Prof. Dr. Judith Zaugg

Sigalova, O. M., Forneris, M., Stojanovska, F., Zhao, B., Viales, R. R., Rabinowitz, A., Hammal, F., Ballester, B., Zaugg, J. B., & Furlong, E. E. M. (2025). Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis [Journal-article]. Genome Research. https://doi.org/10.1101/gr.279652.124

Barzaghi, G., Krebs, A. R., & Zaugg, J. B. (2025). FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.03.31.646464

Baderna, V., Barzaghi, G., Kleinendorst, R., Chatsirisupachai, K., Moniot-Perron, L., Schopp, M., Hochepied, T., Libert, C., Odom, D. T., Zaugg, J. B., & Krebs, A. R. (2025). Cumulative TF binding and H3K27 Acetylation drive enhancer activation frequency [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.03.26.645413

Sigalova, O. M., Forneris, M., Stojanovska, F., Zhao, B., Viales, R. R., Rabinowitz, A., Hamal, F., Ballester, B., Zaugg, J. B., & Furlong, E. E. (2024). Contextualising transcription factor binding during embryogenesis using natural sequence variation [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.10.24.619975

Lim, B., Kamal, A., Gomez Ramos, B., Adrian Segarra, J., Ibarra, I., Dignas, L., Kindinger, T., Volz, K., Rahbari, M., Rahbari, N., Poisel, E., Kafetzopoulou, K., Bose, L., Breinig, M., Heide, D., Gallage, S., Barragan Avila, J., Wiethoff, H., Berest, I., et al. (2024). Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumourigenesis [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.09.10.612045

Sabath, K., Nabih, A., Arnold, C., Moussa, R., Domjan, D., Zaugg, J. B., & Jonas, S. (2024). Basis of gene-specific transcription regulation by the Integrator complex. Molecular Cell, 84(13), 2525–2541. https://doi.org/10.1016/j.molcel.2024.05.027

Costea, J., Rauwolf, K. K., Zafferani, P., Rausch, T., Mathioudaki, A., Zaugg, J., Schrappe, M., Eckert, C., Escherich, G., Bourquin, J. P., Bornhauser, B., Kulozik, A. E., & Korbel, J. O. (2024). Role of Stem-Like Cells in Chemotherapy Resistance and Relapse in pediatric T Cell Acute Lymphoblastic Leukemia [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.06.24.600391

Lindenhofer, D., Bauman, J. R., Hawkins, J. A., Fitzgerald, D., Yildiz, U., Marttinen, J. M., Kueblbeck, M., Zaugg, J. B., Noh, K.-M., Dietrich, S., Huber, W., Stegle, O., & Steinmetz, L. M. (2024). Functional phenotyping of genomic variants using multiomic scDNA-scRNA-seq [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.05.31.596895

Lorenzo, J. P., Molla, L., Amro, E. M., Ibarra, I. L., Ruf, S., Neber, C., Gkougkousis, C., Ridani, J., Subramani, P. G., Boulais, J., Harjanto, D., Vonica, A., Di Noia, J. M., Dieterich, C., Zaugg, J. B., & Papavasiliou, F. N. (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). https://doi.org/10.1073/pnas.2312330121

Mathioudaki, A., Wang, X., Sedloev, D., Huth, R., Kamal, A., Hundemer, M., Liu, Y., Vasileiou, S., Lulla, P., Müller-Tidow, C., Dreger, P., Luft, T., Sauer, T., Schmitt, M., Zaugg, J. B., & Pabst, C. (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), 1269–1281. https://doi.org/10.1182/blood.2023021815

Hauth, A., Panten, J., Kneuss, E., Picard, C., Servant, N., Rall, I., Pérez-Rico, Y. A., Clerquin, L., Servaas, N., Villacorta, L., Jung, F., Luong, C., Chang, H. Y., Zaugg, J. B., Stegle, O., Odom, D. T., Loda, A., & Heard, E. (2024). Escape from X inactivation is directly modulated by levels of Xist non-coding RNA [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.02.22.581559

Miyazawa, H., Rada, J., Sanchez, P. G. L., Esposito, E., Bunina, D., Girardot, C., Zaugg, J., & Aulehla, A. (2024). Glycolysis–Wnt signaling axis tunes developmental timing of embryo segmentation [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.01.22.576629

Daga, N., Servaas, N. H., Kisand, K., Moonen, D., Arnold, C., Reyes-Palomares, A., Kaleviste, E., Kingo, K., Kuuse, R., Ulst, K., Steinmetz, L., Peterson, P., Nakic, N., & Zaugg, J. B. (2024). Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.01.11.575022

Türk, L., Filippov, I., Arnold, C., Zaugg, J., Tserel, L., Kisand, K., & Peterson, P. (2024). Cytotoxic CD8+ Temra cells show loss of chromatin accessibility at genes associated with T cell activation. Frontiers in Immunology, 15. https://doi.org/10.3389/fimmu.2024.1285798

Lobato-Moreno, S., Yildiz, U., Claringbould, A., Servaas, N. H., Vlachou, E. P., Arnold, C., Bauersachs, H. G., Campos-Fornés, V., Prummel, K. D., Noh, K. M., Marttinen, M., & Zaugg, J. B. (2023). Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.12.26.573253

Fitzgerald, D., Roider, T., Baertsch, M.-A., Kibler, A., Horlova, A., Chung, E., Vöhringer, H., Mathioudaki, A., Budeus, B., Passerini, V., Knoll, M., Mammen, J., Li, L., Caillé, L., Czernilofsky, F., Bruch, P.-M., Liebers, N., Meyer-Bender, M., Weigert, O., et al. (2023). A single-cell multi-omic and spatial atlas of B cell lymphomas reveals differentiation drives intratumor heterogeneity [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.11.06.565756

Lazareva, O., Mallm, J.-P., Simovic-Lorenz, M., Philippos, G., Sant, P., Parekh, U., Hammann, L., Li, A., Yildiz, U., Marttinen, M., Zaugg, J., Noh, K. M., Stegle, O., & Ernst, A. (2023). HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.10.09.561487

Kamal, A., Arnold, C., Claringbould, A., Moussa, R., Servaas, N. H., Kholmatov, M., Daga, N., Nogina, D., Mueller-Dott, S., Reyes-Palomares, A., Palla, G., Sigalova, O., Bunina, D., Pabst, C., & Zaugg, J. B. (2023). GRaNIE and GRaNPA: inference and evaluation of enhancer-mediated gene regulatory networks. Molecular Systems Biology, 19(6). https://doi.org/10.15252/msb.202311627

Trovato, M., Bunina, D., Yildiz, U., Marx, N. F.-N., Uckelmann, M., Levina, V., Kori, Y., Janeva, A., Garcia, B. A., Davidovich, C., Zaugg, J. B., & Noh, K.-M. (2023). Histone H3.3 lysine 9 and 27 control repressive chromatin states at cryptic cis -regulatory elements and bivalent promoters in mouse embryonic stem cells [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.05.08.539859

Weigel, B., Tegethoff, J. F., Grieder, S. D., Lim, B., Nagarajan, B., Liu, Y.-C., Truberg, J., Papageorgiou, D., Adrian-Segarra, J. M., Schmidt, L. K., Kaspar, J., Poisel, E., Heinzelmann, E., Saraswat, M., Christ, M., Arnold, C., Ibarra, I. L., Campos, J., Krijgsveld, J., 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), 2122–2135. https://doi.org/10.1038/s41380-023-01959-7

de Teresa-Trueba, I., Goetz, S. K., Mattausch, A., Stojanovska, F., Zimmerli, C. E., Toro-Nahuelpan, M., Cheng, D. W. C., Tollervey, F., Pape, C., Beck, M., Diz-Muñoz, A., Kreshuk, A., Mahamid, J., & Zaugg, J. B. (2023). Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods, 20(2), 284–294. https://doi.org/10.1038/s41592-022-01746-2

Serina Secanechia, Y. N., Bergiers, I., Rogon, M., Arnold, C., Descostes, N., Le, S., López-Anguita, N., Ganter, K., Kapsali, C., Bouilleau, L., Gut, A., Uzuotaite, A., Aliyeva, A., Zaugg, J. B., & Lancrin, C. (2022). Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-20906-0

Zaugg, J. B., Sahlén, P., Andersson, R., Alberich-Jorda, M., de Laat, W., Deplancke, B., Ferrer, J., Mandrup, S., Natoli, G., Plewczynski, D., Rada-Iglesias, A., & Spicuglia, S. (2022). Current challenges in understanding the role of enhancers in disease. Nature Structural and Molecular Biology, 29(12), 1148–1158. https://doi.org/10.1038/s41594-022-00896-3

Kafkia, E., Andres-Pons, A., Ganter, K., Seiler, M., Smith, T. S., Andrejeva, A., Jouhten, P., Pereira, F., Franco, C., Kuroshchenkova, A., Leone, S., Sawarkar, R., Boston, R., Thaventhiran, J., Zaugg, J. B., Lilley, K. S., Lancrin, C., Beck, M., & Patil, K. R. (2022). Operation of a TCA cycle subnetwork in the mammalian nucleus. Science Advances, 8(35). https://doi.org/10.1126/sciadv.abq5206

Bruch, P.-M., Giles, H. A., Kolb, C., Herbst, S. A., Becirovic, T., Roider, T., Lu, J., Scheinost, S., Wagner, L., Huellein, J., Berest, I., Kriegsmann, M., Kriegsmann, K., Zgorzelski, C., Dreger, P., Zaugg, J. B., Müller-Tidow, C., Zenz, T., Huber, W., & Dietrich, S. (2022). Drug-microenvironment perturbations reveal resistance mechanisms and prognostic subgroups in CLL. Molecular Systems Biology, 18(8). https://doi.org/10.15252/msb.202110855

Ibarra, I. L., Ratnu, V. S., Gordillo, L., Hwang, I.-Y., Mariani, L., Weinand, K., Hammarén, H. M., Heck, J., Bulyk, M. L., Savitski, M. M., Zaugg, J. B., & Noh, K.-M. (2022). Comparative chromatin accessibility upon BDNF stimulation delineates neuronal regulatory elements. Molecular Systems Biology, 18(8). https://doi.org/10.15252/msb.202110473

He, L., Arnold, C., Thoma, J., Rohde, C., Kholmatov, M., Garg, S., Hsiao, C.-C., Viol, L., Zhang, K., Sun, R., Schmidt, C., Janssen, M., MacRae, T., Huber, K., Thiede, C., Hébert, J., Sauvageau, G., Spratte, J., Fluhr, H., 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). https://doi.org/10.15252/emmm.202114990

Poisa-Beiro, L., Landry, J. J. M., Raffel, S., Tanaka, M., Zaugg, J., Gavin, A.-C., & Ho, A. D. (2022). Glucose Metabolism and Aging of Hematopoietic Stem and Progenitor Cells. International Journal of Molecular Sciences, 23(6). https://doi.org/10.3390/ijms23063028

Kamal, A., Arnold, C., Claringbould, A., Moussa, R., Servaas, N. H., Kholmatov, M., Daga, N., Nogina, D., Mueller-Dott, S., Reyes-Palomares, A., Palla, G., Sigalova, O., Bunina, D., Pabst, C., & Zaugg, J. B. (2021). GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.12.18.473290

Kleinendorst, R. W. D., Barzaghi, G., Smith, M. L., Zaugg, J. B., & Krebs, A. R. (2021). Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting. Nature Protocols, 16(12), 5673–5706. https://doi.org/10.1038/s41596-021-00630-1

Weidemüller, P., Kholmatov, M., Petsalaki, E., & Zaugg, J. B. (2021). Transcription factors: Bridge between cell signaling and gene regulation. Proteomics, 21(23-24). https://doi.org/10.1002/pmic.202000034

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

Lai, M. C., Ruiz-Velasco, M., Arnold, C., Sigalova, O., Bunina, D., Berest, I., Ding, X., Hennrich, M. L., Poisa-Beiro, L., Claringbould, A., Mathioudaki, A., Pabst, C., Ho, A. D., Gavin, A.-C., & Zaugg, J. B. (2021). Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.03.458728

Bruch, P.-M., Giles, H. A. R., Kolb, C., Herbst, S. A., Becirovic, T., Roider, T., Lu, J., Scheinost, S., Wagner, L., Huellein, J., Berest, I., Kriegsmann, M., Kriegsmann, K., Zgorzelski, C., Dreger, P., Zaugg, J. B., Müller-Tidow, C., Zenz, T., Huber, W., & Dietrich, S. (2021). Combinatorial drug-microenvironment interaction mapping reveals cell-extrinsic drug resistance mechanisms and clinically relevant patient subgroups in CLL [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.07.23.453514

Kim, K.-P., Li, C., Bunina, D., Jeong, H.-W., Ghelman, J., Yoon, J., Shin, B., Park, H., Han, D. W., Zaugg, J. B., Kim, J., Kuhlmann, T., Adams, R. H., Noh, K.-M., Goldman, S. A., & Schöler, H. R. (2021). Donor cell memory confers a metastable state of directly converted cells. Cell Stem Cell, 28(7), 1291–1306. https://doi.org/10.1016/j.stem.2021.02.023

Ibarra, I. L., Ratnu, V. S., Gordillo, L., Hwang, I.-Y., Mariani, L., Weinand, K., Hammarén, H. M., Bulyk, M. L., Savitski, M. M., Zaugg, J. B., & Noh, K.-M. (2021). Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.05.28.446128

Scheller, M., Ludwig, A. K., Göllner, S., Rohde, C., Krämer, S., Stäble, S., Janssen, M., Müller, J.-A., He, L., Bäumer, N., Arnold, C., Gerß, J., Schönung, M., Thiede, C., Niederwieser, C., Niederwieser, D., Serve, H., Berdel, W. E., Thiem, U., 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), 527–544. https://doi.org/10.1038/s43018-021-00213-9

Guha, R., Mathioudaki, A., Doumbo, S., Doumtabe, D., Skinner, J., Arora, G., Siddiqui, S., Li, S., Kayentao, K., Ongoiba, A., Zaugg, J., Traore, B., & Crompton, P. D. (2021). Plasmodium falciparum malaria drives epigenetic reprogramming of human monocytes toward a regulatory phenotype. PLoS Pathogens, 17(4 April). https://doi.org/10.1371/journal.ppat.1009430

Ranzoni, A. M., Tangherloni, A., Berest, I., Riva, S. G., Myers, B., Strzelecka, P. M., Xu, J., Panada, E., Mohorianu, I., Zaugg, J. B., & Cvejic, A. (2021). Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell, 28(3), 472–487. https://doi.org/10.1016/j.stem.2020.11.015

Ibarra, I. L., Hollmann, N. M., Klaus, B., Augsten, S., Velten, B., Hennig, J., & Zaugg, J. B. (2020). Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Nature Communications, 11(1). https://doi.org/10.1038/s41467-019-13888-7

Reyes-Palomares, A., Gu, M., Grubert, F., Berest, I., Sa, S., Kasowski, M., Arnold, C., Shuai, M., Srivas, R., Miao, S., Li, D., Snyder, M. P., Rabinovitch, M., & Zaugg, J. B. (2020). Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-15463-x

Kafkia, E., Andres-Pons, A., Ganter, K., Seiler, M., Jouhten, P., Pereira, F., Zaugg, J. B., Lancrin, C., Beck, M., & Patil, K. R. (2020). Operation of a TCA cycle subnetwork in the mammalian nucleus [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.22.393413

Sigalova, O. M., Shaeiri, A., Forneris, M., Furlong, E. E., & Zaugg, J. B. (2020). Predictive features of gene expression variation reveal mechanistic link with differential expression. Molecular Systems Biology, 16(8). https://doi.org/10.15252/msb.20209539

Grubert, F., Srivas, R., Spacek, D. V., Kasowski, M., Ruiz-Velasco, M., Sinnott-Armstrong, N., Greenside, P., Narasimha, A., Liu, Q., Geller, B., Sanghi, A., Kulik, M., Sa, S., Rabinovitch, M., Kundaje, A., Dalton, S., Zaugg, J. B., & Snyder, M. (2020). Landscape of cohesin-mediated chromatin loops in the human genome. Nature, 583(7818), 737–743. https://doi.org/10.1038/s41586-020-2151-x

Bunina, D., Abazova, N., Diaz, N., Noh, K.-M., Krijgsveld, J., & Zaugg, J. B. (2020). Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Systems, 10(6), 480–494. https://doi.org/10.1016/j.cels.2020.05.003

Maria Ranzoni, A., Tangherloni, A., Berest, I., Riva, S. G., Myers, B., Strzelecka, P. M., Xu, J., Panada, E., Mohorianu, I., Zaugg, J. B., & Cvejic, A. (2020). Integrative Single-cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Haematopoiesis [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.05.06.080259

Gehre, M., Bunina, D., Sidoli, S., Lübke, M. J., Diaz, N., Trovato, M., Garcia, B. A., Zaugg, J. B., & Noh, K.-M. (2020). Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nature Genetics, 52(3), 273–282. https://doi.org/10.1038/s41588-020-0586-5

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Giles, H., Bruch, P.-M., Huber, W., Dietrich, S., Helin, K., & Zaugg, J. B. (2019). Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Reports, 29(10), 3147–3159. https://doi.org/10.1016/j.celrep.2019.10.106

Garg, S., Reyes-Palomares, A., He, L., Bergeron, A., Lavallée, V.-P., Lemieux, S., Gendron, P., Rohde, C., Xia, J., Jagdhane, P., Müller-Tidow, C., Lipka, D. B., Imren, S., Humphries, R. K., Waskow, C., Vick, B., Jeremias, I., Richard-Carpentier, G., Hébert, J., 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), 263–276. https://doi.org/10.1182/blood.2018862383

Rasmussen, K. D., Berest, I., Keβler, S., Nishimura, K., Simón-Carrasco, L., Vassiliou, G. S., Pedersen, M. T., Christensen, J., Zaugg, J. B., & Helin, K. (2019). TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research, 29(4), 564–575. https://doi.org/10.1101/gr.239277.118

Hennrich, M. L., Romanov, N., Horn, P., Jaeger, S., Eckstein, V., Steeples, V., Ye, F., Ding, X., Poisa-Beiro, L., Lai, M. C., Lang, B., Boultwood, J., Luft, T., Zaugg, J. B., Pellagatti, A., Bork, P., Aloy, P., Gavin, A.-C., & Ho, A. D. (2018). Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-06353-4

Berest, I., Arnold, C., Reyes-Palomares, A., Palla, G., Rasmussen, K. D., Helin, K., & Zaugg, J. B. (2018). Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors: diffTF [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/368498

Ruiz-Velasco, M., Kumar, M., Lai, M. C., Bhat, P., Solis-Pinson, A. B., Reyes, A., Kleinsorg, S., Noh, K.-M., Gibson, T. J., & Zaugg, J. B. (2017). CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell Systems, 5(6), 628–637. https://doi.org/10.1016/j.cels.2017.10.018

Lai, M. C., Bechy, A.-L., Denk, F., Collins, E., Gavriliouk, M., Zaugg, J. B., Ryan, B. J., Wade-Martins, R., & Caffrey, T. M. (2017). Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders. Molecular Neurodegeneration, 12(1). https://doi.org/10.1186/s13024-017-0224-6

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

Cakiroglu, S. A., Zaugg, J. B., & Luscombe, N. M. (2016). Backmasking in the yeast genome: Encoding overlapping information for protein-coding and RNA degradation. Nucleic Acids Research, 44(17), 8065–8072. https://doi.org/10.1093/nar/gkw683

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

Ignatiadis, N., Klaus, B., Zaugg, J. B., & Huber, W. (2016). Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nature Methods, 13(7), 577–580. https://doi.org/10.1038/nmeth.3885

Zaugg LK, Lenherr P, Zaugg JB, Weiger R, & Krastl G. (2016). Influence of the bleaching interval on the luminosity of long-term discolored enamel-dentin discs. Clinical Oral Investigations, 20(3), 451–458. https://doi.org/10.1007/s00784-015-1545-x

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., Heidari, N., Euskirchen, G., Huber, W., Pritchard, J. K., Bustamante, C. D., Steinmetz, L. M., Kundaje, A., & Snyder, M. (2015). Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell, 162(5), 1051–1065. https://doi.org/10.1016/j.cell.2015.07.048

Castelnuovo, M., Zaugg, J. B., Guffanti, E., Maffioletti, A., Camblong, J., Xu, Z., Clauder-Münster, S., Steinmetz, L. M., Luscombe, N. M., & Stutz, F. (2014). Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Nucleic Acids Research, 42(7), 4348–4362. https://doi.org/10.1093/nar/gku100

Kasowski, M., Kyriazopoulou-Panagiotopoulou, S., Grubert, F., Zaugg, J. B., Kundaje, A., Liu, Y., Boyle, A. P., Zhang, Q. C., Zakharia, F., Spacek, D. V., Li, J., Xie, D., Olarerin-George, A., Steinmetz, L. M., Hogenesch, J. B., Kellis, M., Batzoglou, S., & Snyder, M. (2013). Extensive variation in chromatin states across humans. Science, 342(6159), 750–752. https://doi.org/10.1126/science.1242510

Tan-Wong, S. M., Zaugg, J. B., Camblong, J., Xu, Z., Zhang, D. W., Mischo, H. E., Ansari, A. Z., Luscombe, N. M., Steinmetz, L. M., & Proudfoot, N. J. (2012). Gene loops enhance transcriptional directionality. Science, 338(6107), 671–675. https://doi.org/10.1126/science.1224350

Zaugg, J. B., & Luscombe, N. M. (2012). A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Research, 22(1), 84–94. https://doi.org/10.1101/gr.124099.111

Kotte, O., Zaugg, J. B., & Heinemann, M. (2010). Bacterial adaptation through distributed sensing of metabolic fluxes. Molecular Systems Biology, 6. https://doi.org/10.1038/msb.2010.10

Gattin, Z., Zaugg, J., & van Gunsteren, W. F. (2010). Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling. ChemPhysChem, 11(4), 830–835. https://doi.org/10.1002/cphc.200900501

Hoskins, A. A., Morar, M., Kappock, T. J., Mathews, I. I., Zaugg, J. B., Barder, T. E., Peng, P., Okamoto, A., Ealick, S. E., & Stubbe, J. (2007). N5-CAIR mutase: Role of a CO2 binding site and substrate movement in catalysis. Biochemistry, 46(10), 2842–2855. https://doi.org/10.1021/bi602436g