Matters Arising
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Open Access
Featured
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Matters Arising
| Open Access
A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis
- Alan E. Murphy
- & Nathan G. Skene
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Article
| Open Access
Versioning biological cells for trustworthy cell engineering
Full traceability and transparency are important to establish trust in engineered cell lines. Here the authors argue that version control for cell engineering marks a significant step toward more open, reproducible, traceable and ultimately more trustworthy engineering biology.
- Jonathan Tellechea-Luzardo
- , Leanne Hobbs
- & Natalio Krasnogor
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Article
| Open Access
Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data
Calcium imaging is valuable for understanding neuro and cell biology, but is challenging to analyze, organize, and access. Here, the authors present an efficient, expandable and user-friendly platform, which encapsulates the entire analysis process all to way to interactive visualizations.
- Kushal Kolar
- , Daniel Dondorp
- & Marios Chatzigeorgiou
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Article
| Open Access
Replication dynamics of recombination-dependent replication forks
Replication forks that are stalled at obstacles on the DNA template can be restarted by homologous recombination. Here, the authors show replication dynamics during homologous recombination-dependent replication fork restart by combining polymerase usage sequencing and a Monte Carlo mathematical model.
- Karel Naiman
- , Eduard Campillo-Funollet
- & Antony M. Carr
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Article
| Open Access
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.
- Matthew H. Bailey
- , William U. Meyerson
- & Christian von Mering
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Article
| Open Access
Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide
Common Fragile Sites (CFSs) are chromosome regions prone to breakage upon replication stress known to drive chromosome rearrangements during oncogenesis. Here the authors use genome-wide and single cell techniques to assess how replication timing and transcriptional activity correlate with genome stability.
- Olivier Brison
- , Sami El-Hilali
- & Chun-Long Chen
