Category: Uncategorized

Top Reading Papers 2016 at Recomb-RG

Our paper on computational detection of footprints from open chromatin data has been selected as one of the top 10 reading papers by the community of Recomb Regulatory Genomics. Check here the selection of papers.

Computational prediction of HOTAIR binding to DNA

In Kalwa et al, 2016, we have applied for the first time the “Triplex Domain Finder” (TDF) to analyse DNA regions potentially regulated by HOTAIR, i.e. peaks of ChIRP-Seq experiments or regions with DNA methylation changes after siHOTAIR. TDF not

Publication on differential peak caller THOR in NAR

The paper describing our differential peak caller supporting replicates have been published in Nucleic Acids Research. Allhoff, M., Sere K., Freitas, J., Zenke, M.,  Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research,

Congratulations to Manuel Allhoff for his Ph.D. defense!

Manuel Allhoff has successfully defended his Informatics Ph.D. Congrats Batmanu!          

Paper accepted in Aging

Lin Q., Weidner C. I., Costa I. G., Marioni, R., Ferreira M. R. P. , Deary I. J., Wagner W., DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy?, Aging, accepted.

Andre Camara defended his PhD

Andre Camara, who was jointly co-supervised by Prof. Ricardo Prudencio and our group, has successfully completed his Ph.D. degree at the Federal University of Pernambuco. His dissertation proposed a new methodology for prediction of drug-protein interactions by combining multiple information

Uncovering regulatory networks during dendritic cell differentiation in NAR

Together with the cell biology department, we have investigated changes in histone modifications and binding of the master regulator Pu.1 during dendritic cell differentiation. We have derived a computational approach to detect further co-binding partners of PU.1 uncovering an regulatory

New Member – Fabio Ticoni

Fabio Ticconi has just joined the group as a Ph.D. candidate. Welcome!

Talk at IFCS 2015 on Detection of DNA methylation signatures

Marcelo Freitas will give a talk on the International Federation of Classification Societies. He will discuss about this lattest work on prediction of signatures from highly dimensional DNA methylation data for prediction of patient age.    

Publication in Clinical Epigenetics – Senecense and Nuclear Organization

In Hanzellman et al., we show how senescence-associated DNA hypermethylation occurs at specific sites in the genome and reflects functional changes in the course of replicative senescence.