BiCoN: Network-constrained biclustering of patients and omics data

Lazareva O, Canzar S, Yuan K, Baumbach J, Blumenthal DB, Tieri P, Kacprowski T, List M (2020)

Publication Type: Journal article

Publication year: 2020


Original Authors: Olga Lazareva, Stefan Canzar, Kevin Yuan, Jan Baumbach, David B Blumenthal, Paolo Tieri, Tim Kacprowski, Markus List

Book Volume: 37

Pages Range: 2398 - 2404

Journal Issue: 16


DOI: 10.1093/bioinformatics/btaa1076



Unsupervised learning approaches are frequently employed to stratify patients into clinically relevant subgroups and to identify biomarkers such as disease-associated genes. However, clustering and biclustering techniques are oblivious to the functional relationship of genes and are thus not ideally suited to pinpoint molecular mechanisms along with patient subgroups.


We developed the network-constrained biclustering approach BiCoN (Biclustering Constrained by Networks) which (i) restricts biclusters to functionally related genes connected in molecular interaction networks and (ii) maximizes the difference in gene expression between two subgroups of patients. This allows BiCoN to simultaneously pinpoint molecular mechanisms responsible for the patient grouping. Network-constrained clustering of genes makes BiCoN more robust to noise and batch effects than typical clustering and biclustering methods. BiCoN can faithfully reproduce known disease subtypes as well as novel, clinically relevant patient subgroups, as we could demonstrate using breast and lung cancer datasets. In summary, BiCoN is a novel systems medicine tool that combines several heuristic optimization strategies for robust disease mechanism extraction. BiCoN is well-documented and freely available as a python package or a web interface.

Availability and Implementation

PyPI package:

Web interface

Supplementary information

Supplementary data are available at Bioinformatics online.

Authors with CRIS profile

Involved external institutions

How to cite


Lazareva, O., Canzar, S., Yuan, K., Baumbach, J., Blumenthal, D.B., Tieri, P.,... List, M. (2020). BiCoN: Network-constrained biclustering of patients and omics data. Bioinformatics, 37(16), 2398 - 2404.


Lazareva, Olga, et al. "BiCoN: Network-constrained biclustering of patients and omics data." Bioinformatics 37.16 (2020): 2398 - 2404.

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