Clinical transcriptomics - Carsten Daub

Carsten Daub research group
(Daub lab group picture. From left to right: Carsten Daub, Niyaz Yoosuf, Enrichetta Mileti, Tahmina Akhter, Abdul Kadir Mukarram, Matthias Hörtenhuber)

Research interest summary

Our interests focus on the understanding of the molecular basis of gene regulation 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 (miRNA). 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.


Team members

Group leader
Senior researcher

Carsten Daub

Phone: 08-524 812 24
Organizational unit: Daub

I am an Associate Professor (“Docent” in the Swedish academic system) and group leader for the Clinical Transcriptomics research group at the Department of Biosciences and Nutrition at Karolinska Institutet. My educational background is in Chemistry (Masters in 2000 at Technical University Berlin) and Bioinformatics (PhD in 2004 at Max-Planck-Institute in Golm). I spent two years as postdoc with Erik Sonnhammer at Karolinska Institutet 2004-2006 after which I went to work with Yoshihide Hayashizaki at RIKEN Yokohama. In 2007 I became Team Leader and was leading the Bioinformatics Core Facility as Facility Director since 2008. In 2012, I moved back to Karolinska Institutet to lead the Clinical Transcriptomics research group to improve the understanding of gene regulation underlying diseases.
PhD student

Tahmina Akhter

Phone: 08--52481159
Organizational unit: Daub

I am a PhD student in CDA lab. I have a general background of computer science (Bachelor degree) and completed my Masters in Computational and Systems Biology at KTH (The Royal Institute of Technology) in Stockholm. I worked as a research engineer at the department of Computation Biology at KTH and was involved in a project concerning parallelism in neural network using Blue Gene Super Computer. Since late 2013 I am registered as PhD student at the department of BioNut. My project focuses on inflammatory bowel disease (IBD), Asthma  and other inflammatory airway diseases for the identification of diagnostic biomarkers and disease predictive scores, and the establishment of a bioinformatic pipeline for drug repositioning based on computational methods. I have programming skills (R, C++, Python, Java etc.), use different algorithms and bioinformatic software, I have research experience in the field of computational biology, and previous professional experience in software development. I am highly motivated to do research, and my strength is my dedication to work.
PhD student

Matthias Hörtenhuber

Organizational unit: Daub

I came to Carsten Daub’s lab in September 2015, where I will be doing my PhD as a part of the Zencode ITN. For this project I will work on the establishment of a zebrafish genome database (daniocode), including its database schema, data input design, data views/visualizations and genome annotation. I will also study gene regulation during cell differentiation in zebrafish via the analysis of next generation sequencing data (RNA-seq, ChIP-seq, CAGE) and compare it with the human genome.Before coming to Sweden I studied mathematics as well as biomedical engineering in Vienna, Austria.
PhD student

Enrichetta Mileti

Phone: 08--52481159
Organizational unit: Daub

I obtained my bachelor degree in Biology in December 2012 at University of L’Aquila.In the meanwhile, the importance of Bioinformatics in biological analysis has become more and more important and my curiosity in use it as well. This prompted me to join the International Master in Bioinformatics in 2013 at Bologna University and I received my Master degree in Bioinformatics in July 2014. In October 2014, I joined the Carsten Daub group as Scientific Trainee and since February 2015 I am registered as PhD student.The main focus of my PhD project is the study of gene regulatory basis of insulin resistance in human subcutaneous white adipose tissue.Further, my interest is not only the identification of genes expressed in different insulin conditions, but also identifying biological factors which can influence the transcription of insulin-related genes, such as promoter-distal regulatory regions like enhancers.
PhD student

Abdul Kadir Mukarram

Organizational unit: Daub

I joined Carsten's group in September 2015 as a Scientific Trainee and will start my PhD studies as an early-stage researcher of the Marie Curie project “ZENCODE-ITN” in December 2015.  My research focus is mainly in the area of genome annotation and comparative genomics to strengthen zebrafish as a model organism for studying human disease. RNA-Seq, CAGE, and ChIP-Seq integrative data analyses are among my main activities to decode the genome regulatory networks in zebrafish to answer medically relevant problems in human.

Niyaz Yoosuf

Organizational unit: Daub

I am a computational biologist with a strong interest in applying high throughput biological data in genomic studies. In collaboration with Prof. Joakim Lundberg, KTH and SciLifeLab, my current research focuses on classifying the heterogeneous cell types in multicellular tissues using spatial transcriptomics, a new method, which was, developed to combine morphological and gene expression data. I will also address the role of post-transcriptional regulations, primarily the tissue/cell specific differential usage of polyadenylation. My research interests also extend in developing clustering based expression signatures to characterize the cell types and outperform traditional gene-based analysis.

Previous team members

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

Key publications

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.
Yu N, Hallström B, Fagerberg L, Ponten F, Kawaji H, Carninci P, et al
Nucleic Acids Res. 2015 Aug;43(14):6787-98
Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.
Persson H, Kwon A, Ramilowski J, Silberberg G, Söderhäll C, Orsmark-Pietras C, et al
J. Allergy Clin. Immunol. 2015 Sep;136(3):638-48
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.
Arner E, Daub C, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, et al
Science 2015 Feb;347(6225):1010-4
A promoter-level mammalian expression atlas.
, Forrest A, Kawaji H, Rehli M, Baillie J, de Hoon M, et al
Nature 2014 Mar;507(7493):462-70
Adipose tissue microRNAs as regulators of CCL2 production in human obesity.
Arner E, Mejhert N, Kulyté A, Balwierz P, Pachkov M, Cormont M, et al
Diabetes 2012 Aug;61(8):1986-93

Participation in consortia