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[FG] Zaugg Judith

Publications

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Sigalova, O.M. et al. (2025) ‘Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis’, Genome Research [Preprint]. Available at: https://doi.org/10.1101/gr.279652.124.

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Barzaghi, G., Krebs, A.R. and Zaugg, J.B. (2025) ‘FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.03.31.646464.

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Baderna, V. et al. (2025) ‘Cumulative TF binding and H3K27 Acetylation drive enhancer activation frequency’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2025.03.26.645413.

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Sigalova, O.M. et al. (2024) ‘Contextualising transcription factor binding during embryogenesis using natural sequence variation’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.10.24.619975.

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Lim, B. et al. (2024) ‘Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.09.10.612045.

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Sabath, K. et al. (2024) ‘Basis of gene-specific transcription regulation by the Integrator complex’, Molecular Cell, 84(13), pp. 2525–2541.e12. Available at: https://doi.org/10.1016/j.molcel.2024.05.027.

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Costea, J. et al. (2024) ‘Role of Stem-Like Cells in Chemotherapy Resistance and Relapse in pediatric T Cell Acute Lymphoblastic Leukemia’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.06.24.600391.

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Lindenhofer, D. et al. (2024) ‘Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.05.31.596895.

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Lorenzo, J.P. et al. (2024) ‘APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation’, Proceedings of the National Academy of Sciences of the United States of America, 121(17). Available at: https://doi.org/10.1073/pnas.2312330121.

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Mathioudaki, A. et al. (2024) ‘The remission status of AML patients after allo-HCT is associated with a distinct single-cell bone marrow T-cell signature’, Blood, 143(13), pp. 1269–1281. Available at: https://doi.org/10.1182/blood.2023021815.

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Hauth, A. et al. (2024) ‘Escape from X inactivation is directly modulated by levels of Xist non-coding RNA’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.02.22.581559.

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Daga, N. et al. (2024) ‘Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2024.01.11.575022.

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Türk, L. et al. (2024) ‘Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation’, Frontiers in Immunology, 15. Available at: https://doi.org/10.3389/fimmu.2024.1285798.

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Lobato-Moreno, S. et al. (2023) ‘Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.12.26.573253.

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Fitzgerald, D. et al. (2023) ‘A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2023.11.06.565756.

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Kamal, A. et al. (2023) ‘GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks’, Molecular Systems Biology, 19(6). Available at: https://doi.org/10.15252/msb.202311627.

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Weigel, B. et al. (2023) ‘MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention’, Molecular Psychiatry, 28(5), pp. 2122–2135. Available at: https://doi.org/10.1038/s41380-023-01959-7.

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de Teresa-Trueba, I. et al. (2023) ‘Convolutional networks for supervised mining of molecular patterns within cellular context’, Nature Methods, 20(2), pp. 284–294. Available at: https://doi.org/10.1038/s41592-022-01746-2.

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Serina Secanechia, Y.N. et al. (2022) ‘Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition’, Scientific Reports, 12(1). Available at: https://doi.org/10.1038/s41598-022-20906-0.

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Zaugg, J.B. et al. (2022) ‘Current challenges in understanding the role of enhancers in disease’, Nature Structural and Molecular Biology, 29(12), pp. 1148–1158. Available at: https://doi.org/10.1038/s41594-022-00896-3.

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Bruch, P.-M. et al. (2022) ‘Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL’, Molecular Systems Biology, 18(8). Available at: https://doi.org/10.15252/msb.202110855.

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Ibarra, I.L. et al. (2022) ‘Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements’, Molecular Systems Biology, 18(8). Available at: https://doi.org/10.15252/msb.202110473.

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He, L. et al. (2022) ‘CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia’, EMBO Molecular Medicine, 14(4). Available at: https://doi.org/10.15252/emmm.202114990.

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Kleinendorst, R.W.D. et al. (2021) ‘Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting’, Nature Protocols, 16(12), pp. 5673–5706. Available at: https://doi.org/10.1038/s41596-021-00630-1.

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Weidemüller, P. et al. (2021) ‘Transcription factors: Bridge between cell signaling and gene regulation’, Proteomics, 21(23-24). Available at: https://doi.org/10.1002/pmic.202000034.

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Claringbould, A. and Zaugg, J.B. (2021) ‘Enhancers in disease: molecular basis and emerging treatment strategies’, Trends in Molecular Medicine, 27(11), pp. 1060–1073. Available at: https://doi.org/10.1016/j.molmed.2021.07.012.

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Lai, M.C. et al. (2021) ‘Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.09.03.458728.

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Ibarra, I.L. et al. (2021) ‘Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements’. Cold Spring Harbor Laboratory. Available at: https://doi.org/10.1101/2021.05.28.446128.

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Scheller, M. et al. (2021) ‘Hotspot DNMT3A mutations in clonal hematopoiesis and acute myeloid leukemia sensitize cells to azacytidine via viral mimicry response’, Nature Cancer, 2(5), pp. 527–544. Available at: https://doi.org/10.1038/s43018-021-00213-9.

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Ranzoni, A.M. et al. (2021) ‘Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis’, Cell Stem Cell, 28(3), pp. 472–487.e7. Available at: https://doi.org/10.1016/j.stem.2020.11.015.

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Ibarra, I.L. et al. (2020) ‘Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions’, Nature Communications, 11(1). Available at: https://doi.org/10.1038/s41467-019-13888-7.

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Reyes-Palomares, A. et al. (2020) ‘Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension’, Nature Communications, 11(1). Available at: https://doi.org/10.1038/s41467-020-15463-x.

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Sigalova, O.M. et al. (2020) ‘Predictive features of gene expression variation reveal mechanistic link with differential expression’, Molecular Systems Biology, 16(8). Available at: https://doi.org/10.15252/msb.20209539.

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Grubert, F. et al. (2020) ‘Landscape of cohesin-mediated chromatin loops in the human genome’, Nature, 583(7818), pp. 737–743. Available at: https://doi.org/10.1038/s41586-020-2151-x.

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Bunina, D. et al. (2020) ‘Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons’, Cell Systems, 10(6), pp. 480–494.e8. Available at: https://doi.org/10.1016/j.cels.2020.05.003.

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Berest, I. et al. (2019) ‘Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF’, Cell Reports, 29(10), pp. 3147–3159.e12. Available at: https://doi.org/10.1016/j.celrep.2019.10.106.

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Garg, S. et al. (2019) ‘Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML’, Blood, 134(3), pp. 263–276. Available at: https://doi.org/10.1182/blood.2018862383.

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Rasmussen, K.D. et al. (2019) ‘TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells’, Genome Research, 29(4), pp. 564–575. Available at: https://doi.org/10.1101/gr.239277.118.

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Hennrich, M.L. et al. (2018) ‘Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline’, Nature Communications, 9(1). Available at: https://doi.org/10.1038/s41467-018-06353-4.

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Ruiz-Velasco, M. et al. (2017) ‘CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals’, Cell Systems, 5(6), pp. 628–637.e6. Available at: https://doi.org/10.1016/j.cels.2017.10.018.

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Ruiz-Velasco, M. and Zaugg, J.B. (2017) ‘Structure meets function: How chromatin organisation conveys functionality’, Current Opinion in Systems Biology, 1, pp. 129–136. Available at: https://doi.org/10.1016/j.coisb.2017.01.003.

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Arnold, C., Bhat, P. and Zaugg, J.B. (2016) ‘SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data’, Bioinformatics, 32(15), pp. 2359–2360. Available at: https://doi.org/10.1093/bioinformatics/btw127.

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Ignatiadis, N. et al. (2016) ‘Data-driven hypothesis weighting increases detection power in genome-scale multiple testing’, Nature Methods, 13(7), pp. 577–580. Available at: https://doi.org/10.1038/nmeth.3885.

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Grubert, F. et al. (2015) ‘Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions’, Cell, 162(5), pp. 1051–1065. Available at: https://doi.org/10.1016/j.cell.2015.07.048.

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Kasowski, M. et al. (2013) ‘Extensive variation in chromatin states across humans’, Science, 342(6159), pp. 750–752. Available at: https://doi.org/10.1126/science.1242510.

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