H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions
Cai, Yichao, Zhang, Ying, Loh, Yan Ping, Tng, Jia Qi, Lim, Mei Chee, Cao, Zhendong, Raju, Anandhkumar, Lieberman Aiden, Erez, Li, Shang, Manikandan, Lakshmanan, Tergaonkar, Vinay, Tucker-Kellogg, Greg, Fullwood, Melissa Jane
Published in Nature communications (29.01.2021)
Published in Nature communications (29.01.2021)
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Journal Article
Using deep learning and Google Street View to estimate the demographic makeup of neighborhoods across the United States
Gebru, Timnit, Krause, Jonathan, Wang, Yilun, Chen, Duyun, Deng, Jia, Aiden, Erez Lieberman, Fei-Fei, Li
Published in Proceedings of the National Academy of Sciences - PNAS (12.12.2017)
Published in Proceedings of the National Academy of Sciences - PNAS (12.12.2017)
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Journal Article
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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Journal Article
De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture
Di Pierro, Michele, Cheng, Ryan R., Aiden, Erez Lieberman, Wolynes, Peter G., Onuchic, José N.
Published in Proceedings of the National Academy of Sciences - PNAS (14.11.2017)
Published in Proceedings of the National Academy of Sciences - PNAS (14.11.2017)
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Journal Article
CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions
Kaushal, Anjali, Mohana, Giriram, Dorier, Julien, Özdemir, Isa, Omer, Arina, Cousin, Pascal, Semenova, Anastasiia, Taschner, Michael, Dergai, Oleksandr, Marzetta, Flavia, Iseli, Christian, Eliaz, Yossi, Weisz, David, Shamim, Muhammad Saad, Guex, Nicolas, Lieberman Aiden, Erez, Gambetta, Maria Cristina
Published in Nature communications (12.02.2021)
Published in Nature communications (12.02.2021)
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Journal Article
The fundamental role of chromatin loop extrusion in physiological V(D)J recombination
Zhang, Yu, Zhang, Xuefei, Ba, Zhaoqing, Liang, Zhuoyi, Dring, Edward W., Hu, Hongli, Lou, Jiangman, Kyritsis, Nia, Zurita, Jeffrey, Shamim, Muhammad S., Presser Aiden, Aviva, Lieberman Aiden, Erez, Alt, Frederick W.
Published in Nature (London) (26.09.2019)
Published in Nature (London) (26.09.2019)
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Journal Article
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
Sanborn, Adrian L, Yeh, Benjamin T, Feigerle, Jordan T, Hao, Cynthia V, Townshend, Raphael Jl, Lieberman Aiden, Erez, Dror, Ron O, Kornberg, Roger D
Published in eLife (27.04.2021)
Published in eLife (27.04.2021)
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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 (18.12.2014)
Published in Cell (18.12.2014)
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Journal Article
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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Journal Article
Transferable model for chromosome architecture
Di Pierro, Michele, Zhang, Bin, Aiden, Erez Lieberman, Wolynes, Peter G., Onuchic, José N.
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
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Journal Article
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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Journal Article
A simple rule for the evolution of cooperation on graphs and social networks
Nowak, Martin A, Ohtsuki, Hisashi, Hauert, Christoph, Lieberman, Erez
Published in Nature (25.05.2006)
Published in Nature (25.05.2006)
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Journal Article
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
Phanstiel, Douglas H., Van Bortle, Kevin, Spacek, Damek, Hess, Gaelen T., Shamim, Muhammad Saad, Machol, Ido, Love, Michael I., Aiden, Erez Lieberman, Bassik, Michael C., Snyder, Michael P.
Published in Molecular cell (21.09.2017)
Published in Molecular cell (21.09.2017)
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Journal Article
Genome Organization Drives Chromosome Fragility
Canela, Andres, Maman, Yaakov, Jung, Seolkyoung, Wong, Nancy, Callen, Elsa, Day, Amanda, Kieffer-Kwon, Kyong-Rim, Pekowska, Aleksandra, Zhang, Hongliang, Rao, Suhas S.P., Huang, Su-Chen, Mckinnon, Peter J., Aplan, Peter D., Pommier, Yves, Aiden, Erez Lieberman, Casellas, Rafael, Nussenzweig, André
Published in Cell (27.07.2017)
Published in Cell (27.07.2017)
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Journal Article
Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals
Rowley, M Jordan, Poulet, Axel, Nichols, Michael H, Bixler, Brianna J, Sanborn, Adrian L, Brouhard, Elizabeth A, Hermetz, Karen, Linsenbaum, Hannah, Csankovszki, Gyorgyi, Lieberman Aiden, Erez, Corces, Victor G
Published in Genome research (01.03.2020)
Published in Genome research (01.03.2020)
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Journal Article
A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
El Khattabi, Laila, Zhao, Haiyan, Kalchschmidt, Jens, Young, Natalie, Jung, Seolkyoung, Van Blerkom, Peter, Kieffer-Kwon, Philippe, Kieffer-Kwon, Kyong-Rim, Park, Solji, Wang, Xiang, Krebs, Jordan, Tripathi, Subhash, Sakabe, Noboru, Sobreira, Débora R., Huang, Su-Chen, Rao, Suhas S.P., Pruett, Nathanael, Chauss, Daniel, Sadler, Erica, Lopez, Andrea, Nóbrega, Marcelo A., Aiden, Erez Lieberman, Asturias, Francisco J., Casellas, Rafael
Published in Cell (22.08.2019)
Published in Cell (22.08.2019)
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Journal Article
Quantitative Analysis of Culture Using Millions of Digitized Books
Michel, Jean-Baptiste, Shen, Yuan Kui, Aiden, Aviva Presser, Veres, Adrian, Gray, Matthew K, Pickett, Joseph P, Hoiberg, Dale, Clancy, Dan, Norvig, Peter, Orwant, Jon, Pinker, Steven, Nowak, Martin A, Aiden, Erez Lieberman
Published in Science (American Association for the Advancement of Science) (14.01.2011)
Published in Science (American Association for the Advancement of Science) (14.01.2011)
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Journal Article
Cohesin depleted cells rebuild functional nuclear compartments after endomitosis
Cremer, Marion, Brandstetter, Katharina, Maiser, Andreas, Rao, Suhas S. P., Schmid, Volker J., Guirao-Ortiz, Miguel, Mitra, Namita, Mamberti, Stefania, Klein, Kyle N., Gilbert, David M., Leonhardt, Heinrich, Cardoso, M. Cristina, Aiden, Erez Lieberman, Harz, Hartmann, Cremer, Thomas
Published in Nature communications (01.12.2020)
Published in Nature communications (01.12.2020)
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