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With the advent of sequencing technology, numerous gene expression data are generated. Identifying differentially expressed genes play an important role in the gene therapy of cancer patients. As an useful mathematical tool, nonnegative matrix factorization (NMF) has been successfully used for identifying differentially expressed genes. In this paper, a novel method named robust graph regularized...
Depression is one of the most common and disabling mental disorders that has a relevant impact on society. Semiautomatic and/or automatic health monitoring systems could be crucial and important to improve depression detection and follow-up. Sentiment Analysis refers to the use of natural language processing and text mining methodologies aiming to identify opinion or sentiment. Affective Computing...
Understanding the nature of many diseases, including cancer, requires locating somatically acquired rearrangements corresponding to large-scale chromosomal aberrations. Computational methods to detect inter-chromosomal rearrangements based on next-generation sequencing platforms face the big challenge of accurately predicting the location of sites spanned by a typically small number of reads, while...
The aim of this paper is (i)to study breast cancer growth by mean of a mathematical model describing cell population dynamics during cancer growth, and (ii)to use this model to reproduce and explain experimental data. We started from a linear model describing cancer subpopulations evolution based on the Cancer Stem Cell (CSC) theory, and we added feedback mechanisms from the cell populations to mimic...
Ginger is widely used as a spice and traditional Chinese medicine achieving warming interior for dispelling cold during its long time clinical observations and practices. However, its mechanism is still obscure. In this study, interior is restricted to stomach and small intestine. 6-gingerol, ginger's quality control and main bio-active chemical compound, is chosen to represent ginger. Started with...
Health surveillance is an important task to track the happenings related to human health, and one of its areas is pharmacovigilance. Pharmacovigilance tracks and monitors safe use of pharmaceutical products. Pharmacovigilance involves tracking side effects that may be caused by medicines and other health related drugs. Medical professionals have a difficult time collecting this information. It is...
It is well known that gout and hyperuricemia are comorbidity due to the high level of uric acid in the blood and its crystallization. However, the pathological mechanism underlying the comorbidity of gout and hyperuricemia is still obscure. In this study, focused on the genes associated with hyperuricemia and gout, three functional protein networks were constructed. They illustrate the pathological...
Despite the linear relation between the number of observed spectra and the searching time, the current protein search engines, even the parallel versions, could take several hours to search a large amount of MS/MS spectra, which can be generated in a short time. After a laborious searching process, some (and at times, majority) of the observed spectra are labeled as non-identifiable. We evaluate the...
This study investigates a novel technique of tissues segmentation of high-grade (HG) glioma. Segmentation of tumor and edema for treatment planning is crucial. Anisotropic diffusion filter removes the noise and preserves the tumor tissues in MRI images. K-mean clustering algorithm clusters the brain tissues in normal and tumor tissues. The healthy tissues surround tumor tissues. Hierarchical centroid...
NB-UVB Phototherapy is one of the most common treatments administrated by dermatologists for psoriasis patients. Although in general, the treatment results in improving the condition, it also can worsen it. If a model can predict the treatment response before hand, the dermatologists can adjust the treatment accordingly. In this paper, we use data mining techniques and conduct four experiments. The...
Information technology is increasingly being used in healthcare paramedic sector with the goal to improve management of resources and enhance medical services to save lives. In this paper, we introduce EMTriage, a distributed Android application with the ability to access patients EHR's, and depending on the data and inputs, assess and distribute an acuity level to patients in need of resources. We...
The rapidly increasing availability of healthcare data from multiple heterogeneous sources has spearheaded the adoption of data-driven approaches for improved clinical research, decision making, and patient management. The patient healthcare data are usually longitudinal and can be expressed as medical event sequences, where the events include clinical diagnosis, medications, laboratory reports, etc...
Breast cancer is the most common type of invasive cancer in females. It accounts for 18.2% of all cancer deaths worldwide. Although somatic mutations play important roles in cancer development and prognosis, the outcome predictions are largely based on the expression of marker genes. We submit that developing an innovative prognostic model incorporating somatic mutations with gene expression can improve...
It is important for data scientists to have a good understanding of the availability of relevant datasets as well as the content, structure, and existing analyses of these datasets. While a number of efforts are underway to integrate the large amount and variety of datasets, there is a lack of information resources that focus on specific learning needs of some targeted audiences. To address this gap,...
Predicting patients' risk of developing certain diseases is an important research topic in healthcare. Personalized predictive modeling, which focuses on building specific models for individual patients, has shown its advantages on utilizing heterogeneous health data compared to global models trained on the entire population. Personalized predictive models use information from similar patient cohorts,...
Functional region identification is of fundamental importance for protein sequences analysis for a protein family. Such knowledge not only provides a better scientific understanding but also assists drug discovery. Domain annotation is one approach but it needs to leverage existing databases. For de novo discovery, motif discovery locates and aligns locally similar sub-sequences and represents them...
Proteins from the same family have similar functions. Hence, it is important to discover from a protein family conserved sequence patterns with variations to unveil the functionality of a functional domain. Aligned Pattern Clusters (APCs) are knowledge-rich representations comparing with probabilistic models. If significant aligned residue associations (ARAs) were discovered in APCs, they could reveal...
Protein-DNA docking is an important computational technique for generating native or near-native complex models. A docking program typically generates a number of complex conformations and predicts the docking solution based on interaction energies. However, incomplete sampling and energy function deficiencies can result in false positive protein-DNA complex models, which hampers its application in...
The alignment of protein-protein interaction (PPI) networks is an effective approach to uncover the functionally conserved sub-structure between networks. A wealth of approaches have been developed for global PPI network alignment in recent years. However, due to the computational intractability caused by its NP-completeness, global PPI network alignment remains challenging in finding large conserved...
The recognized significance of rumen microbiome has inspired efforts to examine the composition of rumen microbial communities in a large scale. One of the key research areas is to infer association and dependencies between members of rumen microbial communities through correlation analysis. However, it has been found that due to the compositional nature of data, simply applying correlation-based...
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