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Papers in PNAS, Leukemia and Molecular Cell

A few successful collaborative efforts were recently published in top biomedical journals. With Zirkel and colleagues we used HINT footprint analysis to characterize transcription factor binding underlying DNA looping via HMGB2. With Sonntag and colleagues, we have leveraged molecular information

Footprinting in ATAC-seq – Preprint and Talk at ISMB

We have recently presented our new approach for fooptring with atac-seq using HINT at ISMB 2018.  A pre-print with preliminary results has been deposited in Biorxv, while HINT-ATAC is available in our software repository.  

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

Project funded by DFG – Bioinformatics of Open Chromatin

The DFG has approved a “sachbeihilfe” project for the research on computational methods for analysis of open chromatin from single cell sequencing.

Collaborative work published in Nature Communications, Genome Research and Gut

The Costa lab has participated in several collaborative works, which has been published in important journals in  the recent months. In Axelsson et al., Nature Communications, we have contributed on inference of gene expression based networks from type 2 diabetes patients. This

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.

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,