Preprints:

• Daga N, H. Servaas N, Kisand K, Moonen D, Arnold C, Reyes-Palomares A, Kaleviste E, Kingo K, Kuuse R, Ulst K, Steinmetz L, Peterson P, Nakic N, Zaugg JB (2024). Integration of genetic and epigenetic data pinpoints autoimmune specific remodelling of enhancer landscape in CD4+ T cells. BioRxiv
• Lobato-Moreno S, Yildiz U, Claringbould A, Servaas N, Vlachou E, Arnold C, Bauersachs H, Campos-Fornes V, Prummel K, Noh K, Marttinen M, Zaugg JB (2023). Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease. BioRxiv
• Lai MC, Ruiz-Velasco M, Arnold C, Sigalova O, Bunina D, Berest I, Ding X, Hennrich ML, Poisa-Beiro L, Claringbould A, Mathioudaki A, Pabst C, Ho AD, Gavin A-C & Zaugg JB (2021) Enhancer-priming in ageing human bone marrow mesenchymal stromal cells contributes to immune traits. BioRxiv
• Bunina D+, Germain P-L, Lopez Tobon A, Fernandez-Novel Marx N, Arnold C, Ó hEachteirn A, Claringbould A, Lai MC, Rangasamy S, Narayanan V, Testa G, Zaugg JB+ & Noh K-M+ (2021) Pathological LSD1 mutations cause HDAC-mediated aberrant gene repression during early cell differentiation. BioRxiv.

2023

• de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB (2023) Convolutional networks for supervised mining of molecular patterns within cellular context. Nature Methods.
  • Press release from EMBL Communications

2022

Coming soon

2021

• Claringbould A & Zaugg JB (2021) Enhancers in disease: molecular basis and emerging treatment strategies. Trends Mol Med 27(11):1060–1073.
  • Selected for cover of the November issue
• Weidemüller P, Kholmatov M, Petsalaki E & Zaugg JB (2021) Transcription factors: Bridge between cell signaling and gene regulation. Proteomics, e2000034.
  • Link to data and analysis performed in this study (including annotations and classification of transcription factors)

2020

• Sigalova OM, Shaeiri A, Forneris M, Furlong EEM+, Zaugg JB+. Predictive features of gene expression variation reveal mechanistic link with differential expression (2020). Molecular Systems Biology 16 (8), e9539
  • The paper was featured on EMBL news
  • Thanks to the MSB team for selecting the article fo the August cover of the issue
  • Code is available here
  • Data used in the study (gene-specific features) are available here
• Grubert F, Srivas R, Spacek DV, 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 JB, Snyder M. Landscape of cohesin-mediated chromatin loops in the human genome. Nature 583(7818):737-743.
  • The paper was part of the ENCODE project and featured on the cover
• Bunina D, Abazova N, Diaz N, Noh K-M+, Krijgsveld J+, Zaugg JB+ (2020): Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Systems 10, 6 (2020) 459-460
  • The paper was featured on EMBL news
• Reyes-Palomares A, Gu M, Grubert F, Berest I, Sa S, Kasowski M, Arnold C, Shuai M, Srivas R, Miao S, Li D, Snyder MP, Rabinovitch M & Judith Zaugg JB (2020). Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nat Commun 11, 1673 (2020). https://doi.org/10.1038/s41467-020-15463-x
  • The paper was featured in the monthly highlights of Genomes and Epigenomes at Nature Communications
  • For a lay summary: check out the article covered on EMBL news
• Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J & Zaugg JB (2020). Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Nat Commun 11, 124 (2020) doi:10.1038/s41467-019-13888-7
  • Software is available here
  • The paper was featured in the monthly highlights of Genomes and Epigenomics at Nature communications
  • For a lay summary: check the article covered on EMBL news

2019

• Berest I*, Arnold C*, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch PM, Huber W, Dietrich S, Helin K, Zaugg JB (2019). Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF. Cell Reports 29, 10, 3 (2019) 3147-3159.e12
  • Software is available on our git repository
  • Documentation is available on readthedocs
  • For a lay summary: check the article covered on EMBL news
• 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., Zaugg, J.B.+, Sauvageau, G.+ and Pabst, C+. 2019. Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML.Blood (2019) 134 (3): 263–276.
  • The paper was highlighted in an editorial at Blood

2017

• Ruiz-Velasco M, Kumar M*, Lai ML*, Bhat P, Solis-Pinson AB, Reyes A, Kleinsorg A, Noh K-M, Gibson TJ, Zaugg JB (2017). CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals. Cell Systems Volume 5 , Issue 6 , 628 – 637.e6 ; link to download the pdf
  • This article was featured in the EMBL News.

2015

• Grubert F*, Zaugg JB*, Kasowski M*, Ursu O*, et al. (2015) Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.Cell. 162 (5): 1051-1065
  • This article was highlighted in Cell, and Nature Genetics, and also covered by an EMBL press release

Before 2012

• Kotte O, Zaugg JB, Heinemann M. (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 6: 355.
• Hoskins AA, Morar M, Kappock TJ, Mathews II, Zaugg JB, Barder TE, Peng P, Okamoto A, Ealick SE, Stubbe J. (2007) N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis. Biochemistry 46(10):2842-55.