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Additional Information

Competing Interests

Phil Arnold is an employee of Novartis Institutes for BioMedical Research. The authors declare that they have no competing interests.

Author Contributions

Mikhail Pachkov performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.

Piotr J Balwierz conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Phil Arnold performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.

Andreas J Gruber performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.

Mihaela Zavolan performed the experiments, analyzed the data, contributed reagents/materials/analysis tools.

Erik van Nimwegen conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The annotation data used by the ISMARA pipeline is available from SwissregulonDB (swissregulon.unibas.ch). The examples presented in the poster are available on ISMARA web-server (ismara.unibas.ch)

Funding

This work was supported by Grant SNF 3100A0-118318 from the Swiss National Science Foundation and by SystemsX.ch, the Swiss Initiative in Systems Biology, through the CellPlasticity project. Andreas J Gruber was supported by the Werner Siemens-Foundation. Mikhail Pachkov was supported by a grant from the Swiss Institute of Bioinformatics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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