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 ...

The influx of high-throughput biotechnologies has resulted in considerable amounts of available and untapped data, useful for both interpretation and extrapolation. Due to the fact that the noise to signal ratio in most biological databases are non-...

Small-angle x-ray scattering (SAXS) is an experimental biophysical method used for gaining insight into the structure of large biomolecular complexes. Under appropriate chemical conditions, the information obtained from a SAXS experiment can be equated ...

We propose a Robust Non-negative Matrix Factorization (RNMF) formulation by introducing L₁-norm regularization terms for decomposed factors to cluster noisy biological networks for identification of functional modules. To solve robust NMF, we develop an ...

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 ...

Typically, a vast amount of experience and data is needed to successfully determine cancer prognosis in the face of (1) the inherent stochasticity of cell dynamics, (2) incomplete knowledge of healthy cell regulation, and (3) the inherent uncertain and ...

Dynamic Programming (DP) provides optimal solutions to a problem by combining optimal solutions to many overlapping subproblems. DP algorithms exploit this overlapping property to explore otherwise exponential-sized problem spaces in polynomial time, ...

We established a bioinformatics procedure at our laboratory that processes sequencing data, identifies single nucleotide variants (SNVs) and small insertions/deletions (indels), annotates the variants based on the curated variant databases and ...

Many cancers appear to have an increased somatic mutation rate. Intriguingly, increased numbers of tumor-infiltrating T cells are often found in cancers with defective DNA repair, which especially accumulate high numbers of somatic mutations. These ...

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between ...

Motivation: Because susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and their ...

Signaling pathways play an important role in the cell's response to its environment. Signaling pathways are often represented as directed graphs, which are not adequate for modeling reactions such as complex assembly and dissociation, combinatorial ...

With the abundance of vast amounts of "-omic" biological data from multiple sources that span diverse biological processes, approaches for answering critical questions become a vital mission. To grasp more comprehensive view of the biology of the ...

Recent US government initiatives have led to wide adoption of Electronic Health Records (EHRs). More and more health care institutions are storing patients' data in an electronic format. These EHRs contain valuable information which can be used in ...

Since human aging is hard to study experimentally due to long lifespan and ethical constraints, current "ground truth" knowledge about human aging has mostly been predicted computationally or statistically by transferring the knowledge from well-studied ...

Detection of differentially expressed (DE) genes across conditions within RNA-Seq datasets yields insight into the differences in biological processes at work in these conditions. Most methods available for discovering DE genes use statistical methods ...

Protein-protein docking methods aim to compute the correct bound form of two or more proteins. One of the major challenges for docking methods is to accurately discriminate native-like structures. The protein docking community agrees on the existence of ...