IEEE/ACM Transactions on Computational Biology and Bioinformatics

Smoking is the major cause of lung cancer and the leading cause of cancer-related death in the world. The most current view about lung cancer is no longer limited to individual genes being mutated by any carcinogenic insults from smoking. Instead, ...

This article presents two new deterministic algorithms for constructing consensus trees. Given an input of $k$ phylogenetic trees with identical leaf label sets and $n$ leaves each, the first algorithm constructs the majority rule + consensus tree in $...

Protein-protein interactions PPIs play a vital role in the biological processes involved in the cell functions and disease pathways. The experimental methods known to predict PPIs require tremendous efforts and the results are often hindered by the ...

The research detailed in this paper focuses on the processing of Electroencephalography EEG data to identify attention during the learning process. The identification of affect using our procedures is integrated into a simulated distance learning system ...

Recent advances in high-throughput technologies have given rise to collecting large amounts of multidimensional heterogeneous data that provide diverse information on the same biological samples. Integrative analysis of such multisource datasets may ...

In this study, the expected time required to eradicate HIV-1 completely was found as the conditional absorbing time in a finite state space continuous-time Markov chain model. The Markov chain has two absorbing states: one corresponds to HIV eradication ...

Gene-expression-based phenotype classification is used for disease diagnosis and prognosis relating to treatment strategies. The present paper considers classification based on sequential measurements of multiple genes using gene regulatory network GRN ...

The tandem duplication random loss operation TDRL is an important genome rearrangement operation in metazoan mitochondrial genomes. A TDRL consists of a duplication of a contiguous set of genes in tandem followed by a random loss of one copy of each ...

Hajirasouliha and Raphael WABI 2014 proposed a model for deconvoluting mixed tumor samples measured from a collection of high-throughput sequencing reads. This is related to understanding tumor evolution and critical cancer mutations. In short, their ...

The identification of essential proteins in protein-protein interaction PPI networks is of great significance for understanding cellular processes. With the increasing availability of large-scale PPI data, numerous centrality measures based on network ...

Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to ...

When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with ...

Heme is an essential biomolecule that widely exists in numerous extant organisms. Accurately identifying heme binding residues HEMEs is of great importance in disease progression and drug development. In this study, a novel predictor named HEMEsPred was ...

This study proposes a new method to determine the functions of an unannotated protein. The proteins and amino acid residues mentioned in biomedical texts associated with an unannotated protein $p$ can be considered as characteristics terms for $p$, ...

Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes are still ...

The application of machine learning methods for the identification of candidate genes responsible for phenotypes of interest, such as cancer, is a major challenge in the field of bioinformatics. These lists of genes are often called genomic signatures ...

This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to ...

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with ...

In systems biology, network models are often used to study interactions among cellular components, a salient aim being to develop drugs and therapeutic mechanisms to change the dynamical behavior of the network to avoid undesirable phenotypes. Owing to ...

Epidermal Growth Factor Receptor EGFR signaling to the Ras-MAPK pathway is implicated in the development and progression of cancer and is a major focus of targeted combination therapies. Physiochemical models have been used for identifying and testing ...

In extreme cold weather, living organisms produce Antifreeze Proteins AFPs to counter the otherwise lethal intracellular formation of ice. Structures and sequences of various AFPs exhibit a high degree of heterogeneity, consequently the prediction of ...

Collective motion of swimmers can be detected by hydrodynamic interactions through the effective macroscopic viscosity. It follows from the general hydrodynamics that the effective viscosity of non-dilute random suspensions depends on the shape of ...

We describe a specialized methodology for segmenting 2D microscopy digital images of freshwater green microalgae. The goal is to obtain representative algae shapes to extract morphological features to be employed in a posterior step of taxonomical ...

This paper deals with the sampled-data stabilization problem for Takagi-Sugeno T-S fuzzy genetic regulatory networks with leakage delays. A novel Lyapunov-Krasovskii functional LKF is established by the non-uniform division of the delay intervals with ...

Computing similarity or dissimilarity between protein structures is an important task in structural biology. A conventional method to compute protein structure dissimilarity requires structural alignment of the proteins. However, defining one best ...

Interleukin-8 IL-8, CXCL8 is a neutrophil chemotactic factor belonging to the family of chemokines. IL-8 was shown to resist pepsin cleavage displaying its high resistance to this protease. However, the molecular mechanisms underlying this resistance ...

MicroRNAs miRNAs play an essential role in many biological processes by regulating the target genes, especially in the initiation and development of cancers. Therefore, the identification of the miRNA-mRNA regulatory modules is important for ...

Genome-wide association study GWAS has been widely witnessed as a powerful tool for revealing suspicious loci from various diseases. However, real world GWAS tasks always suffer from the data imbalance problem of sufficient control samples and limited ...

In existing works, the filters designed for delayed genetic regulatory networks GRNs contain time delay. If the time delay is unknown, the filters do not work in practical applications. In order to overcome the shortcoming in such existing works, this ...

Network Alignment over graph-structured data has received considerable attention in many recent applications. Global network alignment tries to uniquely find the best mapping for a node in one network to only one node in another network. The mapping is ...