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
Published in Nature cell biology (01.11.2019)
Published in Nature cell biology (01.11.2019)
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Journal Article
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
Published in Nature methods (01.09.2021)
Published in Nature methods (01.09.2021)
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Journal Article
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
Published in Genes & development (15.11.2017)
Published in Genes & development (15.11.2017)
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Journal Article
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.
Published in Molecular cell (16.01.2020)
Published in Molecular cell (16.01.2020)
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Journal Article
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
Published in Genome Biology (19.03.2019)
Published in Genome Biology (19.03.2019)
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Journal Article
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
Published in Nature communications (03.01.2019)
Published in Nature communications (03.01.2019)
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Journal Article
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
Published in eLife (11.09.2020)
Published in eLife (11.09.2020)
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Journal Article
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution
Chacko, Jonathan, Ozadam, Hakan, Cenik, Can
Published in Bioinformatics (Oxford, England) (03.06.2024)
Published in Bioinformatics (Oxford, England) (03.06.2024)
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Journal Article
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
Published in Nature (London) (30.07.2020)
Published in Nature (London) (30.07.2020)
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Journal Article
Single-cell quantification of ribosome occupancy in early mouse development
Ozadam, Hakan, Tonn, Tori, Han, Crystal M, Segura, Alia, Hoskins, Ian, Rao, Shilpa, Ghatpande, Vighnesh, Tran, Duc, Catoe, David, Salit, Marc, Cenik, Can
Published in Nature (London) (29.06.2023)
Published in Nature (London) (29.06.2023)
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Journal Article
Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein
Rao, Shilpa, Hoskins, Ian, Tonn, Tori, Garcia, P Daniela, Ozadam, Hakan, Sarinay Cenik, Elif, Cenik, Can
Published in RNA (Cambridge) (01.09.2021)
Published in RNA (Cambridge) (01.09.2021)
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Journal Article
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
Published in Nature (London) (14.09.2017)
Published in Nature (London) (14.09.2017)
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Journal Article
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.
Published in Molecular cell (15.11.2018)
Published in Molecular cell (15.11.2018)
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Journal Article
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
Published in Nature genetics (01.10.2018)
Published in Nature genetics (01.10.2018)
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Journal Article
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
Published in Nature (London) (30.07.2020)
Published in Nature (London) (30.07.2020)
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Journal Article
Loss of coordinated expression between ribosomal and mitochondrial genes revealed by comprehensive characterization of a large family with a rare Mendelian disorder
Panici, Brendan, Nakajima, Hosei, Carlston, Colleen M., Ozadam, Hakan, Cenik, Can, Cenik, Elif Sarinay
Published in Genomics (San Diego, Calif.) (01.07.2021)
Published in Genomics (San Diego, Calif.) (01.07.2021)
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Journal Article
Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling
Chen, Weijun, Moore, Jill, Ozadam, Hakan, Shulha, Hennady P., Rhind, Nicholas, Weng, Zhiping, Moore, Melissa J.
Published in Cell (03.05.2018)
Published in Cell (03.05.2018)
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Journal Article
An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments
Heyer, Erin E, Ozadam, Hakan, Ricci, Emiliano P, Cenik, Can, Moore, Melissa J
Published in Nucleic acids research (01.01.2015)
Published in Nucleic acids research (01.01.2015)
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