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Discovering statistically significant biclusters in gene expression data
TLDR
We propose a new method to detect significant biclusters in large expression datasets, which combines graph theoretic and statistical modelling of the data. Expand
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Associating Genes and Protein Complexes with Disease via Network Propagation
TLDR
We provide a global, network-based method for prioritizing disease genes and inferring protein complex associations, which we call PRINCE. Expand
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Conserved patterns of protein interaction in multiple species.
To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, DrosophilaExpand
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Network-based prediction of protein function
Functional annotation of proteins is a fundamental problem in the post‐genomic era. The recent availability of protein interaction networks for many model species has spurred on the development ofExpand
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PREDICT: a method for inferring novel drug indications with application to personalized medicine
Inferring potential drug indications, for either novel or approved drugs, is a key step in drug development. Previous computational methods in this domain have focused on either drug repositioning orExpand
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Conserved pathways within bacteria and yeast as revealed by global protein network alignment
We implement a strategy for aligning two protein–protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways andExpand
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Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.
Dissection of regulatory networks that control gene transcription is one of the greatest challenges of functional genomics. Using human genomic sequences, models for binding sites of knownExpand
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Protein networks in disease.
During a decade of proof-of-principle analysis in model organisms, protein networks have been used to further the study of molecular evolution, to gain insight into the robustness of cells toExpand
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CLICK: a clustering algorithm with applications to gene expression analysis.
Novel DNA microarray technologies enable the monitoring of expression levels of thousands of genes simultaneously. This allows a global view on the transcription levels of many (or all) genes whenExpand
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Cluster Graph Modification Problems
TLDR
We show that Cluster Editing isNP-complete, Cluster Deletion is NP-hard to approximate to within some constant factor, and Cluster Completion is polynomial. Expand
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