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.

 
 
IMG_6036.JPG

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, web: danio-code.zfin.org 

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 (DANIO-CODE), 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.

 
 
Tahmina_pic 2018 June.jpeg

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.

 
 

Amitha Raman - Lab engineer 

amitha.raman@ki.se

I work as a lab engineer for Carsten Daub’s clinical transcriptomics research group with a strong interest in Molecular biology and NGS technologies. I obtained my Master of Science degree in Molecular Genetics from Linköping University, Sweden in May 2012 and worked as a technician for Dominic Wright’s research team for a short time.
I was part of Carsten Daub’s and Juha Kere’s research group from 2012 – 2014 and my main focus has been on NGS technologies, lab automation and molecular biology techniques, especially CAGE (Cap Analysis of Gene Expression) and STRT (Single-cell tagged reverse transcription). Additionally, I have successfully set up a research laboratory including sample preparation and library production, optimization, testing and methods development and Illumina sequencing for the above high throughput techniques at ISO/SWEDAC accredited clinical laboratory at MAF (Mutation Analysis Core facility). I spent two years working on CAGE library production for insulin sensitivity project from 2014 – 2016 as part of the Lipid laboratory under Profs. Mikael Ryden and Peter Arner. I moved back to Daub’s lab in Jan 2017 and since then I have been working on the functional annotation of the dog genome project using CAGE technology.

amitha.raman@ki.se Linked-in Final Retouched headshot.jpg
 
 

Michael Dong - Bioinformatics Lab Technician 

michael.dong@ki.se

I work as a Laboratory Technician in Bioinformatics at the Department of Biosciences and Nutrition, under the supervision of Ph.D Carsten Daub.

My educational background is in Bioinformatics and molecular biology. After getting my license degree in Health Biology at the University of Paris-Sud, Orsay, France (now Paris-Saclay), I chose to orient my studies towards Computational Biology. I then graduated with a master degree in bioinformatics and biostatistics in 2016, as well as a Magistery degree in Biology and Biotechnology, after completing my 6-months end-of-course internship in Umeå, Sweden.

 

 
 
 

 

Been here, done that ...

Previous team members

 
  • 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