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At least 901 records · Page 50Linked to original sources
PubMed2004

CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs.

UNLABELLED: Cluster and set-cover algorithms are developed to obtain a set of tag single nucleotide polymorphisms (SNPs) that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2>C with at least one tag SNP, where C is specified by the user. AVAILABILITY: http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html CONTACT: mng@maths.hku.hk.

Algorithms↗
PubMed2006

Protein classification using probabilistic chain graphs and the Gene Ontology structure.

MOTIVATION: Probabilistic graphical models have been developed in the past for the task of protein classification. In many cases, classifications obtained from the Gene Ontology have been used to validate these models. In this work we directly incorporate the structure of the Gene Ontology into the graphical representation for protein classification. We present a method in which each protein is represented by a replicate of the Gene Ontology structure, effectively modeling each protein in its own 'annotation space'. Proteins are also connected to one another according to different measures of functional similarity, after which belief propagation is run to make predictions at all ontology terms. RESULTS: The proposed method was evaluated on a set of 4879 proteins from the Saccharomyces Genome Database whose interactions were also recorded in the GRID project. Results indicate that direct utilization of the Gene Ontology improves predictive ability, outperforming traditional models that do not take advantage of dependencies among functional terms. Average increase in accuracy (precision) of positive and negative term predictions of 27.8% (2.0%) over three different similarity measures and three subontologies was observed. AVAILABILITY: C/C++/Perl implementation is available from authors upon request.

Algorithms↗
PubMed2006

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.

MOTIVATION: B cells responding to antigenic stimulation can fine-tune their binding properties through a process of affinity maturation composed of somatic hypermutation, affinity-selection and clonal expansion. The mutation rate of the B cell receptor DNA sequence, and the effect of these mutations on affinity and specificity, are of critical importance for understanding immune and autoimmune processes. Unbiased estimates of these properties are currently lacking due to the short time-scales involved and the small numbers of sequences available. RESULTS: We have developed a bioinformatic method based on a maximum likelihood analysis of phylogenetic lineage trees to estimate the parameters of a B cell clonal expansion model, which includes somatic hypermutation with the possibility of lethal mutations. Lineage trees are created from clonally related B cell receptor DNA sequences. Important links between tree shapes and underlying model parameters are identified using mutual information. Parameters are estimated using a likelihood function based on the joint distribution of several tree shapes, without requiring a priori knowledge of the number of generations in the clone (which is not available for rapidly dividing populations in vivo). A systematic validation on synthetic trees produced by a mutating birth-death process simulation shows that our estimates are precise and robust to several underlying assumptions. These methods are applied to experimental data from autoimmune mice to demonstrate the existence of hypermutating B cells in an unexpected location in the spleen.

Algorithms↗
PubMed2006

AliBaba: PubMed as a graph.

UNLABELLED: The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. AVAILABILITY: http://alibaba.informatik.hu-berlin.de/

Abstracting and Indexing↗
PubMed1984

A reassessment of the validity of the iso-shunt graph.

The iso-shunt diagram was introduced in 1973 to simplify the selection of the optimal inspired oxygen concentration in patients undergoing intensive therapy. A further study of 25 patients in a District General Hospital showed that plots of arterial PO2 against inspired oxygen concentration closely follow predicted iso-shunt lines. There was no significant difference in calculated mean values for shunt with inspired oxygen concentrations between 30 and 100%. Results are compared with other studies and it is suggested that some reported discrepancies may be explained by the reduced response of many polarographic electrodes when measuring high values for arterial PO2.

Adult↗
PubMed2000

Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.

It is shown that partial self-fertilization can be introduced into neutral population genetic models with recombination as a simple change in the scaling of the parameters. This means that statistical and computational methods that have been developed under the assumption of random mating can be used without modification, provided the appropriate parameter changes are made. An important prediction is that all forms of linkage disequilibrium will be more extensive in selfing species. The implications of this are discussed.

Linkage Disequilibrium↗
PubMed1982

Clinical determination of energy cost and walking velocity via stopwatch or speedometer cane and conversion graphs.

Work rate and relative exercise intensity are basic considerations in developing optimal exercise training prescriptions in cardiopulmonary rehabilitation. Velocity and energy cost of walking are directly related to work rate and indirectly related to exercise intensity. This article describes two methods of measuring walking velocity and estimating oxygen uptake. The validity and accuracy of the methods are discussed. We believe both methods are clinically useful. Because one method uses a specially instrumented speedometer cane, technical information concerning its design and construction is also included.

Canes↗
PubMed1990

The earliest graph?

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History, Medieval↗