Publications

Preprints:

  • Kamal A, Arnold C, Claringbould A, Moussa R, Daga N, Nogina D, Kholmatov M, Servaas N, Mueller-Dott S, Reyes-Palomaresv A, Palla G, Sigalova O, Bunina D, Pabst C, Zaugg JB (2021). GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages. 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.
  • Bruch P-M, Giles H, Kolb C, Herbst SA, Becirovic T, Roider T, Lu J, Scheinost S, Wagner L, Hüllein J, Berest I, Kriegsmann M, Kriegsmann K, Zgorzelski C, Dreger P, Zaugg JB, Müller-Tidow C, Zenz T, Huber W & Dietrich S (2021) Mapping drug-microenvironment-genetic interplay in CLL reveals trisomy 12 as a modulator of microenvironmental signals. 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.
  • Ibarra IL, Ratnu VS, Gordillo L, Hwang I-Y, Mariani L, Weinand K, Hammaren HM, Bulyk ML, Savitski MM, Zaugg JB+ & Noh K-M+ (2021) Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements. BioRxiv.

2021

2020

  • 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

2019

  • 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.
  • Rasmussen, KD*, Berest, I.*, Keβler, S., Nishimura, K., Simón-Carrasco, L., Vassiliou, GS, Pedersen, MT, Christensen, J., Zaugg, JB+ and Helin, K+. 2019. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research 29(4), pp. 564–575.

2018

  • Hennrich  ML*, Romanov N*, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Bork P, Aloy P, Gavin AC+, Ho AD+ (2018). Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature Communications, DOI: 10.1038/s41467-018-06353-4 

2017

  • Ruiz-Velasco M, Zaugg JB (2017). Structure meets function: How chromatin organisation conveys functionality. Current Opinion in Systems Biology: 1, Feb 2017,129-136, ISSN 2452-3100
  • Lai MC, Bechy AL, Denk F, Collins E, Gavriliouk M, Zaugg JB, Ryan BJ, Wade-Martins R and Caffrey TM (2017): Haplotype-specific MAPT exon 3 expression regulated by common intronic polymorphisms associated with Parkinsonian disorders. Mol Neurodegener, 2017 vol. 12 (1) p. 79

2016

2015

2014

  • Castelnuovo M*, Zaugg JB*+, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Luscombe NM, Steinmetz LM, Stutz F+. (2014) Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast Nucleic Acids Res. 42 (7): 4348-4362.

2013

  • Kasowski M*, Kyriazopoulou-Panagiotopoulou S*, Grubert F*, Zaugg JB*, Kundaje A*, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, et al. (2013) Extensive Variation in Chromatin States Across Humans. Science 342 (6159), 750-752.

2012

  • Tan-Wong SM*, Zaugg JB*, Camblong J*, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. (2012) Gene Loops Enhance Transcriptional Directionality. Science 338 (6107), 671-675.
  • Zaugg JB, Luscombe NM. (2012) A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res 22: 84–94.

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 catalysisBiochemistry 46(10):2842-55.