F U N D I N G

 

We are thankful for past and present support from 

• The Lundbeck Foundation 

• The Novo Nordisk Foundation

• The European Research Commission (ERC) 

• The Danish Cancer Society

• The EU Joint Programme – Neurodegenerative Disease Research (JPND)

• Danish Center for Scientific Computing

• Innovation Fund Denmark

• Elixir

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F O C U S   A R E A S

​Our group is both computational and experimental, and we work with both fundamental gene regulation and medical transcriptomics. In particular, we specialize in tag-based sequencing analysis to find alternative promoters and enhancers, and gene regulation bioinformatics. 

 

Highlights include

• The definition of an enhancer atlas over human tissues and cells, 

• The widely  used JASPAR database

• The discovery of degradation mechanisms of enhancer RNAs

• A code for transcription  initiation in human genomes

• Inflammation-specific enhancers and promoters

N E W S   I N   B R I E F

 

 

R E S O U R C E S

 

• JASPAR - High quality transcription factor binding site motifs. A standard resource in bioinformatics with >800 citations

• SpliceR - a tool to analyze RNA-seq alternative splice events in R.

• Enhancer/promoter selector -  A slider-based interface to selecting tissue/cell-restricted enhancers or promoters from the FANTOM set

• NHR-scan - a  HMM-based prediction of nuclear receptor binding sites 

 

S E L E C T E D   P A P E R S 

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​Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner et al, Science 2015 

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Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Andersson et al,  Nature Communications 201

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A promoter level mammalian expression atlas. The FANTOM Consortium Nature 2014 

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An atlas of active enhancers across human cell types and tissues. Andersson  et al, Nature 2014 

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 Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Ntini et al, Nature Structural and Molecular Biology  2013

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Metazoan promoters: emerging characteristics and insights into transcriptional regulation.  Lenhard et al. Nature Reviews Genetics 2012

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Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Valen et al . Nature Structural and Molecular Biology  2011

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 A code for transcription initiation in mammalian genomes. Frith et al. Genome Research  2007

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Genome-wide analysis of mammalian promoter architecture and evolution.  Carninci et al. Nature Genetics 2006

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        See all papers here.