Bioinformatik og RNA Biologi
Ole Maaløesvej 5, Biocenteret 2.2.27
2200 København N
Computational genomicist with strong interests in transcription and transcriptional regulation.
My current work is primarily focused on transcriptional regulation via enhancers and their emanating RNAs. My major accomplishments during my postdoc are work done with the FANTOM consortium (http://fantom.gsc.riken.jp/5). My major work has been to use human transcription initiation sites to produce an unprecedented atlas of active enhancers across the vast majority of human cell types and tissues (Andersson R, et al. 2014. Nature. http://doi.org/r35).
BRIEF SYNOPSIS ON RESEARCH EXPERIENCE AND RESULTS
My research experience is broad and covers multiple aspects of genome and chromatin characteristics that influence gene expression, from large-scale chromosomal variations and abnormalities to fine-grained positioning of nucleosomes and enhancers and their associations with gene expression.
Major achievements during my PhD studies include a Bayesian framework for accurate detection of chromosomal aberrations (Andersson et al. 2008), which has been the foundation for several in-depth studies on DNA copy number deviations in healthy (Diaz de Ståhl et al. 2008) and diseased states (e.g., Nord et al. 2009; Sandgren et al. 2010). We were the first to show the existence of somatic variations in DNA copy number between differentiated tissues (Piotrowski et al. 2008) and between phenotypically concordant and discordant monozygotic twins (Bruder et al. 2008). I further have a strong interest in transcriptional regulation by chromatin. Major results include the observations of a preferential positioning of nucleosomes at internal exons and a strong association between certain histone modifications and exon inclusion rate, suggesting a functional role in splicing (Andersson et al. 2009).
In my postdoctoral research I have shifted focus from large-scale chromosomal aberrations to study the transcriptomics and chromatin at promoters, alternative promoters and long-distance regulatory elements. My major accomplishments during this time are work done with the FANTOM consortium, resulting in two Nature publications (Andersson et al. 2014; Forrest et al. 2014). I have played an important role in the analysis of transcription initiation sites in man and mouse (Forrest et al. 2014). My major work has been to use the initiation sites to produce an unprecedented atlas of active enhancers across the vast majority of human cell types and tissues (Andersson et al. 2014). Using enhancer transcription as a proxy for activity, I was able to assess their cell-type specific usage and infer models of gene regulation by enhancers.
ONGOING WORK AND FUTURE PLANS
My work on transcribed enhancers and the resulting FANTOM enhancer atlas (Andersson et al. 2014) pave the way for a paradigm shift in genome-wide assessment of enhancer activities and their regulatory architectures. Via massive validation we show enhancer transcription to the most accurate predictor of enhancer activity to date (3-fold increase in validation rate compared to state-of-the-art approaches). Via systematic analysis of enhancer activities determined from enhancer RNA we may hence more precisely determine the specificity of enhancers and their context-dependent regulatory architectures and determinants.
I am now pursuing several studies to gain insight into the regulatory complexities and diversities of human cell types. By systematic integrative analysis of dynamics in enhancer activities and DNA methylation we have shown regulatory DNA hypomethylation to be highly associated with increased enhancer activities during granulopoiesis (Rönnerblad et al. 2014). The current phase of FANTOM builds on the results of my enhancer work. We are studying the dynamics of enhancers and their regulation of gene promoters in a large number of human and mouse time courses.
To investigate the biogenesis of enhancer RNAs and their differences with other long non-coding RNAs, I am currently making a resource delineating the properties and fates of human long RNAs. This resource will be utilized to improve assays for enhancer detection and investigate how the wide repertoire of lncRNAs compares to known functional lncRNAs.
Undervisnings- og vejledningsområder
2013 – 2014
Lecturer – Statistics for Molecular Biomedicine, University of Copenhagen
2011 – 2013
Teaching Assistant – Statistics for Molecular Biomedicine, University of Copenhagen
2013 – 2014
Lecturer - Bioinformatics of High-throughput analysis, University of Copenhagen
2007 – 2008
Guest Lecturer – Introduction to Biotechnology and Bioinformatics, Uppsala University
Lecturer – Advanced practical and theoretical course in array-based analyses, University of Alabama at Birmingham
2004 – 2007
Lecturer - Knowledge-based Systems in Bioinformatics, Uppsala University
Lecturer – Molecular Bioinformatics, Uppsala University
2005 – 2006
Lecturer – Boolean Reasoning, Uppsala University
Lecturer – Bioinformatics – Models and Algorithms, Uppsala University
2003 – 2004
Teaching Assistant – Programming in Ada 95, Linköping University