Visualization of three-way comparisons of omics data

Background  

Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However, the current color-codings limit the visualizations to single datasets or pairwise comparisons.     

Predicting cancer involvement of genes from heterogeneous data

Background  

Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data.     

Quantifying robustness of biochemical network models

Background  

Robustness of mathematical models of biochemical networks is important for validation purposes and can be used as a means of selecting between different competing models. Tools for quantifying parametric robustness are needed.     

Phylogenomic reconstruction of lactic acid bacteria: an update

Background  

Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets.     

A reference dataset for verifying numerical electrophysiological heart models

Background  

The evaluation, verification and comparison of different numerical heart models are difficult without a commonly available database that could be utilized as a reference. Our aim was to compile an exemplary dataset.     

Characterization of the microheterogeneity of transthyretin in plasma and urine using SELDI-TOF-MS immunoassay

Background  

It has been shown that transthyretin (TTR) exists in different molecular variants. Besides point mutations associated with different diseases such as amyloidosis, other posttranslational modifications occur that might be of diagnostic interest.     

Degradation or excretion of quantum dots in mouse embryonic stem cells

Background  

Quantum dots (QDs) have been considered as a new and efficient probe for labeling cells non-invasively in vitro and in vivo, but fairly little is known about how QDs are eliminated from cells after labeling. The purpose of this study is to investigate the metabolism of QDs in different type of cells.     

Direct observation of molecular arrays in the organized smooth endoplasmic reticulum

Background  

Tubules and sheets of endoplasmic reticulum perform different functions and undergo inter-conversion during different stages of the cell cycle. Tubules are stabilized by curvature inducing resident proteins, but little is known about the mechanisms of endoplasmic reticulum sheet stabilization. Tethering of endoplasmic reticulum membranes to the cytoskeleton or to each other has been proposed as a plausible way of sheet stabilization.     

Ultra-high throughput sequencing-based small RNA discovery and discrete statistical biomarker analysis in a collection of cervical tumours and matched controls

Background  

Ultra-high throughput sequencing technologies provide opportunities both for discovery of novel molecular species and for detailed comparisons of gene expression patterns. Small RNA populations are particularly well suited to this analysis, as many different small RNAs can be completely sequenced in a single instrument run.     

Missing value imputation improves clustering and interpretation of gene expression microarray data

Background  

Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation approaches are available to the microarray users and new ones are constantly being developed, there is no general consensus on how to choose between the different methods since their performance seems to vary drastically depending on the dataset being used.     

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

Background  

Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe.     

On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence

Background  

In eukaryotes, most DNA-binding proteins exert their action as members of large effector complexes. The presence of these complexes are revealed in high-throughput genome-wide assays by the co-occurrence of the binding sites of different complex components. Resampling tests are one route by which the statistical significance of apparent co-occurrence can be assessed.     

Loss of Dictyostelium HSPC300 causes a scar-like phenotype and loss of SCAR protein

Background  

SCAR/WAVE proteins couple signalling to actin polymerization, and are thus fundamental to the formation of pseudopods and lamellipods. They are controlled as part of a five-membered complex that includes the tiny HSPC300 protein. It is not known why SCAR/WAVE is found in such a large assembly, but in Dictyostelium the four larger subunits have different, clearly delineated functions.     

Evolutionary rate patterns of the Gibberellin pathway genes

Background  

Analysis of molecular evolutionary patterns of different genes within metabolic pathways allows us to determine whether these genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution of proteins in an interacting system. Although previous studies found that upstream genes in the pathway evolved more slowly than downstream genes, the correlation between evolutionary rate and position of the genes in metabolic pathways as well as its implications in molecular evolution are still less understood.     

In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

Background  

Housekeeping genes are commonly used as endogenous reference genes for the relative quantification of target genes in gene expression studies. No conclusive systematic study comparing the suitability of different candidate reference genes in clear cell renal cell carcinoma has been published to date. To remedy this situation, 10 housekeeping genes for normalizing purposes of RT-PCR measurements already recommended in various studies were examined with regard to their usefulness as reference genes.     

Comparative rates of evolution in endosymbiotic nuclear genomes

Background  

The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded.     

Meta-analysis of gene expression microarrays with missing replicates

Background  

Many different microarray experiments are publicly available today. It is natural to ask whether different experiments for the same phenotypic conditions can be combined using meta-analysis, in order to increase the overall sample size. However, some genes are not measured in all experiments, hence they cannot be included or their statistical significance cannot be appropriately estimated in traditional meta-analysis. Nonetheless, these genes, which we refer to as incomplete genes, may also be informative and useful.     

A mechanism for the sharp transition of morphogen gradient interpretation in <Emphasis Type="Italic">Xenopus</Emphasis>

Background  

One way in which positional information is established during embryonic development is through the graded distribution of diffusible morphogens. Unfortunately, little is known about how cells interpret different concentrations of morphogen to activate different genes or how thresholds are generated in a morphogen gradient.