The calculation of information and organismal complexity

Background  

It is difficult to measure precisely the phenotypic complexity of living organisms. Here we propose a method to calculate the minimal amount of genomic information needed to construct organism (effective information) as a measure of organismal complexity, by using permutation and combination formulas and Shannon's information concept.     

Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation

Background  

Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic effects arising from the procedures used to generate these libraries.     

Biochemical pathways analysis of microarray results: regulation of myogenesis in pigs

Background  

Combining microarray results and biological pathway information will add insight into biological processes. Pathway information is widely available in databases through the internet.     

From bit to it: How a complex metabolic network transforms information into living matter

Background  

Organisms live and die by the amount of information they acquire about their environment. The systems analysis of complex metabolic networks allows us to ask how such information translates into fitness. A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide.     

Protein family comparison using statistical models and predicted structural information

Background  

This paper presents a simple method to increase the sensitivity of protein family comparisons by incorporating secondary structure (SS) information. We build upon the effective information theory approach towards profile-profile comparison described in [Yona & Levitt 2002]. Our method augments profile columns using PSIPRED secondary structure predictions and assesses statistical similarity using information theoretical principles.     

Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases

Background  

All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, but this is not represented by the known genetic code.     

GeneLibrarian: an effective gene-information summarization and visualization system

Background  

Abundant information about gene products is stored in online searchable databases such as annotation or literature. To efficiently obtain and digest such information, there is a pressing need for automated information-summarization and functional-similarity clustering of genes.     

ProFAT: a web-based tool for the functional annotation of protein sequences

Background  

The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches.     

PathSys: integrating molecular interaction graphs for systems biology

Background  

The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.     

Natural hybridization in heliconiine butterflies: the species boundary as a continuum

Background  

To understand speciation and the maintenance of taxa as separate entities, we need information about natural hybridization and gene flow among species.     

A traveling salesman approach for predicting protein functions

Background  

Protein-protein interaction information can be used to predict unknown protein functions and to help study biological pathways.     

Inferring functional modules of protein families with probabilistic topic models

Background  

Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.     

eCOMPAGT – efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology

Background  

High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-related personal information, which needs to be handled with care by following data privacy protection guidelines. In addition, genotyping core facilities handling cooperative projects require a straightforward solution to monitor the status and financial resources of the different projects.     

Evolution of mantis shrimps (Stomatopoda,Malacostraca) in the light of new Mesozoic fossils

Background  

We describe new specimens of Mesozoic mantis shrimps (Stomatopoda, Malacostraca) that exhibit morphological and developmental information previously unknown.     

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of <Emphasis Type="Italic">Oryza sativa</Emphasis>

Background  

Pollen development in flowering plants requires strict control of the gene expression program and genetic information stability by mechanisms possibly including the miRNA pathway. However, our understanding of the miRNA pathway in pollen development remains limited, and the dynamic profile of miRNAs in developing pollen is unknown.     

BIGSdb: Scalable analysis of bacterial genome variation at the population level

Background  

The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner.     

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

Background  

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.     

Altered expression of hypothetical proteins in hippocampus of transgenic mice overexpressing human Cu/Zn-superoxide dismutase 1

Background  

The rapid completion of genome sequences has created an infrastructure of biological information and provided essential information to link genes to gene products, proteins, the building blocks for cellular functions. In addition, genome/cDNA sequences make it possible to predict proteins for which there is no experimental evidence. Clues for function of hypothetical proteins are provided by sequence similarity with proteins of known function in model organisms.     

MANET: tracing evolution of protein architecture in metabolic networks

Background  

Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics.