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We have developed a statistical method named IsoDOT to assess differential isoform expression (DIE) and differential isoform usage (DIU) using RNA-seq data. Here isoform usage refers to relative isoform expression given the total expression…
In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling…
To investigate GRBs in depth, it is crucial to develop an effective method for identifying GRBs accurately. Current criteria, e.g., onboard blind search, ground blind search, and target search, are limited by manually set thresholds and…
An RNA-seq experiment with 48 biological replicates in each of 2 conditions was performed to determine the number of biological replicates ($n_r$) required, and to identify the most effective statistical analysis tools for identifying…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
BACKGROUND: Breast cancer has emerged as one of the most prevalent cancers among women leading to a high mortality rate. Due to the heterogeneous nature of breast cancer, there is a need to identify differentially expressed genes associated…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Benefiting from the advancements in deep learning, various genomic analytical techniques, such as survival analysis, classification of tumors and their subtypes, and exploration of specific pathways, have significantly enhanced our…
Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. While significant…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
This analysis report presents an in-depth exploration of multiple hypothesis testing in the context of Genomics RNA-seq differential expression (DE) analysis, with a primary focus on techniques designed to control the false discovery rate…
We present a multi-species partial differential equation (PDE) model for tumor growth and a an algorithm for calibrating the model from magnetic resonance imaging (MRI) scans. The model is designed for glioblastoma (GBM) brain tumors. The…
For numerous parameter and state estimation problems, assimilating new data as they become available can help produce accurate and fast inference of unknown quantities. While most existing algorithms for solving those kind of ill-posed…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
Genetic variants identified to date by genome-wide association studies only explain a small fraction of total heritability. Gene-by-gene interaction is one important potential source of unexplained heritability. In the first part of this…
The ongoing opioid crisis highlights the urgent need for novel therapeutic strategies that can be rapidly deployed. This study presents a novel approach to identify potential repurposable drugs for the treatment of opioid addiction, aiming…
Glioblastoma Multiforme (GBM) is a highly aggressive brain tumour with limited therapeutic options and poor prognosis. This study presents a mathematical framework to investigate the efficacy of immunotherapy strategies based on cytotoxic…
This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). We performed a detailed comparison of both…
Interpretability of deep learning is widely used to evaluate the reliability of medical imaging models and reduce the risks of inaccurate patient recommendations. For models exceeding human performance, e.g. predicting RNA structure from…