IEEE/ACM Transactions on Computational Biology and Bioinformatics

Computational genomics is an emerging field that is enabling us to reveal the origins of life and the genetic basis of diseases such as cancer. Next Generation Sequencing NGS technologies have unleashed a wealth of genomic information by producing ...

External control of gene regulatory networks GRNs has received much attention in recent years. The aim is to find a series of actions to apply to a gene regulation system making it avoid its diseased states. In this work, we propose a novel method for ...

The research in DNA data compression lacks a standard dataset to test out compression tools specific to DNA. This paper argues that the current state of achievement in DNA compression is unable to be benchmarked in the absence of such scientifically ...

In the midst of the important genomic variants associated to the susceptibility and resistance to complex diseases, Copy Number Variations CNV has emerged as a prevalent class of structural variation. Following the flood of next-generation sequencing ...

Next Generation Sequencing NGS, a family of technologies for reading DNA and RNA, is changing biological research, and will soon change medical practice, by quickly providing sequencing data and high-level features of numerous individual genomes in ...

Aberrant changes to interactions among cellular components have been conjectured to be potential causes of abnormalities in cellular functions. By systematic analysis of high-throughput-omics data, researchers hope to detect potential associations among ...

Owing to the innate noise in the biological data sources, a single source or a single measure do not suffice for an effective disease gene prioritization. So, the integration of multiple data sources or aggregation of multiple measures is the need of ...

De novo protein structure prediction aims to search for low-energy conformations as it follows the thermodynamics hypothesis that places native conformations at the global minimum of the protein energy surface. However, the native conformation is not ...

With recent advances in high-throughput cell biology, the amount of cellular biological data has grown drastically. Such data is often modeled as graphs also called networks and studying them can lead to new insights into molecule-level organization. A ...

The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor pre-miRNA. These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are ...

Named Entity Recognition NER is a basic step for large number of consequent text mining tasks in the biochemical domain. Increasing the performance of such recognition systems is of high importance and always poses a challenge. In this study, a new ...

Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from deterministic partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. ...

Human diseases involve a sequence of complex interactions between multiple biological processes. In particular, multiple genomic data such as Single Nucleotide Polymorphism SNP, Copy Number Variation CNV, DNA Methylation DM, and their interactions ...

As costs of genome sequencing have dropped precipitously, development of efficient bioinformatic methods to analyze genome structure and evolution have become ever more urgent. For example, most published phylogenomic studies involve either massive ...

Segmentation and analysis of histological images provides a valuable tool to gain insight into the biology and function of microglial cells in health and disease. Common image segmentation methods are not suitable for inhomogeneous histology image ...

Next generation sequencing technologies enable efficient and cost-effective genome sequencing. However, sequencing errors increase the complexity of the de novo assembly process, and reduce the quality of the assembled sequences. Many error correction ...

Protein-DNA interactions are ubiquitous in a wide variety of biological processes. Correctly locating DNA-binding residues solely from protein sequences is an important but challenging task for protein function annotations and drug discovery, especially ...

Since proteins are digested into a mixture of peptides in the preprocessing step of tandem mass spectrometry MS, it is difficult to determine which specific protein a shared peptide belongs to. In recent studies, besides tandem MS data and peptide ...

Genome-scale metabolic network models GEMs have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, ...

One of the most significant research issues in functional genomics is insilico identification of disease related genes. In this regard, the paper presents a new gene selection algorithm, termed as SiFS, for identification of disease genes. It integrates ...

Background: Large amounts of metabolomics data have been accumulated in recent years and await analysis. Previously, we had developed a systems biology approach to infer biochemical mechanisms underlying metabolic alterations observed in cancers and ...

Network alignment has extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the ...

Metagenomic contigs binning is a necessary step of metagenome analysis. After assembly, the number of contigs belonging to different genomes is usually unequal. So a metagenomic contigs dataset is a kind of imbalanced dataset and traditional fuzzy c-...

The discovery of human disease-related miRNA is a challenging problem for complex disease biology research. For existing computational methods, it is difficult to achieve excellent performance with sparse known miRNA-disease association verified by ...

Various mechanical models of live amnioserosa cells during Drosophila melanogaster’s dorsal closure are proposed. Such models account for specific biomechanical oscillating behaviors and depend on a different set of parameters. The identification of the ...

Remote homology detection represents a central problem in bioinformatics, where the challenge is to detect functionally related proteins when their sequence similarity is low. Recent solutions employ representations derived from the sequence profile, ...