Group Members 

 

Carsten O. Daub - Group Leader

carsten.daub@ki.se - +46852481224 - Twitter: @carsten.daub - Publications - CV

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.

 
 
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Kelvin Kwok - Postdoc

ho-man.kwok@ki.se

I am a functional biologist specializing in endocrinology and adipose tissue biology. During my PhD studies at the University of Hong Kong, I investigated the detrimental role of visceral adipose tissue inflammation in the accelerated development of atherosclerosis in an obese mouse model. In October 2017, I started my Novo Nordisk Postdoctoral Fellowship in Carsten Daub’s lab. It has recently been demonstrated in humans that white adipose tissue exhibits a markedly altered insulin-induced gene expression regulation in vivo in obesity. The objective of my current project is to validate and functionally characterize the responsible regulatory elements identified by CAGE. Specifically, I aim to investigate the regulatory roles of lncRNA and enhancers upon insulin stimulation in adipocytes using in vitro systems.

 
 

Niyaz Yoosuf - Postdoc

niyaz.yoosuf@ki.se

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.

 
 

Enrichetta Mileti - PhD Student

enrichetta.mileti@ki.se

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.

 
 

Abdul Kadir Mukarram - PhD Student

abdul.kadir.mukarram@ki.se

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.

 
 

Matthias Hörtenhuber - PhD Student

matthias.hortenhuber@ki.se

I came to Carsten Daub’s lab in September 2015, where I am be doing my PhD as part of the Zencode ITN. For this project I will work on the establishment of a zebrafish genome database (DANIO-CODE DCC), 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 data. Before coming to Sweden I studied mathematics as well as biomedical engineering in Vienna, Austria.

 
 

Tahmina Akther - PhD Student

tahmina.akhter@ki.se

I am a PhD student in the CDA lab. I have a general background in 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 in the department of Computation Biology at KTH involved in a project about parallelism in neural networks using the Blue Gene Super Computer. My PhD project goal is to understand and characterize differences between severe and controlled asthma. The aim is to find asthma biomarkers for steroid response using bioinformatics methodsand also to identify key regulatory mechanism (enhancers, transcription factors and promoters) of genes linked to severe and mild asthma. I have programming skills (R, C++, Python and Java etc.), use different algorithms and bioinformatics software as well as professional experience in software development. I am highly motivated to do research and my strength is my dedication to work.

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Rasha Fahad - PhD Student

Rasha.fj@gmail.com

I got my master degree in Biotechnology from the University of Queensland, AU in 2015 and joined Carsten’s group in 2019 as a Phd student. In my research I will study the RNA profile of different types of breast cancer tissues using spatial transcriptomics. I’ll investigate breast cancer types based on the pathological characterizations combined with their RNA profiles and I’ll identify breast cancer associated risks using sequencing data (genomic variants) and molecular profiling.

 
 

Irene Stevens - Bioinformatics Lab Technician

irene.stevens@ki.se

I joined Carsten Daub’s lab in July 2018 as an Early Stage Researcher, as part of the Marie Curie ZENCODE Initial Training Network. My educational background is in Medicine (Oradea Medical College) and Computational Biology (NIH Postbac Program, Weill Cornell Tri-I Internship). I obtained my Bachelor’s in Biophysics from Hunter College City University of New York.  

Currently, my research project is focused on genome annotation of model organisms (dog, zebrafish) using high-throughput sequencing. I am learning about data management and database quality control.

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Marine Tessarech – Masters student

marine.tessarech@gmail.com

I am a medical resident in clinical genetics from Angers University Hospital in France. I am currently taking a year off from the medical course to do a masters degree in research. I joined Carsten Daub’s lab in January 2019 for an internship of 10 months. I will be working on gene expression of insulin pathway in human white adipose tissue, according to fasting and hyperinsulinemia states. I will mostly be performing bioinformatics analyses on CAGE sequencing data, in order to study the global transcription profile of human subcutaneous white adipose tissue and correlate the results with clinical data.

 
 

Been here, done that ...

Previous team members

 
  • Michael Dong, Bioinformatics Lab Technician (2016-2018)

  • Amitha Raman, Lab engineer (2013-2018)

  • Jiarui Mi, Master student (2017-2018)

  • Marta Dias, Erasmus master student (2015-2016)

  • Johanna Labate, Erasmus summer student, 2015

  • Olga Hrydziuszko, Postdoc (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)