Data-driven hypothesis weighting increases detection power in genome-scale multiple testing
Ignatiadis, Nikolaos, Klaus, Bernd, Zaugg, Judith B, Huber, Wolfgang
Published in Nature methods (01.07.2016)
Published in Nature methods (01.07.2016)
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Journal Article
Transcription factors: Bridge between cell signaling and gene regulation
Weidemüller, Paula, Kholmatov, Maksim, Petsalaki, Evangelia, Zaugg, Judith B.
Published in Proteomics (Weinheim) (01.12.2021)
Published in Proteomics (Weinheim) (01.12.2021)
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Journal Article
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
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
Published in Cell stem cell (04.03.2021)
Published in Cell stem cell (04.03.2021)
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Journal Article
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
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
Published in Cell (27.08.2015)
Published in Cell (27.08.2015)
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Journal Article
Convolutional networks for supervised mining of molecular patterns within cellular context
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.
Published in Nature methods (01.02.2023)
Published in Nature methods (01.02.2023)
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Journal Article
Landscape of cohesin-mediated chromatin loops in the human genome
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
Published in Nature (London) (30.07.2020)
Published in Nature (London) (30.07.2020)
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Journal Article
Basis of gene-specific transcription regulation by the Integrator complex
Sabath, Kevin, Nabih, Amena, Arnold, Christian, Moussa, Rim, Domjan, David, Zaugg, Judith B., Jonas, Stefanie
Published in Molecular cell (11.07.2024)
Published in Molecular cell (11.07.2024)
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Journal Article
Extensive Variation in Chromatin States Across Humans
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
Published in Science (American Association for the Advancement of Science) (08.11.2013)
Published in Science (American Association for the Advancement of Science) (08.11.2013)
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Journal Article
TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
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
Published in Genome research (01.04.2019)
Published in Genome research (01.04.2019)
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Journal Article
Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension
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.
Published in Nature communications (03.04.2020)
Published in Nature communications (03.04.2020)
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Journal Article
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions
Ibarra, Ignacio L., Hollmann, Nele M., Klaus, Bernd, Augsten, Sandra, Velten, Britta, Hennig, Janosch, Zaugg, Judith B.
Published in Nature communications (08.01.2020)
Published in Nature communications (08.01.2020)
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Journal Article
Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF
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.
Published in Cell reports (Cambridge) (03.12.2019)
Published in Cell reports (Cambridge) (03.12.2019)
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Journal Article
GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks
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
Published in Molecular systems biology (12.06.2023)
Published in Molecular systems biology (12.06.2023)
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Journal Article
Gene Loops Enhance Transcriptional Directionality
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.
Published in Science (American Association for the Advancement of Science) (02.11.2012)
Published in Science (American Association for the Advancement of Science) (02.11.2012)
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Journal Article
Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters
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
Published in Nature communications (30.08.2024)
Published in Nature communications (30.08.2024)
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Journal Article
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline
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.
Published in Nature communications (01.10.2018)
Published in Nature communications (01.10.2018)
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Journal Article
Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy
Gehre, Maja, Bunina, Daria, Sidoli, Simone, Lübke, Marlena J., Diaz, Nichole, Trovato, Matteo, Garcia, Benjamin A., Zaugg, Judith B., Noh, Kyung-Min
Published in Nature genetics (01.03.2020)
Published in Nature genetics (01.03.2020)
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