Carsten Daub

Carsten Daub
Clinical Transcriptomics
Karolinska Institutet

Research interests

Our interests focus on the understanding of the molecular basis of diseases through translational research, specifically, but not exclusively, related to inflammation. The key aspects of our work include genome-wide gene expression analysis from human patient samples employing technologies such as RNA-Seq, Cap Analysis of Gene Expression (CAGE) or small RNA sequencing. Our analysis goes beyond differentially expressed genes and identifies a variety of candidate elements responsible for the observed expression differences in the disease patients and the associated clinical phenotypes. Application of sequencing technology to the transcriptome previously has been utilized to uncover a range of regulatory elements and mechanisms, including regulation through transcription factors (TFs), nearby but distinct alternative promoters resulting in the same protein but employing different sets of regulatory TFs, expression of anti-sense RNA to modulate the sense-RNA and the regulatory role of expressed repeat elements and miRNAs. Subsequent functional validation studies confirm the suggested regulatory relationships.

Group members

Carsten O. Daub, PI
Niyaz Yoosuf, Postdoc
Enrichetta Mileti, PhD student
Tahmina Akhter, PhD student
Abdul Kadir Mukarram, PhD student
Matthias Hörtenhuber, PhD student

Previous group members
Olga Hrydziuszko, Postdoc (2012-2014)
Amitha Raman, Laboratory technician (2012-2014)
Nancy Yu, Postdoc (2012-2014)
Wenjing Kang, Masters student (Feb-June 2014)
Jacqueline Nowak, Masters student (April-August 2014)
Kubra Altinel,  Erasmus summer student, 2014
Johanna Labate, Erasmus summer student, 2015

Graduated PhD students
Morana Vitezic, 2013 

Key publications

  • Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR, Fantom Consortium T, Hayashizaki Y, Uhlén M, Daub CO. Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium. Nucleic Acids Res. 2015 Aug 18;43(14):6787-98. 

  • Persson H, Kwon AT, Ramilowski JA, Silberberg G, Söderhäll C, Orsmark-Pietras C, Nordlund B, Konradsen JR, de Hoon MJ, Melén E, Hayashizaki Y, Hedlin G, Kere J, Daub CO. Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles. J Allergy Clin Immunol. 2015 Apr 9. pii: S0091-6749(15)00328-0.

  • Arner E*, Daub CO*, Vitting-Seerup K*, Andersson R*, et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. 

  • FANTOM Consortium and the RIKEN PMI and CLST (DGT), et al. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. 

  • Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P. Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes. 2012 Aug;61(8):1986-93.

    Publication summary
    Total number of peer-reviewed publications: 56, first author: 4, last author: 13
    H-index: 28 (Google scholar)
    Total number of citations: Google scholar: >4000

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