GeneNetFinder2: improved inference of dynamic gene regulatory relations with multiple regulators
A gene involved in complex regulatory interactions may have multiple regulators since gene expression in such interactions is often controlled by more than one gene. Another thing that makes gene regulatory interactions complicated is that regulatory ...
Hybrid framework using multiple-filters and an embedded approach for an efficient selection and classification of microarray data
A hybrid framework composed of two stages for gene selection and classification of DNA microarray data is proposed. At the first stage, five traditional statistical methods are combined for preliminary gene selection (Multiple Fusion Filter). Then, ...
Predicting hub genes associated with cervical cancer through gene co-expression networks
Cervical cancer is the third most common malignancy in women worldwide. It remains a leading cause of cancer-related death for women in developing countries. In order to contribute to the treatment of the cervical cancer, in our work, we try to find a ...
Predicting the subcellular localization of proteins with multiple sites based on multiple features fusion
Protein sub-cellular localization prediction has attracted much attention in recent years because of its importance for protein function studying and targeted drug discovery, and that makes it to be an important research field in bioinformatics. ...
A faster cDNA microarray gene expression data classifier for diagnosing diseases
Profiling cancer molecules has several advantages; however, using microarray technology in routine clinical diagnostics is challenging for physicians. The classification of microarray data has two main limitations: 1) the data set is unreliable for ...
ChIP-PIT: enhancing the analysis of ChIP-seq data using convex-relaxed pair-wise interaction tensor decomposition
In recent years, thanks to the efforts of individual scientists and research consortiums, a huge amount of chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experimental data have been accumulated. Instead of investigating ...
Practical guidelines for incorporating knowledge-based and data-driven strategies into the inference of gene regulatory networks
Modeling gene regulatory networks (GRNs) is essential for conceptualizing how genes are expressed and how they influence each other. Typically, a reverse engineering approach is employed; this strategy is effective in reproducing possible fitting models ...
The intrinsic geometric structure of protein-protein interaction networks for protein interaction prediction
Recent developments in high-throughput technologies for measuring protein-protein interaction (PPI) have profoundly advanced our ability to systematically infer protein function and regulation. However, inherently high false positive and false negative ...
A novel teaching-learning-based optimization for improved mutagenic primer design in mismatch PCR-RFLP SNP genotyping
Many single nucleotide polymorphisms (SNPs) for complex genetic diseases are genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in small-scale basic research studies. It is an essential work to design feasible PCR-...
Discovering motifs in biological sequences using the micron automata processor
Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l ...
Fractal behavior of the pancreatic β-cell near the percolation threshold: effect of the KATP channel on the electrical response
The molecular system built with true chemical bonds or strong molecular interaction can be described using conceptual mathematical tools. Modeling of the natural generated ionic currents on the human pancreatic β-cell activity had been already studied ...
gEFM: an algorithm for computing elementary flux modes using graph traversal
Computational methods to engineer cellular metabolism promise to play a critical role in producing pharmaceutical, repairing defective genes, destroying cancer cells, and generating biofuels. Elementary Flux Mode (EFM) analysis is one such powerful ...
Globally asymptotic stability analysis for genetic regulatory networks with mixed delays: an m-matrix-based approach
This paper deals with the problem of globally asymptotic stability for nonnegative equilibrium points of genetic regulatory networks (GRNs) with mixed delays (i.e., time-varying discrete delays and constant distributed delays). Up to now, all existing ...
Identification of glucose-binding pockets in human serum albumin using support vector machine and molecular dynamics simulations
Human Serum Albumin (HSA) has been suggested to be an alternate biomarker to the existing Hemoglobin-A1c (HbA1c) marker for glycemic monitoring. Development and usage of HSA as an alternate biomarker requires the identification of glycation sites, or ...
Relational agreement measures for similarity searching of cheminformatic data sets
Research on similarity searching of cheminformatic data sets has been focused on similarity measures using fingerprints. However, nominal scales are the least informative of all metric scales, increasing the tied similarity scores, and decreasing the ...
2015 reviewers list
The publication offers a note of thanks and lists its reviewers.
2015 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 12
This index covers all technical items - papers, correspondence, reviews, etc. - that appeared in this periodical during the year, and items from previous years that were commented upon or corrected in this year. Departments and other items may also be ...