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Summary: Most cellular tasks are performed not by individual proteins, but by groups of functionally associated proteins, often referred to as modules. In a protein assocation network modules appear as groups of densely interconnected…
Fingerprint evidence plays an important role in a criminal investigation for the identification of individuals. Although various techniques have been proposed for fingerprint classification and feature extraction, automated fingerprint…
Due to the recent advances in high-throughput sequencing technologies, it becomes possible to directly analyze microbial communities in the human body and in the environment. Knowledge of how microbes interact with each other and form…
In this paper, we describe the algorithms we implemented in FDPS to make efficient use of accelerator hardware such as GPGPUs. We have developed FDPS to make it possible for many researchers to develop their own high-performance parallel…
Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. Identification of co-expressed genes and coherent patterns is the central goal in microarray or…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
Protein inference plays a vital role in the proteomics study. Two major approaches could be used to handle the problem of protein inference; top-down and bottom-up. This paper presents a framework for protein inference, which uses hardware…
PPINtonus is a system for the early detection of Parkinson's Disease (PD) utilizing deep-learning tonal analysis, providing a cost-effective and accessible alternative to traditional neurological examinations. Partnering with the…
Computational neuroscience is being revolutionized with the advent of multi-electrode arrays that provide real-time, dynamic, perspectives into brain function. Mining event streams from these chips is critical to understanding the firing…
Epilepsy is a neurological disorder classified as the second most serious neurological disease known to humanity, after stroke. Localization of the epileptogenic zone is an important step for epileptic patient treatment, which starts with…
It is more and more common to explore the genome at diverse levels and not only at a single omic level. Through integrative statistical methods, omics data have the power to reveal new biological processes, potential biomarkers, and…
The schooling behavior of fish can be studied through simulations involving a large number of interacting particles. In such systems, each individual particle is guided by behavior rules, which include aggregation towards a centroid,…
Epilepsy is a neurological brain disorder which life threatening and gives rise to recurrent seizures that are unprovoked. It occurs due to the abnormal chemical changes in our brain. Over the course of many years, studies have been…
Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods…
This paper proposes a novel Extended Particle Swarm Optimization model (EPSO) that potentially enhances the search process of PSO for optimization problem. Evidently, gene expression profiles are significantly important measurement factor…
The expression levels of many thousands of genes can be measured simultaneously by DNA microarrays (chips). This novel experimental tool has revolutionized research in molecular biology and generated considerable excitement. A typical…
This paper presents a new major release of the program FIESTA (Feynman Integral Evaluation by a Sector decomposiTion Approach). The new release is mainly aimed at optimal performance at large scales when one is increasing the number of…
Performance in modern GPU-centric systems increasingly depends on resource management policies, including memory placement, scheduling, and observability. However, uniform policies typically yield suboptimal performance across diverse…
Identification of essential genes is one of the ultimate goals of drug designs. Here we introduce an {\it in silico} method to select essential genes through the microarray assay. We construct a graph of genes, called the gene transcription…
Multiparty session types are designed to abstractly capture the structure of communication protocols and verify behavioural properties. One important such property is progress, i.e., the absence of deadlock. Distributed algorithms often…