Predictive features of gene expression variation reveal mechanistic link with differential expression von Sigalova, Olga M, Shaeiri, Amirreza, Forneris, Mattia, Furlong, Eileen EM, Zaugg, Judith B

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

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Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity von Khoueiry, Pierre, Girardot, Charles, Ciglar, Lucia, Peng, Pei-Chen, Gustafson, E Hilary, Sinha, Saurabh, Furlong, Eileen Em

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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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To loop or not to loop: what is the role of TADs in enhancer function and gene regulation? von Cavalheiro, Gabriel R, Pollex, Tim, Furlong, Eileen EM

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Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements von Erceg, Jelena, Pakozdi, Tibor, Marco-Ferreres, Raquel, Ghavi-Helm, Yad, Girardot, Charles, Bracken, Adrian P, Furlong, Eileen E M

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The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection von Liu, Jialin, Viales, Rebecca R., Khoueiry, Pierre, Reddington, James P., Girardot, Charles, Furlong, Eileen E. M., Robinson-Rechavi, Marc

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A core transcriptional network for early mesoderm development in Drosophila melanogaster von Sandmann, Thomas, Girardot, Charles, Brehme, Marc, Tongprasit, Waraporn, Stolc, Viktor, Furlong, Eileen E M

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Cis-acting variation is common across regulatory layers but is often buffered during embryonic development von Floc'hlay, Swann, Wong, Emily S., Zhao, Bingqing, Viales, Rebecca R., Thomas-Chollier, Morgane, Thieffry, Denis, Garfield, David A., Furlong, Eileen E. M.

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Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation von Schauer, Tamás, Ghavi‐Helm, Yad, Sexton, Tom, Albig, Christian, Regnard, Catherine, Cavalli, Giacomo, Furlong, Eileen EM, Becker, Peter B

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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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A conserved role for Snail as a potentiator of active transcription von Rembold, Martina, Ciglar, Lucia, Yáñez-Cuna, J Omar, Zinzen, Robert P, Girardot, Charles, Jain, Ankit, Welte, Michael A, Stark, Alexander, Leptin, Maria, Furlong, Eileen E M

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A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development von Sandmann, Thomas, Jensen, Lars J., Jakobsen, Janus S., Karzynski, Michal M., Eichenlaub, Michael P., Bork, Peer, Furlong, Eileen E.M.

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Challenges for modeling global gene regulatory networks during development: Insights from Drosophila von Wilczynski, Bartek, Furlong, Eileen E.M.

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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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Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis von Ciglar, Lucia, Girardot, Charles, Wilczyński, Bartek, Braun, Martina, Furlong, Eileen E M

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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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Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network von Seyres, Denis, Ghavi-Helm, Yad, Junion, Guillaume, Taghli-Lamallem, Ouarda, Guichard, Céline, Röder, Laurence, Girardot, Charles, Furlong, Eileen E M, Perrin, Laurent

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Fragmentation of DNA in a sub-microliter microfluidic sonication device von Tseng, Qingzong, Lomonosov, Alexey M, Furlong, Eileen E M, Merten, Christoph A

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Conservation and divergence in developmental networks: a view from Drosophila myogenesis von Ciglar, Lucia, Furlong, Eileen EM

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