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Third Place at the ENCODE DREAM Challenge – Conference Round

The HINT team, which was formed by Eduardo Gusmao, Li Zhijian and Ivan G. Costa, obtained the third place in the conference round of the ENCODE DREAM Challengee . The challenge task was the prediction of transcription factor ChIP-Seq peaks. Our approach,

Eduardo Gusmao has successfully defended his Ph.D. !

Congrats to Eduardo on his conclusion to his Ph.D. in Computer Science! Eduardo has started his Posdoc in Shirley Liu’s Lab at Dana Farber Institute / Harvard School of Public Health.

New name – Institute for Computational Genomics

From November 2017, the IZKF Research group Bioinformatics will be called “Institute for Computational Genomics”. We will expand our activities in cutting edge research and teaching on computational and genomic methods for understanding complex biological systems. The new institute is

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