Author: Ivan Costa

Decoding the function of lncRNAs – New sequencing protocols for detection of RNA-DNA Triple Helices

In a colaboration with Grummt Lab, we have performed computational analysis of TripleRNA-seq and TriplexDNA-seq; two novel protocols for returning DNA/RNA molecules forming triple helices. Check here for more details.

Open positions

We perform research on computational methods for analysis of epigenomics and transcriptomics data. Over the past years, we have developed methods for prediction of cell specific binding sites from open chromatin data (Gusmao et al., Bioinformatics, 2015; Nature Methods, 2016),

Decoding the function of lncRNAs – Paper in Cell Stem Cell

Together with Kurian lab, we have delineated bionformatics framework to uncover novel antisense lncRNAs during cardiomyocite differentiation. These were particularly positioned up-stream of transcription factors, and showed a high positive correlation with these anti-sense partners.In this paper, Frank and colleagues

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.  

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.

Paper published on Nature Methods – Footprint Analysis of DNase-Seq data

Our paper revisiting footprinting analysis from DNase-Seq with HINT-BC has been accepted in Nature Methods. Check the paper here.

Tutorial on Inference of Regulatory Networks at ISMB/ECCB 2017

In a joint effort with Marcel Schulz (MPI Saarbrucken) and Matthias Heinig (Helmholtz Center Munich) , we will offer a tutorial on bioinformatics methods for detection of regulatory networks from NGS data. The tutorial will take place this summer within the international bioinformatics

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,