Page 207 of 247
A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases) might refer to more than one gene. The task of Gene Symbol Disambiguation (GSD) – a...
HLA haplotype analysis has been used in population genetics and in the investigation of disease-susceptibility locus, due to its high polymorphism. Several methods for inferring haplotype genotypic data have b...
Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph re...
The development and improvement of reliable computational methods designed to evaluate the quality of protein models is relevant in the context of protein structure refinement, which has been recently identifi...
Quantitative characterization of the topological characteristics of protein-protein interaction (PPI) networks can enable the elucidation of biological functional modules. Here, we present a novel clustering m...
Gene expression measurements from breast cancer (BrCa) tumors are established clinical predictive tools to identify tumor subtypes, identify patients showing poor/good prognosis, and identify patients likely t...
Prediction of bacterial virulent protein sequences has implications for identification and characterization of novel virulence-associated factors, finding novel drug/vaccine targets against proteins indispensa...
Identification of RNA homologs within genomic stretches is difficult when pairwise sequence identity is low or unalignable flanking residues are present. In both cases structure-sequence or profile/family-sequ...
Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene...
In the present investigation, we have used an exhaustive metabolite profiling approach to search for biomarkers in recombinant Aspergillus nidulans (mutants that produce the 6- methyl salicylic acid polyketide mo...
The identification of specific gene expression signature for distinguishing sample groups is a dominant field in cancer research. Although a number of tools have been developed to identify optimal gene express...
In general, gene function prediction can be formalized as a classification problem based on machine learning technique. Usually, both labeled positive and negative samples are needed to train the classifier. F...
The previous studies of genome-wide expression patterns show that a certain percentage of genes are cell cycle regulated. The expression data has been analyzed in a number of different ways to identify cell cy...
Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, n...
In many research areas it is necessary to find differences between treatment groups with several variables. For example, studies of microarray data seek to find a significant difference in location parameters ...
Regulation of gene expression at the level of transcription is a major control point in many biological processes. Transcription factors (TFs) can activate and/or repress the transcriptional rate of target gen...
Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline th...
Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are tolerated. The rise in available protein s...
A fundamental problem when trying to define the functional relationships between proteins is the difficulty in quantifying functional similarities, even when well-structured ontologies exist regarding the acti...
Protein secondary structure prediction method based on probabilistic models such as hidden Markov model (HMM) appeals to many because it provides meaningful information relevant to sequence-structure relations...
Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also provide the means for identifying and discr...
Outer membrane proteins (OMPs) perform diverse functional roles in Gram-negative bacteria. Identification of outer membrane proteins is an important task.
Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have s...
In this paper, it is proposed an optimization approach for producing reduced alphabets for peptide classification, using a Genetic Algorithm. The classification task is performed by a multi-classifier system w...
With the completion of the HapMap project, a variety of computational algorithms and tools have been proposed for haplotype inference, tag SNP selection and genome-wide association studies. Simulated data are ...
Optimization theory has been applied to complex biological systems to interrogate network properties and develop and refine metabolic engineering strategies. For example, methods are emerging to engineer cells...
Hierarchical clustering is a widely applied tool in the analysis of microarray gene expression data. The assessment of cluster stability is a major challenge in clustering procedures. Statistical methods are r...
Protein-protein interactions (PPIs) play key roles in various cellular functions. In addition, some critical inter-species interactions such as host-pathogen interactions and pathogenicity occur through PPIs. ...
Prediction of 3-dimensional protein structures from amino acid sequences represents one of the most important problems in computational structural biology. The community-wide Critical Assessment of Structure P...
MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA transcripts. Previously, experime...
The discovery of biomarkers is an important step towards the development of criteria for early diagnosis of disease status. Recently electrospray ionization (ESI) and matrix assisted laser desorption (MALDI) t...
The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used t...
To meet the needs of gene annotation for newly sequenced organisms, optimized spaced seeds can be implemented into cross-species sequence alignment programs to accurately align gene sequences to the genome of ...
It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i....
The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive data...
Aligning multiple RNA sequences is essential for analyzing non-coding RNAs. Although many alignment methods for non-coding RNAs, including Sankoff's algorithm for strict structural alignments, have been propos...
The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed ...
This paper discusses the problem of automated annotation. It is a continuation of the previous work on the A4-algorithm (Adaptive algorithm of automated annotation) developed by Leontovich and others.
Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods,...
Analysis of complex samples with tandem mass spectrometry (MS/MS) has become routine in proteomic research. However, validation of database search results creates a bottleneck in MS/MS data processing. Recentl...
MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE...
The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models) have also been applied on the level of sequence repeats inside a gene/protein. Ph...
The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have th...
Normalization is essential in dual-labelled microarray data analysis to remove non-biological variations and systematic biases. Many normalization methods have been used to remove such biases within slides (Gl...
A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data ...
DNA methylation is an important epigenetic modification of the genome. Abnormal DNA methylation may result in silencing of tumor suppressor genes and is common in a variety of human cancer cells. As more epige...
In the last decade, sequencing projects have led to the development of a number of annotation systems dedicated to the structural and functional annotation of protein-coding genes. These annotation systems man...
Prediction of disulfide bridges from protein sequences is useful for characterizing structural and functional properties of proteins. Several methods based on different machine learning algorithms have been ap...
Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally develope...
Transposable elements are abundant in eukaryotic genomes and it is believed that they have a significant impact on the evolution of gene and chromosome structure. While there are several completed eukaryotic g...
View featured videos from across the BMC-series journals
2022 Citation Impact
3.0 - 2-year Impact Factor
4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
1.100 - SJR (SCImago Journal Rank)
2023 Speed
19 days submission to first editorial decision for all manuscripts (Median)
146 days submission to accept (Median)
2023 Usage
5,987,678 downloads
4,858 Altmetric mentions