Transcriptional regulation and epigenetics


The regulatory processes that govern cell proliferation and differentiation are central to developmental biology. Particularly well studied in this respect is the hematopoietic system. Gene expression, regulation and epigenetic data of cells of various distinguishable developmental stages fosters the elucidation of the underlying molecular processes, which change gradually over time and lock cells in certain lineages or induce cell potency. We are interested in developing statistical framework for tasks as finding modules of functionally related genes and characterizing cell potency and commitment from expression and epigenetic signatures.


Joseph Kuo 

Eduardo Gade Gusmao (former member)

Sonja Hanzelmann (former member)

Selected Publications

Kolovos, P.,  Georgomanolis, T.,  Koeferle A.,  Larkin J. DBrant L.,  Nikolic M., Gusmao E.G., Zirkel A.,  Knoch T. A., Costa I.G., van Ijcken W. F ,  Cook P. R., Grosveld F. G.Papantonis A., Binding of nuclear factor kappa B to non-canonical consensus sites reveals its multimodal role during the early inflammatory response, Genome Research,  26:1478-1489 [paper].

Lin Q*, Chauvistre H*, Costa IG*, Mitzka S, Gusmao EG, Haenzelmann S, Baying B, Hennuy B, Smeets H, Hoffmann K, Benes V, Sere K, Zenke M, Epigenetic and Transcriptional Architecture of Dendritic Cell Development, Nucleic Acids Research, 43:9680-9693, [paper][data][genome tracks].

Haenzelmann S, Beier F., Gusmao EG ,  Koch CM, Hummel S., Charapitsa I, Joussen S, Benes V, Brümmendorf TH , Reid G, Costa, IG, Wagner, W (2015) Replicative Senescence is Associated with Nuclear Reorganization and with DNA Methylation at Specific Transcription Factor Binding Sites, Clinical Epigenetics, 7:9 [paper].

do Rego, T. G., Roider, H,  de Carvalho, F. A. T., Costa, I.G., Inferring Epigenetic and Transcriptional Regulation during Blood Cell Development with a Mixture of Sparse Linear Models, Bioinformatics. , accepted.

I. G. Costa, S. Roepcke, C. Hafemeister, and A. Schliep, Inferring Differentiation Pathways from Gene Expression. Bioinformatics, v 24, p. i156-i164, 2008, [paper] [Supp].