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Influence of western diet in immune cells with single cell sequencing

Collaborative work with Krenkel and Tacke dissect changes in immune cells of mice subjected to high fat / high sugar diets.

Footprinting in ATAC-seq published in Genome Biology

Our paper on HINT-ATAC  is finally out in Genome Biology!

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

A paper describing TDF- a framework for detection of triple helix forming RNAs  – is finally out in NAR! Moreover with Grummt Lab, we have performed computational analysis of TripleRNA-seq and TriplexDNA-seq; two novel protocols for returning DNA/RNA molecules forming

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

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.