SANDELIN LAB
medical transcriptomics and computational biology
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
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The definition of an enhancer atlas over human tissues and cells,
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The widely used JASPAR database
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The discovery of degradation mechanisms of enhancer RNAs
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A code for transcription initiation in human genomes
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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
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JASPAR - High quality transcription factor binding site motifs. A standard resource in bioinformatics with >800 citations
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SpliceR - a tool to analyze RNA-seq alternative splice events in R.
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Enhancer/promoter selector - A slider-based interface to selecting tissue/cell-restricted enhancers or promoters from the FANTOM set
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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
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner et al, Science 2015
Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Andersson et al, Nature Communications 201
A promoter level mammalian expression atlas. The FANTOM Consortium Nature 2014
An atlas of active enhancers across human cell types and tissues. Andersson et al, Nature 2014
Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality. Ntini et al, Nature Structural and Molecular Biology 2013
Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Lenhard et al. Nature Reviews Genetics 2012
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes. Valen et al . Nature Structural and Molecular Biology 2011
A code for transcription initiation in mammalian genomes. Frith et al. Genome Research 2007
Genome-wide analysis of mammalian promoter architecture and evolution. Carninci et al. Nature Genetics 2006
See all papers here.






