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

• 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.

• Ranzoni AM*, Tangherloni A*, Berest I*, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB & Cvejic A (2021) Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 28, 472-487.e7.

• Kim K-P, Li C*, Bunina D*, Jeong H-W, Ghelman J, Yoon J, Shin B, Park H, Han DW, Zaugg JB, Kim J, Kuhlmann T, Adams RH, Noh K-M, Goldman SA & Schöler HR (2021) Donor cell memory confers a metastable state of directly converted cells. Cell Stem Cell 28, 1291-1306.e10.

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

• Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB & 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. Nat Genet52, 273–282 (2020). https://doi.org/10.1038/s41588-020-0586-5

• 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

• 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, 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.

• 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

• Cakiroglu SA, Zaugg JB, Luscombe NM. (2016)  Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.  Nucleic Acids Res. 44 (17): 8065-8072
• Ignatiadis N, Klaus B, Zaugg JB, Huber W. (2016) Data-driven hypothesis weighting increases detection power in genome-scale multiple testing. Nat Methods. Jul;13(7):577-80
• Arnold C, Bhat P,  Zaugg JB. (2016) SNPhood: Investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. Bioinformatics. doi:10.1093/bioinformatics/btw127

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

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 catalysis. Biochemistry 46(10):2842-55.