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Undisclosed, unmet and neglected challenges in multi-omics studies


Multi-omics approaches have become a reality in both large genomics projects and small laboratories. However, the multi-omics research community still faces a number of issues that have either not been sufficiently discussed or for which current solutions are still limited. In this Perspective, we elaborate on these limitations and suggest points of attention for future research. We finally discuss new opportunities and challenges brought to the field by the rapid development of single-cell high-throughput molecular technologies.

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Fig. 1: Schematic representation of analysis goals in multi-omics studies.
Fig. 2: Challenges and opportunities in multi-omics data-integration.
Fig. 3: Comparison of the properties of omics data types.

Data availability

The data used for Fig. 3 were taken from the publicly available STATegra dataset125. Pre-processed values used to generate graphs are provided together with the code.

Code availability

The code and data used to generate Fig. 3 are available on GitHub at


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This work has been funded by the Spanish Ministry of Science and Innovation with grant number BES-2016-076994 to A.A.-L.

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A.C. drafted the structure of the manuscript and integrated author contributions. A.A.-L., S.T. and A.C. drafted the manuscript, reviewed the literature, contributed to figures and approved the final version of the manuscript.

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Correspondence to Ana Conesa.

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The authors declare no competing interests.

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Peer review information Nature Computational Science thanks Casey Greene and Terry Speed for their contribution to the peer review of this work. Handling editor: Fernando Chirigati, in collaboration with the Nature Computational Science team.

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Tarazona, S., Arzalluz-Luque, A. & Conesa, A. Undisclosed, unmet and neglected challenges in multi-omics studies. Nat Comput Sci 1, 395–402 (2021).

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