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Microarray image analysis processes scanned digital images of hybridized arrays to produce the input spot-level data for downstream analysis, so it can have a potentially large impact on those and subsequent a...
Infections due to parasitic nematodes are common causes of morbidity and fatality around the world especially in developing nations. At present however, there are only three major classes of drugs for treating...
This article is part of a Supplement: Volume 12 Supplement 13
The dengue virus is the most significant arthropod-borne human pathogen, and an increasing number of cases have been reported over the last few decades. Currently neither vaccines nor drugs against the dengue ...
This article is part of a Supplement: Volume 12 Supplement 13
The cervical cancer is the second most prevalent cancer for the woman in the world. It is caused by the oncogenic human papilloma virus (HPV). The inhibition activity of histone deacetylase (HDAC) is a potenti...
This article is part of a Supplement: Volume 12 Supplement 13
Prediction of short stretches in protein sequences capable of forming amyloid-like fibrils is important in understanding the underlying cause of amyloid illnesses thereby aiding in the discovery of sequence-ta...
This article is part of a Supplement: Volume 12 Supplement 13
Schizophrenia, bipolar disorder, and major depression are devastating mental diseases, each with distinctive yet overlapping epidemiologic characteristics. Microarray and proteomics data have revealed genes wh...
This article is part of a Supplement: Volume 12 Supplement 13
Essential events of cell development and homeostasis are revealed by the associated changes of cell morphology and therefore have been widely used as a key indicator of physiological states and molecular pathw...
This article is part of a Supplement: Volume 12 Supplement 13
While contemporary methods of microarray analysis are excellent tools for studying individual microarray datasets, they have a tendency to produce different results from different datasets of the same disease....
This article is part of a Supplement: Volume 12 Supplement 13
LRP6 is a membrane protein crucial in the initiation of canonical Wnt/β-catenin signalling. Its function is dependent on its proline-serine rich intracellular domain. LRP6 has five PPP(S/T)P motifs that are ph...
This article is part of a Supplement: Volume 12 Supplement 13
Previously, the hypothetical protein, KPN00728 from Klebsiella pneumoniae MGH78578 was the Succinate dehydrogenase (SDH) chain C subunit via structural prediction and molecular docking simulation studies. However...
This article is part of a Supplement: Volume 12 Supplement 13
Carboxylation is a modification of glutamate (Glu) residues which occurs post-translation that is catalyzed by γ-glutamyl carboxylase in the lumen of the endoplasmic reticulum. Vitamin K is a critical co-facto...
This article is part of a Supplement: Volume 12 Supplement 13
One of the primary goals of comparative metagenomic projects is to study the differences in the microbial communities residing in diverse environments. Besides providing valuable insights into the inherent str...
This article is part of a Supplement: Volume 12 Supplement 13
Clustering-based methods on gene-expression analysis have been shown to be useful in biomedical applications such as cancer subtype discovery. Among them, Matrix factorization (MF) is advantageous for clusteri...
This article is part of a Supplement: Volume 12 Supplement 13
Many learning approaches to predicting RNA-binding residues in a protein sequence construct a non-redundant training dataset based on the sequence similarity. The sequence similarity-based method either takes ...
This article is part of a Supplement: Volume 12 Supplement 13
Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA–protein interactions. Although some successful computational tools have been reported to recognize RNA bin...
This article is part of a Supplement: Volume 12 Supplement 13
The collection of gene expression profiles from DNA microarrays and their analysis with pattern recognition algorithms is a powerful technology applied to several biological problems. Common pattern recognitio...
This article is part of a Supplement: Volume 12 Supplement 13
Highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs.
This article is part of a Supplement: Volume 12 Supplement 13
A critical aspect of the NIH Translational Research roadmap, which seeks to accelerate the delivery of "bench-side" discoveries to patient's "bedside," is the management of the provenance metadata that keeps trac...
Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to...
Enrichment testing assesses the overall evidence of differential expression behavior of the elements within a defined set. When we have measured many molecular aspects, e.g. gene expression, metabolites, prote...
Traditional strategies for selecting variables in high dimensional classification problems aim to find sets of maximally relevant variables able to explain the target variations. If these techniques may be eff...
Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between...
The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfi...
The iRefIndex addresses the need to consolidate protein interaction data into a single uniform data resource. iRefR provides the user with access to this data source from an R environment.
Computational methods for microRNA target prediction are a fundamental step to understand the miRNA role in gene regulation, a key process in molecular biology. In this paper we present miREE, a novel microRNA...
Along with the rapid digitalization of health data (e.g. Electronic Health Records), there is an increasing concern on maintaining data privacy while garnering the benefits, especially when the data are requir...
This article is part of a Supplement: Volume 12 Supplement 12
One of the drawbacks we face up when analyzing gene to phenotype associations in genomic data is the ugly performance of the designed classifier due to the small sample-high dimensional data structures (n ≪ p) at...
This article is part of a Supplement: Volume 12 Supplement 12
Fold recognition techniques take advantage of the limited number of overall structural organizations, and have become increasingly effective at identifying the fold of a given target sequence. However, in the ...
This article is part of a Supplement: Volume 12 Supplement 12
Protein-protein interaction (PPI) extraction has been a focal point of many biomedical research and database curation tools. Both Active Learning and Semi-supervised SVMs have recently been applied to extract ...
This article is part of a Supplement: Volume 12 Supplement 12
The interactions among genetic factors related to diseases are called epistasis. With the availability of genotyped data from genome-wide association studies, it is now possible to computationally unravel epis...
This article is part of a Supplement: Volume 12 Supplement 12
Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks...
This article is part of a Supplement: Volume 12 Supplement 12
An important analysis performed on microarray gene-expression data is to discover biclusters, which denote groups of genes that are coherently expressed for a subset of conditions. Various biclustering algorit...
This article is part of a Supplement: Volume 12 Supplement 12
Expressed Sequence Tags (ESTs) have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ESTs are ...
Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding ...
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisance...
This research presents three new numerical representations for classifying short exon and intron sequences using discrete Fourier transform period-3 value. Based on the human genome, results indicate that the ...
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
This article is part of a Supplement: Volume 12 Supplement 11
The Student Council (SC) of the International Society for Computational Biology (ISCB) organized their annual symposium in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference.
This article is part of a Supplement: Volume 12 Supplement 11
Successfully modeling high-dimensional data involving thousands of variables is challenging. This is especially true for gene expression profiling experiments, given the large number of genes involved and the ...
RNA sequencing is a flexible and powerful new approach for measuring gene, exon, or isoform expression. To maximize the utility of RNA sequencing data, new statistical methods are needed for clustering, differ...
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