Broad open access to entire clinical research studies data is on the rise. Public access to raw clinical research data has created tremendous opportunity to evaluate new research hypotheses that were not originally formulated in the studies; by ...

To date, our understanding of a normal immune system is far behind that of other healthy organ systems. One reason for this is the lack of standardization in the lab techniques, especially flow cytometry.

To take a step towards the characterization of a ...

In this paper, we present a novel semi-supervised technique for finding privacy-sensitive events in clinical text. Unlike traditional semi-supervised methods, we do not require large amounts of unannotated data. Instead, our approach relies on ...

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process ...

Dysphonia, caused by irregular vocal folds vibration, is one of the major symptoms of benign laryngeal diseases and other organic and functional pathologies. The paper presents a cloud-based system for remote analysis of vocal samples submitted by ...

While efforts have been made to both retrieve genes associated with a phenotype, and model gene regulatory networks (GRNs), no such progress has been made regarding the creation of GRNs from phenotype keywords and reverse engineered large-scale gene ...

With the growth of bio-systems model development, automatic approaches are needed to support systems biologists in model similarity evaluation. Several algorithms have been proposed, but they lack efficiency. We have developed an efficient, intuitive ...

Biosystem comparison plays a major role in system biology. Similar biosystems are identified based on the similarity of species naming. Since the species naming does not follow a standard nomenclature, similarity is not easy to formalize. A single ...

A post-translational modification (PTM) describes a form of biosynthesis for the task of initializing proteins for specific functions. PTMs are complexes which are involved in developing or customizing proteins to increase their functional diversity. In ...

miRNAs are small fragments of RNA composed by 22 nucleotides. Many researchers are involved in studying these molecules that are considered as potential biomarkers and therapeutic targets for many diseases. The interests of computer scientists is ...

Comparative network analysis finds similarities between a query and a target network by aligning them. Biological network evolves over time; and so does the topology of the query network extracted from it. We denote a sequence of query networks where ...

Predicting which peptides can elicit a T cell response (i.e. are immunogenic) is of great importance for many immunological studies. While it is clear that MHC binding is a necessary requirement for peptide immunogenicity, other variables exist that are ...

Computational prediction of HLA class II restricted T cell epitopes has great significance in many immunological studies including vaccine discovery. With the development of novel bioinformatics approaches, prediction of HLA class II binding has ...

B-cell epitope prediction remains relatively underdeveloped as compared with T-cell epitope prediction. To address this deficiency, a generic framework is presented herein for quantitative prediction of biological effects mediated by antipeptide ...

Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from ...

Cryo-Electron Microscopy is a biophysical technique that generates volumetric images of macromolecules. Although it is hard to distinguish the backbone from the density map at medium resolutions such as 5-10Å, the location of major secondary structure ...

Proteins are large flexible biological molecules and conformational flexibility is a shared challenge in comparisons of protein structure. Many tools have been developed to identify remote homologs in cases where backbone flexibilities are considered. ...

Complex diseases such as cancer are known to be highly heterogeneous which results in tumor subtypes that show varying behavior, including different survival time, treatment responses, and recurrence rates. One important problem in biomedical research ...

Biological functions are executed through elaborate collaboration of various biomolecules, and there has been increasing interest in the computational identification of functional modules from large-scale experimental data. In this study, we performed a ...

In this work, we propose a novel context-sensitive random walk model to accurately estimate the node correspondence between two biological networks. We adopt a Markov random walk model that performs a simultaneous walk on two networks. At each step, the ...