Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3 von Ragvin, Anja, Moro, Enrico, Fredman, David, Navratilova, Pavla, Drivenes, Øyvind, Engström, Pär G, Alonso, M. Eva, Mustienes, Elisa de la Calle, Skarmeta, José Luis Gómez, Tavares, Maria J, Casares, Fernando, Manzanares, Miguel, van Heyningen, Veronica, Molven, Anders, Njølstad, Pål R, Argenton, Francesco, Lenhard, Boris, Becker, Thomas S

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CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression von Franke, Martin, De la Calle-Mustienes, Elisa, Neto, Ana, Almuedo-Castillo, María, Irastorza-Azcarate, Ibai, Acemel, Rafael D., Tena, Juan J., Santos-Pereira, José M., Gómez-Skarmeta, José L.

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The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos von Bogdanović, Ozren, Fernández-Miñán, Ana, Tena, Juan J., de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis

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Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis‐regulatory regions in zebrafish von Bessa, José, Tena, Juan J., de la Calle‐Mustienes, Elisa, Fernández‐Miñán, Ana, Naranjo, Silvia, Fernández, Almudena, Montoliu, Lluis, Akalin, Altuna, Lenhard, Boris, Casares, Fernando, Gómez‐Skarmeta, José Luis

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A Polymorphic Enhancer near GREM1 Influences Bowel Cancer Risk through Differential CDX2 and TCF7L2 Binding von Lewis, Annabelle, Freeman-Mills, Luke, de la Calle-Mustienes, Elisa, Giráldez-Pérez, Rosa María, Davis, Hayley, Jaeger, Emma, Becker, Martin, Hubner, Nina C., Nguyen, Luan N., Zeron-Medina, Jorge, Bond, Gareth, Stunnenberg, Hendrik G., Carvajal, Jaime J., Gomez-Skarmeta, Jose Luis, Leedham, Simon, Tomlinson, Ian

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Active DNA demethylation at enhancers during the vertebrate phylotypic period von Bogdanović, Ozren, Smits, Arne H, de la Calle Mustienes, Elisa, Tena, Juan J, Ford, Ethan, Williams, Ruth, Senanayake, Upeka, Schultz, Matthew D, Hontelez, Saartje, van Kruijsbergen, Ila, Rayon, Teresa, Gnerlich, Felix, Carell, Thomas, Veenstra, Gert Jan C, Manzanares, Miguel, Sauka-Spengler, Tatjana, Ecker, Joseph R, Vermeulen, Michiel, Gómez-Skarmeta, José Luis, Lister, Ryan

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A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins von Letelier, Joaquín, de la Calle-Mustienes, Elisa, Pieretti, Joyce, Naranjo, Silvia, Maeso, Ignacio, Nakamura, Tetsuya, Pascual-Anaya, Juan, Shubin, Neil H., Schneider, Igor, Martinez-Morales, Juan Ramón, Gómez-Skarmeta, José Luis

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Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders von Gómez-Marín, Carlos, Tena, Juan J., Acemel, Rafael D., López-Mayorga, Macarena, Naranjo, Silvia, de la Calle-Mustienes, Elisa, Maeso, Ignacio, Beccari, Leonardo, Aneas, Ivy, Vielmas, Erika, Bovolenta, Paola, Nobrega, Marcelo A., Carvajal, Jaime, Gómez-Skarmeta, José Luis

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The little skate genome and the evolutionary emergence of wing-like fins von 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

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Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis von Bogdanovic, Ozren, Fernandez-Miñán, Ana, Tena, Juan J, de la Calle-Mustienes, Elisa, Hidalgo, Carmen, van Kruysbergen, Ila, van Heeringen, Simon J, Veenstra, Gert Jan C, Gómez-Skarmeta, José Luis

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A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation von Acemel, Rafael D, Tena, Juan J, Irastorza-Azcarate, Ibai, Marlétaz, Ferdinand, Gómez-Marín, Carlos, de la Calle-Mustienes, Elisa, Bertrand, Stéphanie, Diaz, Sergio G, Aldea, Daniel, Aury, Jean-Marc, Mangenot, Sophie, Holland, Peter W H, Devos, Damien P, Maeso, Ignacio, Escrivá, Hector, Gómez-Skarmeta, José Luis

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Deep conservation of wrist and digit enhancers in fish von Gehrke, Andrew R., Schneider, Igor, de la Calle-Mustienes, Elisa, Tena, Juan J., Gomez-Marin, Carlos, Chandran, Mayuri, Nakamura, Tetsuya, Braasch, Ingo, Postlethwait, John H., Gómez-Skarmeta, José Luis, Shubin, Neil H.

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Characterization of new otic enhancers of the pou3f4 gene reveal distinct signaling pathway regulation and spatio-temporal patterns von Robert-Moreno, Àlex, Naranjo, Silvia, de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis, Alsina, Berta

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Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus von Kouwenhoven, Evelyn N, van Heeringen, Simon J, Tena, Juan J, Oti, Martin, Dutilh, Bas E, Alonso, M Eva, de la Calle-Mustienes, Elisa, Smeenk, Leonie, Rinne, Tuula, Parsaulian, Lilian, Bolat, Emine, Jurgelenaite, Rasa, Huynen, Martijn A, Hoischen, Alexander, Veltman, Joris A, Brunner, Han G, Roscioli, Tony, Oates, Emily, Wilson, Meredith, Manzanares, Miguel, Gómez-Skarmeta, José Luis, Stunnenberg, Hendrik G, Lohrum, Marion, van Bokhoven, Hans, Zhou, Huiqing

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Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints von Irimia, Manuel, Tena, Juan J, Alexis, Maria S, Fernandez-Miñan, Ana, Maeso, Ignacio, Bogdanovic, Ozren, de la Calle-Mustienes, Elisa, Roy, Scott W, Gómez-Skarmeta, José L, Fraser, Hunter B

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The emergence of the brain non-CpG methylation system in vertebrates von de Mendoza, Alex, Poppe, Daniel, Buckberry, Sam, Pflueger, Jahnvi, Albertin, Caroline B., Daish, Tasman, Bertrand, Stephanie, de la Calle-Mustienes, Elisa, Gómez-Skarmeta, José Luis, Nery, Joseph R., Ecker, Joseph R., Baer, Boris, Ragsdale, Clifton W., Grützner, Frank, Escriva, Hector, Venkatesh, Byrappa, Bogdanovic, Ozren, Lister, Ryan

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Conserved cross‐interactions in Drosophila and Xenopus between Ras/MAPK signaling and the dual‐specificity phosphatase MKP3 von Gómez, Ana Ruiz, López‐Varea, Ana, Molnar, Cristina, de la Calle‐Mustienes, Elisa, Ruiz‐Gómez, Mar, Gómez‐Skarmeta, José Luis, de Celis, Jose F.

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A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts von de la Calle-Mustienes, Elisa, Feijóo, Cármen Gloria, Manzanares, Miguel, Tena, Juan J, Rodríguez-Seguel, Elisa, Letizia, Annalisa, Allende, Miguel L, Gómez-Skarmeta, José Luis

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An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation von Tena, Juan J., Alonso, M. Eva, de la Calle-Mustienes, Elisa, Splinter, Erik, de Laat, Wouter, Manzanares, Miguel, Gómez-Skarmeta, José Luis

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The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild von Prado-Martinez, Javier, Hernando-Herraez, Irene, Lorente-Galdos, Belen, Dabad, Marc, Ramirez, Oscar, Baeza-Delgado, Carlos, Morcillo-Suarez, Carlos, Alkan, Can, Hormozdiari, Fereydoun, Raineri, Emanuele, Estellé, Jordi, Fernandez-Callejo, Marcos, Valles, Mònica, Ritscher, Lars, Schöneberg, Torsten, de la Calle-Mustienes, Elisa, Casillas, Sònia, Rubio-Acero, Raquel, Melé, Marta, Engelken, Johannes, Caceres, Mario, Gomez-Skarmeta, Jose Luis, Gut, Marta, Bertranpetit, Jaume, Gut, Ivo G, Abello, Teresa, Eichler, Evan E, Mingarro, Ismael, Lalueza-Fox, Carles, Navarro, Arcadi, Marques-Bonet, Tomas

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