Transcription factors: from enhancer binding to developmental control von Spitz, François, Furlong, Eileen E. M.

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The role of transcription in shaping the spatial organization of the genome von van Steensel, Bas, Furlong, Eileen E. M.

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Developmental enhancers and chromosome topology von Furlong, Eileen E M, Levine, Michael

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The road ahead in genetics and genomics von McGuire, Amy L., Gabriel, Stacey, Tishkoff, Sarah A., Wonkam, Ambroise, Chakravarti, Aravinda, Furlong, Eileen E. M., Treutlein, Barbara, Meissner, Alexander, Chang, Howard Y., López-Bigas, Núria, Segal, Eran, Kim, Jin-Soo

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The cis-regulatory dynamics of embryonic development at single-cell resolution von Cusanovich, Darren A., Reddington, James P., Garfield, David A., Daza, Riza M., Aghamirzaie, Delasa, Marco-Ferreres, Raquel, Pliner, Hannah A., Christiansen, Lena, Qiu, Xiaojie, Steemers, Frank J., Trapnell, Cole, Shendure, Jay, Furlong, Eileen E. M.

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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development von Bonn, Stefan, Zinzen, Robert P, Girardot, Charles, Gustafson, E Hilary, Perez-Gonzalez, Alexis, Delhomme, Nicolas, Ghavi-Helm, Yad, Wilczyński, Bartek, Riddell, Andrew, Furlong, Eileen E M

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Combinatorial binding predicts spatio-temporal cis -regulatory activity von Gagneur, Julien, Zinzen, Robert P, Girardot, Charles, Furlong, Eileen E. M, Braun, Martina

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Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression von Ghavi-Helm, Yad, Jankowski, Aleksander, Meiers, Sascha, Viales, Rebecca R., Korbel, Jan O., Furlong, Eileen E. M.

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A Versatile, Low-Cost, Multiway Microfluidic Sorter for Droplets, Cells, and Embryos von Utharala, Ramesh, Tseng, Qingzong, Furlong, Eileen E. M, Merten, Christoph A

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Conservation of transcription factor binding specificities across 600 million years of bilateria evolution von Nitta, Kazuhiro R, Jolma, Arttu, Yin, Yimeng, Morgunova, Ekaterina, Kivioja, Teemu, Akhtar, Junaid, Hens, Korneel, Toivonen, Jarkko, Deplancke, Bart, Furlong, Eileen E M, Taipale, Jussi

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Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase? von Mir, Mustafa, Bickmore, Wendy, Furlong, Eileen E M, Narlikar, Geeta

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Enhancer loops appear stable during development and are associated with paused polymerase von Ghavi-Helm, Yad, Klein, Felix A., Pakozdi, Tibor, Ciglar, Lucia, Noordermeer, Daan, Huber, Wolfgang, Furlong, Eileen E. M.

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scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation von Heinen, Tobias, Secchia, Stefano, Reddington, James P, Zhao, Bingqing, Furlong, Eileen E M, Stegle, Oliver

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Model-based method for transcription factor target identification with limited data von Honkela, Antti, Girardot, Charles, Gustafson, E. Hilary, Liu, Ya-Hsin, Furlong, Eileen E.M, Lawrence, Neil D, Rattray, Magnus

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Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes von Mbodj, Abibatou, Gustafson, E Hilary, Ciglar, Lucia, Junion, Guillaume, Gonzalez, Aitor, Girardot, Charles, Perrin, Laurent, Furlong, Eileen E M, Thieffry, Denis

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Gene Expression during the Life Cycle of Drosophila melanogaster von Arbeitman, Michelle N., Eileen E. M. Furlong, Imam, Farhad, Johnson, Eric, Null, Brian H., Baker, Bruce S., Krasnow, Mark A., Scott, Matthew P., Davis, Ronald W., White, Kevin P.

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Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP von Bonn, Stefan, Zinzen, Robert P, Perez-Gonzalez, Alexis, Riddell, Andrew, Gavin, Anne-Claude, Furlong, Eileen E M

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Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development von Zhou, Jian, Schor, Ignacio E, Yao, Victoria, Theesfeld, Chandra L, Marco-Ferreres, Raquel, Tadych, Alicja, Furlong, Eileen E M, Troyanskaya, Olga G

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Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state von Wilczynski, Bartek, Liu, Ya-Hsin, Yeo, Zhen Xuan, Furlong, Eileen E M

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Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers von Girardot, Charles, Scholtalbers, Jelle, Sauer, Sajoscha, Su, Shu-Yi, Furlong, Eileen E M

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