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Article
Stochastic amplification of spatial modes in a system with one diffusing species
The problem of pattern formation in a generic two species reaction–diffusion model is studied, under the hypothesis that only one species can diffuse. For such a system, the classical Turing instability cannot...
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Article
Open AccessMicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes
Colorectal cancer (CRC) transcriptional subtypes have been recently identified by gene expression profiling. Here we describe an analytical pipeline, microRNA master regulator analysis (MMRA), developed to sea...
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Article
Open AccessDetection of gene communities in multi-networks reveals cancer drivers
We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine...
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Article
Open AccessDetermining the optimal number of independent components for reproducible transcriptomic data analysis
Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the nu...
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Article
Open AccessClassification of gene signatures for their information value and functional redundancy
Gene signatures are more and more used to interpret results of omics data analyses but suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. Moreover, many gene signatures...
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Chapter and Conference Paper
Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals
Independent Component Analysis (ICA) can be used to model gene expression data as an action of a set of statistically independent hidden factors. The ICA analysis with a downstream component analysis was succe...
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Article
Open AccessHope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data
After its introduction in 1982, the Hopfield model has been extensively applied for classification and pattern recognition. Recently, its great potential in gene expression patterns retrieval has also been sho...
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Article
Open AccessInterpreting pathways to discover cancer driver genes with Moonlight
Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dep...
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Article
Open AccessPrevalence of microhematuria in renal colic and urolithiasis: a systematic review and meta-analysis
This systematic review and meta-analysis aims to investigate the prevalence of microhematuria in patients presenting with suspected acute renal colic and/or confirmed urolithiasis at the emergency department.
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Article
Open AccessBenchmarking joint multi-omics dimensionality reduction approaches for the study of cancer
High-dimensional multi-omics data are now standard in biology. They can greatly enhance our understanding of biological systems when effectively integrated. To achieve proper integration, joint Dimensionality ...
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Article
Open AccessPaired single-cell multi-omics data integration with Mowgli
The profiling of multiple molecular layers from the same set of cells has recently become possible. There is thus a growing need for multi-view learning methods able to jointly analyze these data. We here pres...
