Rickard Sandberg

Group members:
Rickard Sandberg, group leader
Ilgar Abdullayev, PhD stud
Åsa Björklund, postdoc
Qiaolin Deng, postdoc
Mats Ensterö, postdoc
Ersen Kavak, postdoc
Daniel Ramskiöld, PhD stud
Helena Storvall, PhD stud
Gösta Winberg, Research associate

RICKARD SANDBERG
Department of Cell and Molecular Biology (CMB) and Ludwig Institute for Cancer Research
Rickard.Sandberg@ki.se

We are studying global aspects of gene regulation by combining genome-wide experimental and computational techniques to better understand stem cell characteristics and differentiation processes. We are interested in determining how gene expression patterns are regulated during development through global measurements of e.g. transcripts copy numbers (RNA-Seq) and genome-wide locations of transcription factors (ChIP-Seq). Computational analyses of these data aim to tease out the gene regulatory networks acting in early embryonic development and general patterns in the specification of cell types. To this end we have been developing global RNA-Seq from few or single cells that we are applying to studies on the first differentiation events taking place during mouse preimplantation development.

5 SELECTED PUBLICATIONS:

Shukla S., Kavak E., Gregory M., Imashimizu M., Shutinoski B., Kashlev M., Oberdoerffer P., Sandberg R., and Oberdoerffer, S. (2011) CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, AOP.

Ramsköld D., Wang E.T., Burge C.B., and Sandberg R. (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 5:e1000598.

*Wang E.T., *Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., and Burge C.B.(2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476.

*Sandberg R., *Neilson J.R., Sarma A., Sharp P.A., and Burge C.B. (2008) Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 320:1643-1647

*Sandberg R., *Yasuda R., Pankratz D.G., Carter T.A., Del Rio J.A., Wodicka L., Mayford M., Lockhart D.J., and Barlow C. (2000) Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. USA 97:11038-11043.

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