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Article
Open AccessCAJAL enables analysis and integration of single-cell morphological data using metric geometry
High-resolution imaging has revolutionized the study of single cells in their spatial context. However, summarizing the great diversity of complex cell shapes found in tissues and inferring associations with o...
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Article
Open AccessWidespread redundancy in -omics profiles of cancer mutation states
In studies of cellular function in cancer, researchers are increasingly able to choose from many -omics assays as functional readouts. Choosing the correct readout for a given study can be difficult, and which...
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Article
Open AccessAssessment of network module identification across complex diseases
Many bioinformatics methods have been proposed for reducing the complexity of large gene or protein networks into relevant subnetworks or modules. Yet, how such methods compare to each other in terms of their ...
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Article
Open AccessRetraction Note: detangling PPI networks to uncover functionally meaningful clusters
The authors have retracted this article [1]. After publication they discovered a technical error in the Louvain algorithm with bounded cluster sizes. Correction of this error substantially changed the results ...
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Article
Open AccessRETRACTED ARTICLE: Detangling PPI networks to uncover functionally meaningful clusters
Decomposing a protein-protein interaction network (PPI network) into non-overlap** clusters or communities, sometimes called “network modules,” is an important way to explore functional roles of sets of gene...
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Article
Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs
Off-target effects of the CRISPR–Cas9 system can lead to suboptimal gene-editing outcomes and are a bottleneck in its development. Here, we introduce two interdependent machine-learning models for the predicti...
