Preprints:

• 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.