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Article
Open AccessSuperNoder: a tool to discover over-represented modular structures in networks
Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often (“motifs”). A societal example of a motif might be a household. Replacing such motifs by named supernode...
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Article
Open AccessNetwork Walking charts transcriptional dynamics of nitrogen signaling by integrating validated and predicted genome-wide interactions
Charting a temporal path in gene networks requires linking early transcription factor (TF)-triggered events to downstream effects. We scale-up a cell-based TF-perturbation assay to identify direct regulated ta...
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Article
Open AccessOutPredict: multiple datasets can improve prediction of expression and inference of causality
The ability to accurately predict the causal relationships from transcription factors to genes would greatly enhance our understanding of transcriptional dynamics. This could lead to applications in which one ...
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Article
Open AccessAuthor Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Chapter and Conference Paper
A Data-Efficient Deep Learning Framework for Segmentation and Classification of Histopathology Images
The current study of cell architecture of inflammation in histopathology images commonly performed for diagnosis and research purposes excludes a lot of information available on the biopsy slide. In autoimmune...
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Article
Open AccessShifting to machine supervision: annotation-efficient semi and self-supervised learning for automatic medical image segmentation and classification
Advancements in clinical treatment are increasingly constrained by the limitations of supervised learning techniques, which depend heavily on large volumes of annotated data. The annotation process is not only...
