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Affymetrix GeneChipsâ„¢ are an important tool in many facets of biological research. Recently, notable design changes to the chips have been made. In this study, we use publicly available data from Affymetrix to...
PedGenie software, introduced in 2006, includes genetic association testing of cases and controls that may be independent or related (nuclear families or extended pedigrees) or mixtures thereof using Monte Car...
Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations.
Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cis-regulatory elements have been w...
Classification procedures are widely used in phylogenetic inference, the analysis of expression profiles, the study of biological networks, etc. Many algorithms have been proposed to establish the similarity b...
Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and struct...
Identity by descent (IBD) matrix estimation is a central component in mapping of Quantitative Trait Loci (QTL) using variance component models. A large number of algorithms have been developed for estimation o...
Affymetrix 3' GeneChip microarrays are widely used to profile the expression of thousands of genes simultaneously. They differ from many other microarray types in that GeneChips are hybridised using a single l...
Glycosylation is one of the most complex post-translational modifications (PTMs) of proteins in eukaryotic cells. Glycosylation plays an important role in biological processes ranging from protein folding and ...
Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivated by increasing evidence that some DNA reg...
Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manag...
Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM package...
Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-...
An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.
MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing ...
Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman a...
Many biological networks such as protein-protein interaction networks, signaling networks, and metabolic networks have topological characteristics of a scale-free degree distribution. Preferential attachment h...
Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived...
The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequi...
A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with m...
Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually nee...
As the number of fully sequenced genome increases, the need is greater for bioinformatics to predict or annotate genes of a newly sequenced genome. Ever since Eisenberg and his colleagues introduced phylogenet...
This article is part of a Supplement: Volume 8 Supplement 7
Effective and economical methods for quantitative analysis of high throughput mass spectrometry data are essential to meet the goals of directly identifying, characterizing, and quantifying proteins from a par...
This article is part of a Supplement: Volume 8 Supplement 7
When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated with each protein will be observ...
This article is part of a Supplement: Volume 8 Supplement 7
Comfrey (Symphytum officinale) is a perennial plant and has been consumed by humans as a vegetable, a tea and an herbal medicine for more than 2000 years. It, however, is hepatotoxic and carcinogenic in experimen...
This article is part of a Supplement: Volume 8 Supplement 7
Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especially the binding sites in deoxyribonucleic...
This article is part of a Supplement: Volume 8 Supplement 7
The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions th...
This article is part of a Supplement: Volume 8 Supplement 7
Hidden Markov Models (HMMs) provide an excellent means for structure identification and feature extraction on stochastic sequential data. An HMM-with-Duration (HMMwD) is an HMM that can also exactly model the ...
This article is part of a Supplement: Volume 8 Supplement 7
Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways.
This article is part of a Supplement: Volume 8 Supplement 7
Histopathology, which is one of the most important routines of all laboratory procedures used in pathology, is decisive for the diagnosis of cancer. Experienced histopathologists review the histological slides...
This article is part of a Supplement: Volume 8 Supplement 7
Multiple recent studies have found aberrant expression profiles of microRNAome in human cancers. While several target genes have been experimentally identified for some microRNAs in various tumors, the global ...
This article is part of a Supplement: Volume 8 Supplement 7
It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade ...
This article is part of a Supplement: Volume 8 Supplement 7
Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin tr...
This article is part of a Supplement: Volume 8 Supplement 7
The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlyi...
This article is part of a Supplement: Volume 8 Supplement 7
A nanopore detector has a nanometer-scale trans-membrane channel across which a potential difference is established, resulting in an ionic current through the channel in the pA-nA range. A distinctive channel ...
This article is part of a Supplement: Volume 8 Supplement 7
Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overh...
This article is part of a Supplement: Volume 8 Supplement 7
Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs ...
This article is part of a Supplement: Volume 8 Supplement 7
Nanopore detection is based on observations of the ionic current threading a single, highly stable, nanometer-scale channel. The dimensions are such that small biomolecules and biopolymers (like DNA and peptid...
This article is part of a Supplement: Volume 8 Supplement 7
Mean-based clustering algorithms such as bisecting k-means generally lack robustness. Although componentwise median is a more robust alternative, it can be a poor center representative for high dimensional data. ...
This article is part of a Supplement: Volume 8 Supplement 7
Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test o...
This article is part of a Supplement: Volume 8 Supplement 7
As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR ...
This article is part of a Supplement: Volume 8 Supplement 7
Staphylococcus aureus is a human pathogen that causes a wide variety of life-threatening infections using a large number of virulence factors. One of the major global regulators used by S. aureus is the staphyloc...
This article is part of a Supplement: Volume 8 Supplement 7
Pyrrolizidine alkaloids (PAs) are probably the most common plant constituents that poison livestock, wildlife, and humans worldwide. Riddelliine is isolated from plants grown in the western United States and i...
This article is part of a Supplement: Volume 8 Supplement 7
Urine from male Sprague-Dawley rats 25, 40, and 80 days old was analyzed by NMR and UPLC/MS. The effects of data normalization procedures on principal component analysis (PCA) and quantitative analysis of NMR-...
This article is part of a Supplement: Volume 8 Supplement 7
To better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtai...
This article is part of a Supplement: Volume 8 Supplement 7
This article is part of a Supplement: Volume 8 Supplement 7
The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of protein structures. Therefore, instead of ma...
Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web...
We present a probabilistic topic-based model for content similarity called pmra that underlies the related article search feature in PubMed. Whether or not a document is about a particular topic is computed from ...
An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry). Typically this estimation is done...
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