Data-driven hypothesis weighting increases detection power in genome-scale multiple testing von Ignatiadis, Nikolaos, Klaus, Bernd, Zaugg, Judith B, Huber, Wolfgang

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Enhancers in disease: molecular basis and emerging treatment strategies von Claringbould, Annique, Zaugg, Judith B.

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Transcription factors: Bridge between cell signaling and gene regulation von Weidemüller, Paula, Kholmatov, Maksim, Petsalaki, Evangelia, Zaugg, Judith B.

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Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis von Ranzoni, Anna Maria, Tangherloni, Andrea, Berest, Ivan, Riva, Simone Giovanni, Myers, Brynelle, Strzelecka, Paulina M., Xu, Jiarui, Panada, Elisa, Mohorianu, Irina, Zaugg, Judith B., Cvejic, Ana

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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions von Grubert, Fabian, Zaugg, Judith B., Kasowski, Maya, Ursu, Oana, Spacek, Damek V., Martin, Alicia R., Greenside, Peyton, Srivas, Rohith, Phanstiel, Doug H., Pekowska, Aleksandra, Heidari, Nastaran, Euskirchen, Ghia, Huber, Wolfgang, Pritchard, Jonathan K., Bustamante, Carlos D., Steinmetz, Lars M., Kundaje, Anshul, Snyder, Michael

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Convolutional networks for supervised mining of molecular patterns within cellular context von de Teresa-Trueba, Irene, Goetz, Sara K., Mattausch, Alexander, Stojanovska, Frosina, Zimmerli, Christian E., Toro-Nahuelpan, Mauricio, Cheng, Dorothy W. C., Tollervey, Fergus, Pape, Constantin, Beck, Martin, Diz-Muñoz, Alba, Kreshuk, Anna, Mahamid, Julia, Zaugg, Judith B.

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Landscape of cohesin-mediated chromatin loops in the human genome von Grubert, Fabian, Srivas, Rohith, Spacek, Damek  V, Kasowski, Maya, Ruiz-Velasco, Mariana, Sinnott-Armstrong, Nasa, Greenside, Peyton, Narasimha, Anil, Liu, Qing, Geller, Benjamin, Sanghi, Akshay, Kulik, Michael, Sa, Silin, Rabinovitch, Marlene, Kundaje, Anshul, Dalton, Stephen, Zaugg, Judith B., Snyder, Michael

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Bacterial adaptation through distributed sensing of metabolic fluxes von Heinemann, Matthias, Kotte, Oliver, Zaugg, Judith B

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Basis of gene-specific transcription regulation by the Integrator complex von Sabath, Kevin, Nabih, Amena, Arnold, Christian, Moussa, Rim, Domjan, David, Zaugg, Judith B., Jonas, Stefanie

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Extensive Variation in Chromatin States Across Humans von Kasowski, Maya, Kyriazopoulou-Panagiotopoulou, Sofia, Grubert, Fabian, Zaugg, Judith B., Kundaje, Anshul, Liu, Yuling, Boyle, Alan P., Zhang, Qiangfeng Cliff, Zakharia, Fouad, Spacek, Damek V., Li, Jingjing, Xie, Dan, Olarenn-George, Anthony, Steinmetz, Lars M., Hogenesch, John B., Kellis, Manolis, Batzoglou, Serafim, Snyder, Michael

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TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells von Rasmussen, Kasper D, Berest, Ivan, Keβler, Sandra, Nishimura, Koutarou, Simón-Carrasco, Lucía, Vassiliou, George S, Pedersen, Marianne T, Christensen, Jesper, Zaugg, Judith B, Helin, Kristian

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Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension von Reyes-Palomares, Armando, Gu, Mingxia, Grubert, Fabian, Berest, Ivan, Sa, Silin, Kasowski, Maya, Arnold, Christian, Shuai, Mao, Srivas, Rohith, Miao, Simon, Li, Dan, Snyder, Michael P., Rabinovitch, Marlene, Zaugg, Judith B.

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Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions von Ibarra, Ignacio L., Hollmann, Nele M., Klaus, Bernd, Augsten, Sandra, Velten, Britta, Hennig, Janosch, Zaugg, Judith B.

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Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF von Berest, Ivan, Arnold, Christian, Reyes-Palomares, Armando, Palla, Giovanni, Rasmussen, Kasper Dindler, Giles, Holly, Bruch, Peter-Martin, Huber, Wolfgang, Dietrich, Sascha, Helin, Kristian, Zaugg, Judith B.

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GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks von Kamal, Aryan, Arnold, Christian, Claringbould, Annique, Moussa, Rim, Servaas, Nila H, Kholmatov, Maksim, Daga, Neha, Nogina, Daria, Mueller‐Dott, Sophia, Reyes‐Palomares, Armando, Palla, Giovanni, Sigalova, Olga, Bunina, Daria, Pabst, Caroline, Zaugg, Judith B

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Gene Loops Enhance Transcriptional Directionality von Tan-Wong, Sue Mei, Zaugg, Judith B., Camblong, Jurgi, Xu, Zhenyu, Zhang, David W., Mischo, Hannah E., Ansari, Aseem Z., Luscombe, Nicholas M., Steinmetz, Lars M., Proudfoot, Nick J.

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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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Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters von Trovato, Matteo, Bunina, Daria, Yildiz, Umut, Fernandez-Novel Marx, Nadine, Uckelmann, Michael, Levina, Vita, Perez, Yekaterina, Janeva, Ana, Garcia, Benjamin A., Davidovich, Chen, Zaugg, Judith B., Noh, Kyung-Min

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Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline von Hennrich, Marco L., Romanov, Natalie, Horn, Patrick, Jaeger, Samira, Eckstein, Volker, Steeples, Violetta, Ye, Fei, Ding, Ximing, Poisa-Beiro, Laura, Lai, Mang Ching, Lang, Benjamin, Boultwood, Jacqueline, Luft, Thomas, Zaugg, Judith B., Pellagatti, Andrea, Bork, Peer, Aloy, Patrick, Gavin, Anne-Claude, Ho, Anthony D.

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MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention von Weigel, Bettina, Tegethoff, Jana F., Grieder, Sarah D., Lim, Bryce, Nagarajan, Bhuvaneswari, Liu, Yu-Chao, Truberg, Jule, Papageorgiou, Dimitris, Adrian-Segarra, Juan M., Schmidt, Laura K., Kaspar, Janina, Poisel, Eric, Heinzelmann, Elisa, Saraswat, Manu, Christ, Marleen, Arnold, Christian, Ibarra, Ignacio L., Campos, Joaquin, Krijgsveld, Jeroen, Monyer, Hannah, Zaugg, Judith B., Acuna, Claudio, Mall, Moritz

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