Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,132 bioRxiv papers from 295,346 authors.
Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
By
Davis McCarthy,
Raghd Rostom,
Yuanhua Huang,
Daniel J Kunz,
Petr Danecek,
Marc Jan Bonder,
Tzachi Hagai,
HipSci Consortium,
Wenyi Wang,
Daniel J Gaffney,
Benjamin D Simons,
Oliver Stegle,
Sarah A Teichmann
Posted 10 Sep 2018
bioRxiv DOI: 10.1101/413047
Decoding the clonal substructures of somatic tissues sheds light on cell growth, development and differentiation in health, ageing and disease. DNA-sequencing, either using bulk or using single-cell assays, has enabled the reconstruction of clonal trees from frequency and co-occurrence patterns of somatic variants. However, approaches to systematically characterize phenotypic and functional variations between individual clones are not established. Here we present cardelino (https://github.com/PMBio/cardelino), a computational method for inferring the clone of origin of individual cells that have been assayed using single-cell RNA-seq (scRNA-seq). After validating our model using simulations, we apply cardelino to matched scRNA-seq and exome sequencing data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a key role for cell division genes in non-neutral somatic evolution.
Download data
- Downloaded 3,947 times
- Download rankings, all-time:
- Site-wide: 702 out of 67,143
- In genomics: 182 out of 4,561
- Year to date:
- Site-wide: 254 out of 67,143
- Since beginning of last month:
- Site-wide: 5,614 out of 67,143
Altmetric data
Downloads over time
Distribution of downloads per paper, site-wide
- Home
- Top preprints of 2018
- Paper search
- Author leaderboards
- Overall metrics
- The API
- Email newsletter
- About
News
- 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!