Sandberg Group

PI:
Rickard Sandberg, Assistant Professor, PhD
Participating group members:
PhD studs. Daniel Ramskold, Helena Storvall, Åsa Björklund, Mats Ensterö
Address etc.:
Ludwig Institute for Cancer Research Stockholm, Department of Cell and Molecular Biology, Karolinska Institutet. email: rickard.sandberg@ki.se

Profile of the group:

After returning to Sweden in 2008, R. Sandberg has rapidly built up a competitive research group devoted to studies of gene regulation in early embryonic development using genomic technologies. RS has attracted significant funding from the European Research Council (Starting Grant), the foundation for Strategic Research (SFF, Ingvar Carlsson Award and Future Reseach Leader) and Åke Wiberg Foundation (Special Award). Research is focused on analysis of gene regulation dynamics in early differentiation, proliferation and stem cells. The lab have strong expertise in analyses of transcriptome and epigenetic analyses from massively parallel sequencing and has established computational infrastructure and analyses pipelines to simulteanously process tens of deep-sequenced (~100 Million reads) samples or hundreds of barcoded (~1M reads each) samples in parallel by distributing processor and memory intensive parts using in-house developed programs. The lab has also implemented a functioning RNA-Sequencing protocol for low amounts of RNA, applicable to analyses of single cell transcriptomes. From these data general regulatory principles of gene expression programs of individual cells are explored.

Publications:

  • Daniel Ramsköld, Eric T. Wang, Christopher B. Burge and Rickard Sandberg (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data PLoS Computational Biology, 5(12): e1000598
  • Eric T. Wang*, Rickard Sandberg*, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen Kingsmore, Gary P. Schroth and Christopher B. Burge (2008) Alternative Isoform Regulation in Human Tissue Transcriptomes Nature Nov 27, 456,
  • Sandberg R*, Neilson J.*, Sarma A, Sharp P. A., Burge C. B. (2008) Proliferating cells express mRNAs with shortened 3`UTRs and fewer microRNA target sites.. Science. Vol 320. no. 5883, pp. 1643-1647