Enter the matrix: factorization uncovers knowledge from omics
Genevieve L. Stein-O’Brien,
Aedín C. Culhane,
Alexander V. Favorov,
Lana X. Garmire,
Casey S. Greene,
Loyal A. Goff,
Michael F. Ochs,
Elana J Fertig
Posted 02 Oct 2017
bioRxiv DOI: 10.1101/196915 (published DOI: 10.1016/j.tig.2018.07.003)
Posted 02 Oct 2017
Omics data contains signal from the molecular, physical, and kinetic inter- and intra-cellular interactions that control biological systems. Matrix factorization techniques can reveal low-dimensional structure from high-dimensional data that reflect these interactions. These techniques can uncover new biological knowledge from diverse high-throughput omics data in topics ranging from pathway discovery to time course analysis. We review exemplary applications of matrix factorization for systems-level analyses. We discuss appropriate application of these methods, their limitations, and focus on analysis of results to facilitate optimal biological interpretation. The inference of biologically relevant features with matrix factorization enables discovery from high-throughput data beyond the limits of current biological knowledge-answering questions from high-dimensional data that we have not yet thought to ask.
- Downloaded 3,033 times
- Download rankings, all-time:
- Site-wide: 2,043 out of 100,591
- In systems biology: 50 out of 2,556
- Year to date:
- Site-wide: 33,003 out of 100,591
- Since beginning of last month:
- Site-wide: None out of 100,591
Downloads over time
Distribution of downloads per paper, site-wide
- 20 Oct 2020: Support for sorting preprints using Twitter activity has been removed, at least temporarily, until a new source of social media activity data becomes available.
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!