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Saccharomyces cerevisiae myosin type II-deficient (myo1 Δ) strains remain viable and divide, despite the absence of a cytokinetic ring, by activation of the PKC1-dependent cell wall integrity pathway (CWIP). Sinc...
The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 ...
The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA clust...
Blochmannia are obligately intracellular bacterial mutualists of ants of the tribe Camponotini. Blochmannia perform key nutritional functions for the host, including synthesis of several essential amino acids. We...
Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fr...
An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome sc...
The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. H...
This article is part of a Supplement: Volume 11 Supplement 4
Nuclear Factor kappa B (NF-κB) is a transcription factor involved in the regulation of cell signaling responses and is a key regulator of cellular processes involved in the immune response, differentiation, ce...
This article is part of a Supplement: Volume 11 Supplement 4
Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, maki...
This article is part of a Supplement: Volume 11 Supplement 4
Human disease genes can be distinguished from essential (embryonically lethal) and non-disease genes using gene attributes. Such attributes include gene age, tissue specificity of expression, regulatory capaci...
This article is part of a Supplement: Volume 11 Supplement 4
Changes to the glycosylation profile on HIV gp120 can influence viral pathogenesis and alter AIDS disease progression. The characterization of glycosylation differences at the sequence level is inadequate as t...
This article is part of a Supplement: Volume 11 Supplement 4
The identification of B-cell epitopes on antigens has been a subject of intense research as the knowledge of these markers has great implications for the development of peptide-based diagnostics, therapeutics ...
This article is part of a Supplement: Volume 11 Supplement 4
A key problem in systems biology is estimating dynamical models of gene regulatory networks. Traditionally, this has been done using regression or other ad-hoc methods when the model is linear. More detailed, ...
This article is part of a Supplement: Volume 11 Supplement 4
Developing effective strategies to reveal modular structures in protein interaction networks is crucial for better understanding of molecular mechanisms of underlying biological processes. In this paper, we pr...
This article is part of a Supplement: Volume 11 Supplement 4
A gene regulatory relation often changes over time rather than being constant. But many gene regulatory networks available in databases or literatures are static in the sense that they are either snapshots of ...
This article is part of a Supplement: Volume 11 Supplement 4
Harnessing vast amounts of genomic data in phylogenetic context stemming from massive sequencing of multiple closely related genomes requires new tools and approaches. We present a tool for the genome-wide ana...
This article is part of a Supplement: Volume 11 Supplement 4
While the accuracy and precision of deep sequencing data is significantly better than those obtained by the earlier generation of hybridization-based high throughput technologies, the digital nature of deep se...
This article is part of a Supplement: Volume 11 Supplement 4
When characterizing the structural topology of proteins, protein secondary structure (PSS) plays an important role in analyzing and modeling protein structures because it represents the local conformation of a...
This article is part of a Supplement: Volume 11 Supplement 4
Nucleosome, the fundamental unit of chromatin, is formed by wrapping nearly 147bp of DNA around an octamer of histone proteins. This histone core has many variants that are different from each other by their b...
This article is part of a Supplement: Volume 11 Supplement 4
Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Pre...
De novo assembly of transcript sequences produced by short-read DNA sequencing technologies offers a rapid approach to obtain expressed gene catalogs for non-model organisms. A draft genome sequence will be produ...
Glioblastoma is the most common primary brain tumor in adults. Though a lot of research has been focused on this disease, the causes and pathogenesis of glioblastoma have not been indentified clearly.
This article is part of a Supplement: Volume 11 Supplement 3
Significant interest exists in establishing radiologic imaging as a valid biomarker for assessing the response of cancer to a variety of treatments. To address this problem, we have chosen to study patients wi...
This article is part of a Supplement: Volume 11 Supplement 3
Identifying the regions associated with protein function is a singularly important task in the post-genomic era. Biological studies often identify functional enzyme residues by amino acid sequences, particular...
This article is part of a Supplement: Volume 11 Supplement 3
The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-...
This article is part of a Supplement: Volume 11 Supplement 3
MicroRNAs (miRNAs) are single-stranded non-coding RNAs shown to plays important regulatory roles in a wide range of biological processes and diseases. The functions and regulatory mechanisms of most of miRNAs ...
This article is part of a Supplement: Volume 11 Supplement 3
Response of cells to changing endogenous or exogenous conditions is governed by intricate molecular interactions, or regulatory networks. To lead to appropriate responses, regulatory network should be 1) conte...
This article is part of a Supplement: Volume 11 Supplement 3
The increasing availability of large-scale protein-protein interaction data has made it possible to understand the basic components and organization of cell machinery from the network level. The arising challe...
This article is part of a Supplement: Volume 11 Supplement 3
Small animal MRI at 7 Tesla (T) provides a useful tool for adiposity research. For adiposity researchers, separation of fat from surrounding tissues and its subsequent quantitative or semi- quantitative analys...
This article is part of a Supplement: Volume 11 Supplement 3
The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that b...
This article is part of a Supplement: Volume 11 Supplement 3
Comprehensive exploration of protein-protein interactions is a challenging route to understand biological processes. For efficiently enlarging protein interactions annotated with residue-based binding models, ...
This article is part of a Supplement: Volume 11 Supplement 3
Understanding the biomedical implications of data from high throughput experiments requires solutions for effective cross-scale and cross-domain data exploration. However, existing solutions do not provide suf...
This article is part of a Supplement: Volume 11 Supplement 3
Cancer is a complex disease. So far, many genes have been reported to involve in the development of cancer. Rather than the traditional approach to studying individual genes or loci, a systematic investigation...
This article is part of a Supplement: Volume 11 Supplement 3
Military and industrial activities have lead to reported release of 2,4-dinitrotoluene (2,4DNT) into soil, groundwater or surface water. It has been reported that 2,4DNT can induce toxic effects on humans and ...
This article is part of a Supplement: Volume 11 Supplement 3
The challenge today is to develop a modeling and simulation paradigm that integrates structural, molecular and genetic data for a quantitative understanding of physiology and behavior of biological processes a...
This article is part of a Supplement: Volume 11 Supplement 3
Short interfering RNAs (siRNAs) can be used to knockdown gene expression in functional genomics. For a target gene of interest, many siRNA molecules may be designed, whereas their efficiency of expression inhi...
This article is part of a Supplement: Volume 11 Supplement 3
Effector secretion is a common strategy of pathogen in mediating host-pathogen interaction. Eight EPIYA-motif containing effectors have recently been discovered in six pathogens. Once these effectors enter hos...
This article is part of a Supplement: Volume 11 Supplement 3
Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, tho...
Lantibiotics are lanthionine-containing, post-translationally modified antimicrobial peptides. These peptides have significant, but largely untapped, potential as preservatives and chemotherapeutic agents. Typ...
The molecular mechanisms that modify genome structures to give birth and death to alleles are still not well understood. To investigate the causative chromosomal rearrangements, we took advantage of the alleli...
The computational prediction of transcription start sites is an important unsolved problem. Some recent progress has been made, but many promoters, particularly those not associated with CpG islands, are still...
Treatment of non-small cell lung cancer with novel targeted therapies is a major unmet clinical need. Alternative splicing is a mechanism which generates diverse protein products and is of functional relevance...
Age- and sex-related susceptibility to adverse drug reactions and disease is a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of hepatic genes expres...
Riverine ecosystems, highly sensitive to climate change and human activities, are characterized by rapid environmental change to fluctuating water levels and siltation, causing stress on their biological compo...
Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. G...
Significant interest exists in establishing synergistic research in bioinformatics, systems biology and intelligent computing. Supported by the United States National Science Foundation (NSF), International So...
This article is part of a Supplement: Volume 11 Supplement 3
At present, very little is known about how Burkholderia pseudomallei (B. pseudomallei) interacts with its host to elicit melioidosis symptoms. We established a murine acute-phase melioidosis model and used DNA mi...
Proteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and ...
The Beijing genotype of M. tuberculosis is a virulent strain that is disseminating worldwide and has a strong association with drug resistance. In the Western Cape of South Africa, epidemiological studies have id...
Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs) and also provide a means of assessing their variation. This information is useful for...
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