Fabre, Pierre J, Beccari, Leonardo, El-Idrissi, Imane, Huynh, Thi Hanh Nguyen, Ozadam, Hakan, Dekker, Job, Duboule, Denis
The 4D nucleome project.
Dekker, Job, Belmont, Andrew S, Guttman, Mitchell, Leshyk, Victor O, Lis, John T, Lomvardas, Stavros, Mirny, Leonid A, O'Shea, Clodagh C, Park, Peter J, Ren, Bing
... , Politz, Joan C Ritland, Shendure, Jay, Zhong, Sheng Show all
SMC complexes differentially compact mitotic chromosomes according to genomic context.
Schalbetter, Stephanie Andrea, Goloborodko, Anton, Fudenberg, Geoffrey, Belton, Jon-Matthew, Miles, Catrina, Yu, Miao, Dekker, Job, Mirny, Leonid, Baxter, Jonathan
Corrigendum: CTCF-mediated topological boundaries during development foster appropriate gene regulation.
Narendra, Varun, Bulajić, Milia, Dekker, Job, Mazzoni, Esteban O, Reinberg, Danny
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.
Belaghzal, Houda, Dekker, Job, Gibcus, Johan H
Shelterin components mediate genome reorganization in response to replication stress.
Mizuguchi, Takeshi, Taneja, Nitika, Matsuda, Emiko, Belton, Jon-Matthew, FitzGerald, Peter, Dekker, Job, Grewal, Shiv I S
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Nora, Elphège P, Goloborodko, Anton, Valton, Anne-Laure, Gibcus, Johan H, Uebersohn, Alec, Abdennur, Nezar, Dekker, Job, Mirny, Leonid A, Bruneau, Benoit G
Epigenetic characteristics of the mitotic chromosome in 1D and 3D.
Oomen, Marlies E, Dekker, Job
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation.
Kundu, Sharmistha, Ji, Fei, Sunwoo, Hongjae, Jain, Gaurav, Lee, Jeannie T, Sadreyev, Ruslan I, Dekker, Job, Kingston, Robert E
2016
CTCF-mediated topological boundaries during development foster appropriate gene regulation.
Narendra, Varun, Bulajić, Milica, Dekker, Job, Mazzoni, Esteban O, Reinberg, Danny
Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.
McGeachie, Michael J, Yates, Katherine P, Zhou, Xiaobo, Guo, Feng, Sternberg, Alice L, Van Natta, Mark L, Wise, Robert A, Szefler, Stanley J, Sharma, Sunita, Kho, Alvin T
... , Cho, Michael H, Croteau-Chonka, Damien C, Castaldi, Peter J, Jain, Gaurav, Sanyal, Amartya, Zhan, Ye, Lajoie, Bryan R, Dekker, Job, Stamatoyannopoulos, John, Covar, Ronina A, Zeiger, Robert S, Adkinson, N Franklin, Williams, Paul V, Kelly, H William, Grasemann, Hartmut, Vonk, Judith M, Koppelman, Gerard H, Postma, Dirkje S, Raby, Benjamin A, Houston, Isaac, Lu, Quan, Fuhlbrigge, Anne L, Tantisira, Kelan G, Silverman, Edwin K, Tonascia, James, Strunk, Robert C, Weiss, Scott T Show all
Mapping the 3D genome: Aiming for consilience.
Dekker, Job
RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells.
Barutcu, A Rasim, Hong, Deli, Lajoie, Bryan R, McCord, Rachel Patton, van Wijnen, Andre J, Lian, Jane B, Stein, Janet L, Dekker, Job, Imbalzano, Anthony N, Stein, Gary S
Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites.
Liu, Ce Feng, Brandt, Gabriel S, Hoang, Quyen Q, Naumova, Natalia, Lazarevic, Vanja, Hwang, Eun Sook, Dekker, Job, Glimcher, Laurie H, Ringe, Dagmar, Petsko, Gregory A
SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.
Barutcu, A Rasim, Lajoie, Bryan R, Fritz, Andrew J, McCord, Rachel P, Nickerson, Jeffrey A, van Wijnen, Andre J, Lian, Jane B, Stein, Janet L, Dekker, Job, Stein, Gary S
... , Imbalzano, Anthony N Show all
Structural organization of the inactive X chromosome in the mouse.
Giorgetti, Luca, Lajoie, Bryan R, Carter, Ava C, Attia, Mikael, Zhan, Ye, Xu, Jin, Chen, Chong Jian, Kaplan, Noam, Chang, Howard Y, Heard, Edith
... , Dekker, Job Show all
Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming.
Beagan, Jonathan A, Gilgenast, Thomas G, Kim, Jesi, Plona, Zachary, Norton, Heidi K, Hu, Gui, Hsu, Sarah C, Shields, Emily J, Lyu, Xiaowen, Apostolou, Effie
... , Hochedlinger, Konrad, Corces, Victor G, Dekker, Job, Phillips-Cremins, Jennifer E Show all
A Guide to Packing Your DNA.
Dekker, Job, Guttman, Mitchell, Lomvardas, Stavros
Activation of proto-oncogenes by disruption of chromosome neighborhoods.
Hnisz, Denes, Weintraub, Abraham S, Day, Daniel S, Valton, Anne-Laure, Bak, Rasmus O, Li, Charles H, Goldmann, Johanna, Lajoie, Bryan R, Fan, Zi Peng, Sigova, Alla A
... , Reddy, Jessica, Borges-Rivera, Diego, Lee, Tong Ihn, Jaenisch, Rudolf, Porteus, Matthew H, Dekker, Job, Young, Richard A Show all
The 3D Genome as Moderator of Chromosomal Communication.
Dekker, Job, Mirny, Leonid
Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire.
Montefiori, Lindsey, Wuerffel, Robert, Roqueiro, Damian, Lajoie, Bryan, Guo, Changying, Gerasimova, Tatiana, De, Supriyo, Wood, William, Becker, Kevin G, Dekker, Job
... , Liang, Jie, Sen, Ranjan, Kenter, Amy L Show all
TAD disruption as oncogenic driver.
Valton, Anne-Laure, Dekker, Job
Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus.
Smith, Emily M, Lajoie, Bryan R, Jain, Gaurav, Dekker, Job
2015
The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer.
Belton, Jon-Matthew, Lajoie, Bryan R, Audibert, Sylvain, Cantaloube, Sylvain, Lassadi, Imen, Goiffon, Isabelle, Baù, Davide, Marti-Renom, Marc A, Bystricky, Kerstin, Dekker, Job
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.
Servant, Nicolas, Varoquaux, Nelle, Lajoie, Bryan R, Viara, Eric, Chen, Chong-Jian, Vert, Jean-Philippe, Heard, Edith, Dekker, Job, Barillot, Emmanuel
Structural and functional diversity of Topologically Associating Domains.
Dekker, Job, Heard, Edith
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila.
Ramírez, Fidel, Lingg, Thomas, Toscano, Sarah, Lam, Kin Chung, Georgiev, Plamen, Chung, Ho-Ryun, Lajoie, Bryan R, de Wit, Elzo, Zhan, Ye, de Laat, Wouter
... , Dekker, Job, Manke, Thomas, Akhtar, Asifa Show all
Long-Range Chromatin Interactions.
Dekker, Job, Misteli, Tom
The yeast genome undergoes significant topological reorganization in quiescence.
Rutledge, Mark T, Russo, Mariano, Belton, Jon-Matthew, Dekker, Job, Broach, James R
Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells.
Barutcu, A Rasim, Lajoie, Bryan R, McCord, Rachel P, Tye, Coralee E, Hong, Deli, Messier, Terri L, Browne, Gillian, van Wijnen, Andre J, Lian, Jane B, Stein, Janet L
... , Dekker, Job, Imbalzano, Anthony N, Stein, Gary S Show all
Genome-wide maps of nuclear lamina interactions in single human cells.
Kind, Jop, Pagie, Ludo, de Vries, Sandra S, Nahidiazar, Leila, Dey, Siddharth S, Bienko, Magda, Zhan, Ye, Lajoie, Bryan, de Graaf, Carolyn A, Amendola, Mario
... , Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A, Jalink, Kees, Dekker, Job, van Oudenaarden, Alexander, van Steensel, Bas Show all
Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis.
Wang, Xindan, Le, Tung B K, Lajoie, Bryan R, Dekker, Job, Laub, Michael T, Rudner, David Z
Condensin-driven remodelling of X chromosome topology during dosage compensation.
Crane, Emily, Bian, Qian, McCord, Rachel Patton, Lajoie, Bryan R, Wheeler, Bayly S, Ralston, Edward J, Uzawa, Satoru, Dekker, Job, Meyer, Barbara J
Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C.
Hsieh, Tsung-Han S, Weiner, Assaf, Lajoie, Bryan, Dekker, Job, Friedman, Nir, Rando, Oliver J
Measuring Chromatin Structure in Budding Yeast.
Belton, Jon-Matthew, Dekker, Job
Hi-C in Budding Yeast.
Belton, Jon-Matthew, Dekker, Job
Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast.
Belton, Jon-Matthew, Dekker, Job
Randomized ligation control for chromosome conformation capture.
Belton, Jon-Matthew, Dekker, Job
Chromosome Conformation Capture (3C) in Budding Yeast.
Belton, Jon-Matthew, Dekker, Job
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin.
Ing-Simmons, Elizabeth, Seitan, Vlad C, Faure, Andre J, Flicek, Paul, Carroll, Thomas, Dekker, Job, Fisher, Amanda G, Lenhard, Boris, Merkenschlager, Matthias
The Hitchhiker's guide to Hi-C analysis: practical guidelines.
Lajoie, Bryan R, Dekker, Job, Kaplan, Noam
2014
Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe.
Mizuguchi, Takeshi, Fudenberg, Geoffrey, Mehta, Sameet, Belton, Jon-Matthew, Taneja, Nitika, Folco, Hernan Diego, FitzGerald, Peter, Dekker, Job, Mirny, Leonid, Barrowman, Jemima
... , Grewal, Shiv I S Show all
Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.
Kellis, Manolis, Wold, Barbara, Snyder, Michael P, Bernstein, Bradley E, Kundaje, Anshul, Marinov, Georgi K, Ward, Lucas D, Birney, Ewan, Crawford, Gregory E, Dekker, Job
... , Dunham, Ian, Elnitski, Laura L, Farnham, Peggy J, Feingold, Elise A, Gerstein, Mark, Giddings, Morgan C, Gilbert, David M, Gingeras, Thomas R, Green, Eric D, Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D, Myers, Richard M, Pazin, Michael J, Ren, Bing, Stamatoyannopoulos, John, Weng, Zhiping, White, Kevin P, Hardison, Ross C Show all
Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.
Giorgetti, Luca, Galupa, Rafael, Nora, Elphège P, Piolot, Tristan, Lam, France, Dekker, Job, Tiana, Guido, Heard, Edith
Defining functional DNA elements in the human genome.
Kellis, Manolis, Wold, Barbara, Snyder, Michael P, Bernstein, Bradley E, Kundaje, Anshul, Marinov, Georgi K, Ward, Lucas D, Birney, Ewan, Crawford, Gregory E, Dekker, Job
... , Dunham, Ian, Elnitski, Laura L, Farnham, Peggy J, Feingold, Elise A, Gerstein, Mark, Giddings, Morgan C, Gilbert, David M, Gingeras, Thomas R, Green, Eric D, Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D, Myers, Richard M, Pazin, Michael J, Ren, Bing, Stamatoyannopoulos, John A, Weng, Zhiping, White, Kevin P, Hardison, Ross C Show all
Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture.
Dekker, Job
2013
High-throughput genome scaffolding from in vivo DNA interaction frequency.
Kaplan, Noam, Dekker, Job
Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments.
Seitan, Vlad C, Faure, Andre J, Zhan, Ye, McCord, Rachel Patton, Lajoie, Bryan R, Ing-Simmons, Elizabeth, Lenhard, Boris, Giorgetti, Luca, Heard, Edith, Fisher, Amanda G
... , Flicek, Paul, Dekker, Job, Merkenschlager, Matthias Show all
Organization of the mitotic chromosome.
Naumova, Natalia, Imakaev, Maxim, Fudenberg, Geoffrey, Zhan, Ye, Lajoie, Bryan R, Mirny, Leonid A, Dekker, Job
Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny.
Kumar, Satyendra, Wuerffel, Robert, Achour, Ikbel, Lajoie, Bryan, Sen, Ranjan, Dekker, Job, Feeney, Ann J, Kenter, Amy L
Biological techniques: Chromosomes captured one by one.
Dekker, Job, Mirny, Leonid
Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?
Nora, Elphège P, Dekker, Job, Heard, Edith
Architectural protein subclasses shape 3D organization of genomes during lineage commitment.
Phillips-Cremins, Jennifer E, Sauria, Michael E G, Sanyal, Amartya, Gerasimova, Tatiana I, Lajoie, Bryan R, Bell, Joshua S K, Ong, Chin-Tong, Hookway, Tracy A, Guo, Changying, Sun, Yuhua
... , Bland, Michael J, Wagstaff, William, Dalton, Stephen, McDevitt, Todd C, Sen, Ranjan, Dekker, Job, Taylor, James, Corces, Victor G Show all
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data.
Dekker, Job, Marti-Renom, Marc A, Mirny, Leonid A
Nuclear biology: what's been most surprising?
Dekker, Job, Wysocka, Joanna, Mattaj, Iain, Lieberman Aiden, Erez, Pikaard, Craig
The hierarchy of the 3D genome.
Gibcus, Johan H, Dekker, Job
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.
McCord, Rachel Patton, Nazario-Toole, Ashley, Zhang, Haoyue, Chines, Peter S, Zhan, Ye, Erdos, Michael R, Collins, Francis S, Dekker, Job, Cao, Kan
2012
3C-based technologies to study the shape of the genome.
de Laat, Wouter, Dekker, Job
From cells to chromatin: capturing snapshots of genome organization with 5C technology.
Ferraiuolo, Maria A, Sanyal, Amartya, Naumova, Natalia, Dekker, Job, Dostie, Josée
HiTC: exploration of high-throughput 'C' experiments.
Servant, Nicolas, Lajoie, Bryan R, Nora, Elphège P, Giorgetti, Luca, Chen, Chong-Jian, Heard, Edith, Dekker, Job, Barillot, Emmanuel
Analysis of long-range chromatin interactions using Chromosome Conformation Capture.
Naumova, Natalia, Smith, Emily M, Zhan, Ye, Dekker, Job
Hi-C: a comprehensive technique to capture the conformation of genomes.
Belton, Jon-Matthew, McCord, Rachel Patton, Gibcus, Johan Harmen, Naumova, Natalia, Zhan, Ye, Dekker, Job
Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Imakaev, Maxim, Fudenberg, Geoffrey, McCord, Rachel Patton, Naumova, Natalia, Goloborodko, Anton, Lajoie, Bryan R, Dekker, Job, Mirny, Leonid A
The long-range interaction landscape of gene promoters.
Sanyal, Amartya, Lajoie, Bryan R, Jain, Gaurav, Dekker, Job
The accessible chromatin landscape of the human genome.
Thurman, Robert E, Rynes, Eric, Humbert, Richard, Vierstra, Jeff, Maurano, Matthew T, Haugen, Eric, Sheffield, Nathan C, Stergachis, Andrew B, Wang, Hao, Vernot, Benjamin
... , Garg, Kavita, John, Sam, Sandstrom, Richard, Bates, Daniel, Boatman, Lisa, Canfield, Theresa K, Diegel, Morgan, Dunn, Douglas, Ebersol, Abigail K, Frum, Tristan, Giste, Erika, Johnson, Audra K, Johnson, Ericka M, Kutyavin, Tanya, Lajoie, Bryan, Lee, Bum-Kyu, Lee, Kristen, London, Darin, Lotakis, Dimitra, Neph, Shane, Neri, Fidencio, Nguyen, Eric D, Qu, Hongzhu, Reynolds, Alex P, Roach, Vaughn, Safi, Alexias, Sanchez, Minerva E, Sanyal, Amartya, Shafer, Anthony, Simon, Jeremy M, Song, Lingyun, Vong, Shinny, Weaver, Molly, Yan, Yongqi, Zhang, Zhancheng, Zhang, Zhuzhu, Lenhard, Boris, Tewari, Muneesh, Dorschner, Michael O, Hansen, R Scott, Navas, Patrick A, Stamatoyannopoulos, George, Iyer, Vishwanath R, Lieb, Jason D, Sunyaev, Shamil R, Akey, Joshua M, Sabo, Peter J, Kaul, Rajinder, Furey, Terrence S, Dekker, Job, Crawford, Gregory E, Stamatoyannopoulos, John A Show all
An integrated encyclopedia of DNA elements in the human genome.
An encyclopedia of mouse DNA elements (Mouse ENCODE).
Stamatoyannopoulos, John A, Snyder, Michael, Hardison, Ross, Ren, Bing, Gingeras, Thomas, Gilbert, David M, Groudine, Mark, Bender, Michael, Kaul, Rajinder, Canfield, Theresa
... , Giste, Erica, Johnson, Audra, Zhang, Mia, Balasundaram, Gayathri, Byron, Rachel, Roach, Vaughan, Sabo, Peter J, Sandstrom, Richard, Stehling, A Sandra, Thurman, Robert E, Weissman, Sherman M, Cayting, Philip, Hariharan, Manoj, Lian, Jin, Cheng, Yong, Landt, Stephen G, Ma, Zhihai, Wold, Barbara J, Dekker, Job, Crawford, Gregory E, Keller, Cheryl A, Wu, Weisheng, Morrissey, Christopher, Kumar, Swathi A, Mishra, Tejaswini, Jain, Deepti, Byrska-Bishop, Marta, Blankenberg, Daniel, Lajoie, Bryan R, Jain, Gaurav, Sanyal, Amartya, Chen, Kaun-Bei, Denas, Olgert, Taylor, James, Blobel, Gerd A, Weiss, Mitchell J, Pimkin, Max, Deng, Wulan, Marinov, Georgi K, Williams, Brian A, Fisher-Aylor, Katherine I, Desalvo, Gilberto, Kiralusha, Anthony, Trout, Diane, Amrhein, Henry, Mortazavi, Ali, Edsall, Lee, McCleary, David, Kuan, Samantha, Shen, Yin, Yue, Feng, Ye, Zhen, Davis, Carrie A, Zaleski, Chris, Jha, Sonali, Xue, Chenghai, Dobin, Alex, Lin, Wei, Fastuca, Meagan, Wang, Huaien, Guigo, Roderic, Djebali, Sarah, Lagarde, Julien, Ryba, Tyrone, Sasaki, Takayo, Malladi, Venkat S, Cline, Melissa S, Kirkup, Vanessa M, Learned, Katrina, Rosenbloom, Kate R, Kent, W James, Feingold, Elise A, Good, Peter J, Pazin, Michael, Lowdon, Rebecca F, Adams, Leslie B Show all
MORC family ATPases required for heterochromatin condensation and gene silencing.
Moissiard, Guillaume, Cokus, Shawn J, Cary, Joshua, Feng, Suhua, Billi, Allison C, Stroud, Hume, Husmann, Dylan, Zhan, Ye, Lajoie, Bryan R, McCord, Rachel Patton
... , Hale, Christopher J, Feng, Wei, Michaels, Scott D, Frand, Alison R, Pellegrini, Matteo, Dekker, Job, Kim, John K, Jacobsen, Steven E Show all
CTCF and cohesin help neurons raise their self-awareness.
Dekker, Job
Spatial partitioning of the regulatory landscape of the X-inactivation centre.
Nora, Elphège P, Lajoie, Bryan R, Schulz, Edda G, Giorgetti, Luca, Okamoto, Ikuhiro, Servant, Nicolas, Piolot, Tristan, van Berkum, Nynke L, Meisig, Johannes, Sedat, John
... , Gribnau, Joost, Barillot, Emmanuel, Blüthgen, Nils, Dekker, Job, Heard, Edith Show all
Genome architecture and expression.
Felsenfeld, Gary, Dekker, Job
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.
Zhang, Yu, McCord, Rachel Patton, Ho, Yu-Jui, Lajoie, Bryan R, Hildebrand, Dominic G, Simon, Aline C, Becker, Michael S, Alt, Frederick W, Dekker, Job
The context of gene expression regulation.
Gibcus, Johan H, Dekker, Job
Evidence for transcript networks composed of chimeric RNAs in human cells.
Djebali, Sarah, Lagarde, Julien, Kapranov, Philipp, Lacroix, Vincent, Borel, Christelle, Mudge, Jonathan M, Howald, Cédric, Foissac, Sylvain, Ucla, Catherine, Chrast, Jacqueline
... , Ribeca, Paolo, Martin, David, Murray, Ryan R, Yang, Xinping, Ghamsari, Lila, Lin, Chenwei, Bell, Ian, Dumais, Erica, Drenkow, Jorg, Tress, Michael L, Gelpí, Josep Lluís, Orozco, Modesto, Valencia, Alfonso, van Berkum, Nynke L, Lajoie, Bryan R, Vidal, Marc, Stamatoyannopoulos, John, Batut, Philippe, Dobin, Alex, Harrow, Jennifer, Hubbard, Tim, Dekker, Job, Frankish, Adam, Salehi-Ashtiani, Kourosh, Reymond, Alexandre, Antonarakis, Stylianos E, Guigó, Roderic, Gingeras, Thomas R Show all
The structure and function of chromatin and chromosomes.
Noble, William Stafford, Blau, C Anthony, Dekker, Job, Duan, Zhi-Jun, Mao, Yi
2011
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping.
Reece-Hoyes, John S, Diallo, Alos, Lajoie, Bryan, Kent, Amanda, Shrestha, Shaleen, Kadreppa, Sreenath, Pesyna, Colin, Dekker, Job, Myers, Chad L, Walhout, Albertha J M
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping.
Reece-Hoyes, John S, Barutcu, A Rasim, McCord, Rachel Patton, Jeong, Jun Seop, Jiang, Lizhi, MacWilliams, Andrew, Yang, Xinping, Salehi-Ashtiani, Kourosh, Hill, David E, Blackshaw, Seth
... , Zhu, Heng, Dekker, Job, Walhout, Albertha J M Show all
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.
Umbarger, Mark A, Toro, Esteban, Wright, Matthew A, Porreca, Gregory J, Baù, Davide, Hong, Sun-Hae, Fero, Michael J, Zhu, Lihua J, Marti-Renom, Marc A, McAdams, Harley H
... , Shapiro, Lucy, Dekker, Job, Church, George M Show all
Translocation mapping exposes the risky lifestyle of B cells.
McCord, Rachel Patton, Dekker, Job
Chromatin globules: a common motif of higher order chromosome structure?
Sanyal, Amartya, Baù, Davide, Martí-Renom, Marc A, Dekker, Job
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.
Wang, Kevin C, Yang, Yul W, Liu, Bo, Sanyal, Amartya, Corces-Zimmerman, Ryan, Chen, Yong, Lajoie, Bryan R, Protacio, Angeline, Flynn, Ryan A, Gupta, Rajnish A
... , Wysocka, Joanna, Lei, Ming, Dekker, Job, Helms, Jill A, Chang, Howard Y Show all
A user's guide to the encyclopedia of DNA elements (ENCODE).
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules.
Baù, Davide, Sanyal, Amartya, Lajoie, Bryan R, Capriotti, Emidio, Byron, Meg, Lawrence, Jeanne B, Dekker, Job, Marti-Renom, Marc A
2010
Sister cohesion and structural axis components mediate homolog bias of meiotic recombination.
Kim, Keun P, Weiner, Beth M, Zhang, Liangran, Jordan, Amy, Dekker, Job, Kleckner, Nancy
Genomics tools for unraveling chromosome architecture.
van Steensel, Bas, Dekker, Job
Mediator and cohesin connect gene expression and chromatin architecture.
Kagey, Michael H, Newman, Jamie J, Bilodeau, Steve, Zhan, Ye, Orlando, David A, van Berkum, Nynke L, Ebmeier, Christopher C, Goossens, Jesse, Rahl, Peter B, Levine, Stuart S
... , Taatjes, Dylan J, Dekker, Job, Young, Richard A Show all
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease.
Bradner, James E, Mak, Raymond, Tanguturi, Shyam K, Mazitschek, Ralph, Haggarty, Stephen J, Ross, Kenneth, Chang, Cindy Y, Bosco, Jocelyn, West, Nathan, Morse, Elizabeth
... , Lin, Katherine, Shen, John Paul, Kwiatkowski, Nicholas P, Gheldof, Nele, Dekker, Job, DeAngelo, Daniel J, Carr, Steven A, Schreiber, Stuart L, Golub, Todd R, Ebert, Benjamin L Show all
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.
Gheldof, Nele, Smith, Emily M, Tabuchi, Tomoko M, Koch, Christoph M, Dunham, Ian, Stamatoyannopoulos, John A, Dekker, Job
Integrating one-dimensional and three-dimensional maps of genomes.
Naumova, Natalia, Dekker, Job
Hi-C: a method to study the three-dimensional architecture of genomes.
van Berkum, Nynke L, Lieberman-Aiden, Erez, Williams, Louise, Imakaev, Maxim, Gnirke, Andreas, Mirny, Leonid A, Dekker, Job, Lander, Eric S
2009
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Lieberman-Aiden, Erez, van Berkum, Nynke L, Williams, Louise, Imakaev, Maxim, Ragoczy, Tobias, Telling, Agnes, Amit, Ido, Lajoie, Bryan R, Sabo, Peter J, Dorschner, Michael O
... , Sandstrom, Richard, Bernstein, Bradley, Bender, M A, Groudine, Mark, Gnirke, Andreas, Stamatoyannopoulos, John, Mirny, Leonid A, Lander, Eric S, Dekker, Job Show all
My5C: web tools for chromosome conformation capture studies.
Lajoie, Bryan R, van Berkum, Nynke L, Sanyal, Amartya, Dekker, Job
Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization.
Chang, Howard Y, Cuvier, Olivier, Dekker, Job
Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening.
D'haene, Barbara, Attanasio, Catia, Beysen, Diane, Dostie, Josée, Lemire, Edmond, Bouchard, Philippe, Field, Michael, Jones, Kristie, Lorenz, Birgit, Menten, Björn
... , Buysse, Karen, Pattyn, Filip, Friedli, Marc, Ucla, Catherine, Rossier, Colette, Wyss, Carine, Speleman, Frank, De Paepe, Anne, Dekker, Job, Antonarakis, Stylianos E, De Baere, Elfride Show all
Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions.
Miele, Adriana, Bystricky, Kerstin, Dekker, Job
Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery.
Oza, Pranav, Jaspersen, Sue L, Miele, Adriana, Dekker, Job, Peterson, Craig L
Determining spatial chromatin organization of large genomic regions using 5C technology.
van Berkum, Nynke L, Dekker, Job
Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).
Miele, Adriana, Dekker, Job
2008
Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction.
Dekker, Job
Long-range chromosomal interactions and gene regulation.
Miele, Adriana, Dekker, Job
A mechanism for Ikaros regulation of human globin gene switching.
Keys, Janelle R, Tallack, Michael R, Zhan, Ye, Papathanasiou, Peter, Goodnow, Christopher C, Gaensler, Karin M, Crossley, Merlin, Dekker, Job, Perkins, Andrew C
Gene regulation in the third dimension.
Dekker, Job
2007
Chromosome conformation capture carbon copy technology.
Dostie, Josée, Zhan, Ye, Dekker, Job
Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex.
Lanzuolo, Chiara, Roure, Virginie, Dekker, Job, Bantignies, Frédéric, Orlando, Valerio
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Birney, Ewan, Stamatoyannopoulos, John A, Dutta, Anindya, Guigó, Roderic, Gingeras, Thomas R, Margulies, Elliott H, Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T, Thurman, Robert E
... , Kuehn, Michael S, Taylor, Christopher M, Neph, Shane, Koch, Christoph M, Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A, Andrews, Robert M, Flicek, Paul, Boyle, Patrick J, Cao, Hua, Carter, Nigel P, Clelland, Gayle K, Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C, Dorschner, Michael O, Fiegler, Heike, Giresi, Paul G, Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D, Johnson, Brett E, Johnson, Ericka M, Frum, Tristan T, Rosenzweig, Elizabeth R, Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C, Navas, Patrick A, Neri, Fidencio, Parker, Stephen C J, Sabo, Peter J, Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu, Man, Collins, Francis S, Dekker, Job, Lieb, Jason D, Tullius, Thomas D, Crawford, Gregory E, Sunyaev, Shamil, Noble, William S, Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L, Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A, Sekinger, Edward A, Lagarde, Julien, Abril, Josep F, Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermüller, Jörg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S, Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C, Thomas, Daryl J, Weirauch, Matthew T, Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K G, Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L, Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G, Brown, James B, Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N, Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S, Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M, Rogers, Jane, Stadler, Peter F, Lowe, Todd M, Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E, Fu, Yutao, Green, Eric D, Karaöz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A, Wetterstrand, Kris A, Good, Peter J, Feingold, Elise A, Guyer, Mark S, Cooper, Gregory M, Asimenos, George, Dewey, Colin N, Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I, Löytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R, Holmes, Ian, Mullikin, James C, Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W James, Stone, Eric A, Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C, Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D, Zhang, Zhengdong D, Barrera, Leah, Stuart, Rhona, King, David C, Ameur, Adam, Enroth, Stefan, Bieda, Mark C, Kim, Jonghwan, Bhinge, Akshay A, Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B, Lee, Charlie W H, Ng, Patrick, Shahab, Atif, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J, Inman, David, Singer, Michael A, Richmond, Todd A, Munn, Kyle J, Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C, Couttet, Phillippe, Bruce, Alexander W, Dovey, Oliver M, Ellis, Peter D, Langford, Cordelia F, Nix, David A, Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E, Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Kim, Tae Hoon, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K, Rosenfeld, M Geoff, Aldred, Shelley Force, Cooper, Sara J, Halees, Anason, Lin, Jane M, Shulha, Hennady P, Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N S, Yu, Yong, Ruan, Yijun, Iyer, Vishwanath R, Green, Roland D, Wadelius, Claes, Farnham, Peggy J, Ren, Bing, Harte, Rachel A, Hinrichs, Angie S, Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S, Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M, Karolchik, Donna, Armengol, Lluis, Bird, Christine P, de Bakker, Paul I W, Kern, Andrew D, Lopez-Bigas, Nuria, Martin, Joel D, Stranger, Barbara E, Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrímsdóttir, Ingileif B, Huppert, Julian, Zody, Michael C, Abecasis, Gonçalo R, Estivill, Xavier, Bouffard, Gerard G, Guan, Xiaobin, Hansen, Nancy F, Idol, Jacquelyn R, Maduro, Valerie V B, Maskeri, Baishali, McDowell, Jennifer C, Park, Morgan, Thomas, Pamela J, Young, Alice C, Blakesley, Robert W, Muzny, Donna M, Sodergren, Erica, Wheeler, David A, Worley, Kim C, Jiang, Huaiyang, Weinstock, George M, Gibbs, Richard A, Graves, Tina, Fulton, Robert, Mardis, Elaine R, Wilson, Richard K, Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B, Chang, Jean L, Lindblad-Toh, Kerstin, Lander, Eric S, Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, de Jong, Pieter J Show all
Quantitative analysis of chromosome conformation capture assays (3C-qPCR).
Hagège, Hélène, Klous, Petra, Braem, Caroline, Splinter, Erik, Dekker, Job, Cathala, Guy, de Laat, Wouter, Forné, Thierry
GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p.
Dekker, Job
Mapping networks of physical interactions between genomic elements using 5C technology.
Dostie, Josée, Dekker, Job
2006
Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
Dostie, Josée, Richmond, Todd A, Arnaout, Ramy A, Selzer, Rebecca R, Lee, William L, Honan, Tracey A, Rubio, Eric D, Krumm, Anton, Lamb, Justin, Nusbaum, Chad
... , Green, Roland D, Dekker, Job Show all
The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications.
Gheldof, Nele, Tabuchi, Tomoko M, Dekker, Job
Mapping chromatin interactions by chromosome conformation capture.
Miele, Adriana, Gheldof, Nele, Tabuchi, Tomoko M, Dostie, Josée, Dekker, Job
The three 'C' s of chromosome conformation capture: controls, controls, controls.
Dekker, Job
2005
Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.
Vakoc, Christopher R, Letting, Danielle L, Gheldof, Nele, Sawado, Tomoyuki, Bender, M A, Groudine, Mark, Weiss, Mitchell J, Dekker, Job, Blobel, Gerd A
2004
A mechanical basis for chromosome function.
Kleckner, Nancy, Zickler, Denise, Jones, Gareth H, Dekker, Job, Padmore, Ruth, Henle, Jim, Hutchinson, John
2003
A closer look at long-range chromosomal interactions.
Dekker, Job
2002
Capturing chromosome conformation.
Dekker, Job, Rippe, Karsten, Dekker, Martijn, Kleckner, Nancy