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Artificial intelligence (AI) has been transforming the practice of drug discovery in the past decade. Various AI techniques have been used in a wide range of applications, such as virtual screening and drug design. In this survey, we first…
MicroRNAs (miRs) are robust regulators of gene expression, implicated in most biological processes. microRNAs predominantly downregulate the expression of genes post-transcriptionally and each miR is predicted to target several hundred…
We develop a model-based methodology for integrating gene-set information with an experimentally-derived gene list. The methodology uses a previously reported sampling model, but takes advantage of natural constraints in the…
Artificial Intelligence (AI) technology is based on theory and development of computer systems able to perform tasks that normally require human intelligence. In this context, deep learning is a family of computational methods that allow an…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
This paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment. The groups of genes are externally defined, for example, sets of gene pathways derived from biological databases. Our…
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…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
With the world population rapidly increasing, transforming our agrifood systems to be more productive, efficient, safe, and sustainable is crucial to mitigate potential food shortages. Recently, artificial intelligence (AI) techniques such…
Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after…
Diverse subfields of neuroscience have enriched artificial intelligence for many decades. With recent advances in machine learning and artificial neural networks, many neuroscientists are partnering with AI researchers and machine learning…
In this paper, we present a new approach for analyzing gene expression data that builds on topological characteristics of time series. Our goal is to identify cell cycle regulated genes in micro array dataset. We construct a point cloud out…
Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…
Gene set analysis, a popular approach for analysing high-throughput gene expression data, aims to identify sets of genes that show enriched expression patterns between two conditions. In addition to the multitude of methods available for…
In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and…
Medical imaging is widely used in cancer diagnosis and treatment, and artificial intelligence (AI) has achieved tremendous success in various tasks of medical image analysis. This paper reviews AI-based tumor subregion analysis in medical…
Generative AI (GenAI), which aims to synthesize realistic and diverse data samples from latent variables or other data modalities, has achieved remarkable results in various domains, such as natural language, images, audio, and graphs.…
Fluorescence microscopy, widely used in the study of living cells, tissues, and organisms, often faces the challenge of photodamage. This is primarily caused by the interaction between light and biochemical components during the imaging…
Artificial Intelligence (AI) can potentially transform the industry, enhancing the production process and minimizing manual, repetitive tasks. Accordingly, the synergy between high-performance computing and powerful mathematical models…