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An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA bi...
DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amo...
Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpo...
The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology.
Quantitative simultaneous monitoring of the expression levels of thousands of genes under various experimental conditions is now possible using microarray experiments. However, there are still gaps toward whol...
Cell culture systems are useful in studying toxicological effects of chemicals such as Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), however little is known as to how accurately isolated cells reflect respons...
As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations.
Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video im...
DNA Microarray technology is an innovative methodology in experimental molecular biology, which has produced huge amounts of valuable data in the profile of gene expression. Many clustering algorithms have bee...
Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. U...
Cluster analysis is an integral part of high dimensional data analysis. In the context of large scale gene expression data, a filtered set of genes are grouped together according to their expression profiles u...
Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the re...
Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional...
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The ...
One type of DNA microarray experiment is discovery of gene expression patterns for a cell line undergoing a biological process over a series of time points. Two important issues with such an experiment are the...
The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. It is a key problem in biological sequences analysis. The SCS problem...
One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been d...
Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Orderi...
The amplification of variable regions of immunoglobulins has become a major challenge in the cloning of antibody genes, whether from hybridoma cell lines or splenic B cells. Using conventional protocols, the h...
Recently several statistical methods have been proposed to identify genes with differential expression between two conditions. However, very few studies consider the problem of sample imbalance and there is no...
Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an...
Structure matching plays an important part in understanding the functional role of biological structures. Bioinformatics assists in this effort by reformulating this process into a problem of finding a maximum...
Haplotype analysis has gained increasing attention in the context of association studies of disease genes and drug responsivities over the last years. The potential use of haplotypes has led to the initiation ...
Searching for the longest common sequence (LCS) of multiple biosequences is one of the most fundamental tasks in bioinformatics. In this paper, we present a parallel algorithm named FAST_LCS to speedup the com...
TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear.
The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The...
The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRM...
Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologic...
Expression microarrays represent a powerful technique for the simultaneous investigation of thousands of genes. The evidence that genes are not randomly distributed in the genome and that their coordinated exp...
The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows ...
Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family o...
As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and c...
The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using pattern search algorithms have been valua...
Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide – adenine (A), thymine (T), cytosine (C) or guanine (G) – is altered. Arguably, SNPs account for more than...
The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. A...
Although protein-protein interaction networks determined with high-throughput methods are incomplete, they are commonly used to infer the topology of the complete interactome. These partial networks often show...
Knowing the submitochondria localization of a mitochondria protein is an important step to understand its function. We develop a method which is based on an extended version of pseudo-amino acid composition to...
A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metaboli...
Short interfering RNAs have allowed the development of clean and easily regulated methods for disruption of gene expression. However, while these methods continue to grow in popularity, designing effective siR...
Measuring each protein's importance in signaling networks helps to identify the crucial proteins in a cellular process, find the fragile portion of the biology system and further assist for disease therapy. Ho...
Uncertainty often affects molecular biology experiments and data for different reasons. Heterogeneity of gene or protein expression within the same tumor tissue is an example of biological uncertainty which sh...
Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We co...
Propositional representations of biomedical knowledge are a critical component of most aspects of semantic mining in biomedicine. However, the proper set of propositions has yet to be determined. Recently, the...
Automatic recognition of relations between a specific disease term and its relevant genes or protein terms is an important practice of bioinformatics. Considering the utility of the results of this approach, w...
The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools th...
We study the adaptation of Link Grammar Parser to the biomedical sublanguage with a focus on domain terms not found in a general parser lexicon. Using two biomedical corpora, we implement and evaluate three ap...
Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics...
The availability of genome sequences for many organisms enabled the reconstruction of several genome-scale metabolic network models. Currently, significant efforts are put into the automated reconstruction of ...
Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for t...
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2022 Citation Impact
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4.3 - 5-year Impact Factor
0.938 - SNIP (Source Normalized Impact per Paper)
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