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Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
In many longitudinal microarray studies, the gene expression levels in a random sample are observed repeatedly over time under two or more conditions. The resulting time courses are generally very short, high-dimensional, and may have…
Addressing the reproducibility crisis in artificial intelligence through the validation of reported experimental results is a challenging task. It necessitates either the reimplementation of techniques or a meticulous assessment of papers…
Probe-level models have led to improved performance in microarray studies but the various sources of probe-level contamination are still poorly understood. Data-driven analysis of probe performance can be used to quantify the uncertainty in…
Be it for a malicious or legitimate purpose, packing, a transformation that consists in applying various operations like compression or encryption to a binary file, i.e. for making reverse engineering harder or obfuscating code, is widely…
In the rapidly evolving domain of next generation sequencing and bioinformatics analysis, data generation is one aspect that is increasing at a concomitant rate. The burden associated with processing large amounts of sequencing data has…
In industrial engineering and manufacturing, quality control is an essential part of the production process of a product. To ensure proper functionality of a manufactured good, rigorous testing has to be performed to identify defective…
The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
Free and open source software package ecosystems have existed for a long time and are among the most sophisticated human-made systems. One of the oldest and most popular software package ecosystems is CRAN, the repository of packages of the…
Cell populations are never truly homogeneous; individual cells exist in biochemical states that define functional differences between them. New technology based on microfluidic arrays combined with multiplexed quantitative polymerase chain…
There is a growing need for unbiased clustering methods, ideally automated. We have developed a topology-based analysis tool called Two-Tier Mapper (TTMap) to detect subgroups in global gene expression datasets and identify their…
The greatest challenge in maximizing the use of gene expression data is to develop new computational tools capable of interconnecting and interpreting the results from different organisms and experimental settings. We propose an integrative…
High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…
An important task in microbiome studies is to test the existence of and give characterization to differences in the microbiome composition across groups of samples. Important challenges of this problem include the large within-group…
Applications on inference of biological networks have raised a strong interest in the problem of graph estimation in high-dimensional Gaussian graphical models. To handle this problem, we propose a two-stage procedure which first builds a…
Gene expression datasets are usually of high dimensionality and therefore require efficient and effective methods for identifying the relative importance of their attributes. Due to the huge size of the search space of the possible…
Prostate cancer is among the most common cancer in males and its heterogeneity is well known. Its early detection helps making therapeutic decision. There is no standard technique or procedure yet which is full-proof in predicting cancer…
Malware developers use combinations of techniques such as compression, encryption, and obfuscation to bypass anti-virus software. Malware with anti-analysis technologies can bypass AI-based anti-virus software and malware analysis tools.…
Gaussian processes (GPs) are pervasive in functional data analysis, machine learning, and spatial statistics for modeling complex dependencies. Modern scientific data sets are typically heterogeneous and often contain multiple known…