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BMC Proceedings

Tuan Nhon Dang, Paul Murray, Jillian Aurisano, Angus Graeme Forbes
BACKGROUND: Molecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins...
2015: BMC Proceedings
Shareef M Dabdoub, R Wolfgang Rumpf, Amber D Shindhelm, William C Ray
BACKGROUND: Current visualizations of molecular motion use a Timeline-analogous representation that conveys "first the molecule was shaped like this, then like this...". This scheme is orthogonal to the Pathline-like human understanding of motion "this part of the molecule moved from here to here along this path". We present MoFlow, a system for visualizing molecular motion using a Pathline-analogous representation. RESULTS: The MoFlow system produces high-quality renderings of molecular motion as atom pathlines, as well as interactive WebGL visualizations, and 3D printable models...
2015: BMC Proceedings
Francesco Paduano, Angus Graeme Forbes
BACKGROUND: Biologists make use of pathway visualization tools for a range of tasks, including investigating inter-pathway connectivity and retrieving details about biological entities and interactions. Some of these tasks require an understanding of the hierarchical nature of elements within the pathway or the ability to make comparisons between multiple pathways. We introduce a technique inspired by LineSets that enables biologists to fulfill these tasks more effectively. RESULTS: We introduce a novel technique, Extended LineSets, to facilitate new explorations of biological pathways...
2015: BMC Proceedings
Tuan Nhon Dang, Paul Murray, Angus Graeme Forbes
BACKGROUND: Molecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules. RESULTS: In this paper, we introduce PathwayMatrix, a visualization tool that presents the binary relations between proteins in the pathway via the use of an interactive adjacency matrix...
2015: BMC Proceedings
Daekyoung Jung, Bohyoung Kim, Robert J Freishtat, Mamta Giri, Eric Hoffman, Jinwook Seo
BACKGROUND: MicroRNAs (miRNA) are short nucleotides that down-regulate its target genes. Various miRNA target prediction algorithms have used sequence complementarity between miRNA and its targets. Recently, other algorithms tried to improve sequence-based miRNA target prediction by exploiting miRNA-mRNA expression profile data. Some web-based tools are also introduced to help researchers predict targets of miRNAs from miRNA-mRNA expression profile data. A demand for a miRNA-mRNA visual analysis tool that features novel miRNA prediction algorithms and more interactive visualization techniques exists...
2015: BMC Proceedings
Jan Aerts, G Elisabeta Marai, Kay Nieselt, Cydney Nielsen, Marc Streit, Daniel Weiskopf
No abstract text is available yet for this article.
2015: BMC Proceedings
(no author information available yet)
No abstract text is available yet for this article.
2015: BMC Proceedings
Mamdooh Gari, Mohammed Dakhakhni, Abdullah Gari, Erada Alshihri, Rowan Al-Jahdali, Kothandaraman Narasimhan, Shen Liang, Fatin Al-Sayes, Gauthaman Kalamegam, Adeel Chaudhary, Adel Abuzenadah, Mohammed Al-Qahtani
BACKGROUND: Benign neutropenia often presents in certain populations without any genotype nor phenotype. Middle East countries are among the regions where endemic cases of chronic benign neutropenia are reported in the general population with an incidence of approximately between 10-15%. Not many studies have been performed to ascertain the cause or burden associated with this condition. The objective of the current study was to identify the frequency and characterize the consequences of chronic benign neutropenia in the country of Saudi Arabia...
2015: BMC Proceedings
Morenike Oluwatoyin Folayan, Megan Gottemoeller, Rosemary Mburu, Brandon Brown
BACKGROUND: Over the last few decades, biomedical HIV prevention research had engaged multiple African stakeholders. There have however been few platforms to enable regional stakeholders to engage with one another. In partnership with the World AIDS Campaign International, the Institute of Public Health of Obafemi Awolowo University, and the National Agency for the Control of AIDS in Nigeria, the New HIV Vaccine and Microbicide Advocacy Society hosted a forum on biomedical HIV prevention research in Africa...
2014: BMC Proceedings
(no author information available yet)
No abstract text is available yet for this article.
2014: BMC Proceedings
Joseph O Ogutu, Hans-Peter Piepho
BACKGROUND: Genomic prediction is now widely recognized as an efficient, cost-effective and theoretically well-founded method for estimating breeding values using molecular markers spread over the whole genome. The prediction problem entails estimating the effects of all genes or chromosomal segments simultaneously and aggregating them to yield the predicted total genomic breeding value. Many potential methods for genomic prediction exist but have widely different relative computational costs, complexity and ease of implementation, with significant repercussions for predictive accuracy...
2014: BMC Proceedings
Ricardo Pong-Wong
BACKGROUND: A method for estimating genomic breeding values (GEBV) based on the Horseshoe prior was introduced and used on the analysis of the 16(th) QTLMAS workshop dataset, which resembles three milk production traits. The method was compared with five commonly used methods: Bayes A, Bayes B, Bayes C, Bayesian Lasso and GLUP. METHODS: The main difference between the methods is the prior distribution assumed during the estimation of the SNP effects. The distribution of the Bayesian Lasso is a Laplace distribution; for Bayes A is a Student-t; for Bayes B and Bayes C is a spike and slab prior combining a proportion of SNP without effect and a proportion with effect distributed as a Student-t or Gaussian for Bayes B and C, respectively; for GBLUP is similar to a ridge regression...
2014: BMC Proceedings
Bianca Moioli, Francesco Napolitano, Gennaro Catillo
BACKGROUND: Identification of QTLs for important phenotypic traits, through the use of medium-density genome-wide SNP panels, is one of the most challenging areas in animal genetics, for preventing the time-consuming direct sequencing of putative candidate genes, when searching for the mutations that affect the trait. Appropriate statistical analyses allow the identification of genomic regions associated with the investigated trait in the genotyped population. METHODS: The selective genotyping technique was applied to 1000 genotyped animals with known phenotype...
2014: BMC Proceedings
Giulietta Minozzi, Andrea Pedretti, Stefano Biffani, Ezequiel Luis Nicolazzi, Alessandra Stella
BACKGROUND: Genome wide association studies are now widely used in the livestock sector to estimate the association among single nucleotide polymorphisms (SNPs) distributed across the whole genome and one or more trait. As computational power increases, the use of machine learning techniques to analyze large genome wide datasets becomes possible. METHODS: The objective of this study was to identify SNPs associated with the three traits simulated in the 16th MAS-QTL workshop dataset using the Random Forest (RF) approach...
2014: BMC Proceedings
Valentina Riggio, Ricardo Pong-Wong
BACKGROUND: Genome-wide association studies can have limited power to identify QTL, partly due to the stringent correction for multiple testing and low linkage-disequilibrium between SNPs and QTL. Regional Heritability Mapping (RHM) has been advanced as an alternative approach to capture underlying genetic effects. In this study, RHM was used to identify loci underlying variation in the 16(th) QTLMAS workshop simulated traits. METHODS: The method was implemented by fitting a mixed model where a genomic region and the overall genetic background were added as random effects...
2014: BMC Proceedings
Christine Grosse-Brinkhaus, Sarah Bergfelder, Ernst Tholen
BACKGROUND: Different genome wide association methods (GWAS) including multivariate analysis techniques were applied to identify quantitative trait loci (QTL) and pleiotropy in the simulated data set provided by the QTL-MAS workshop 2012 held in Alghero (Italy). METHODS: Genetic correlations and heritabilities for all three quantitative traits were obtained by a multivariate animal model. In a second step the data were corrected for a polygenic component containing the genomic-based kinship matrix...
2014: BMC Proceedings
M Graziano Usai, Giustino Gaspa, Nicolò Pp Macciotta, Antonello Carta, Sara Casu
BACKGROUND: A common dataset was simulated and made available to participants of the XVI(th) QTL-MAS workshop. Tasks for the participants were to detect QTLs affecting three traits, to assess their possible pleiotropic effects, and to evaluate the breeding values in a candidate population without phenotypes using genomic information. METHODS: Four generations consisting of 20 males and 1000 females were generated by mating each male with 50 females. The genome consisted of 5 chromosomes, each of 100 Mb size and carrying 2,000 equally distributed SNPs...
2014: BMC Proceedings
Rajesh Talluri, Sanjay Shete
Graphical models are increasingly used in genetic analyses to take into account the complex relationships between genetic and nongenetic factors influencing the phenotypes. We propose a model for determining the network structure of quantitative traits while accounting for the correlated nature of the family-based samples using the kinship coefficient. The Gaussian graphical model of age, systolic blood pressure, diastolic blood pressure, hypertension, blood pressure medication use, and smoking status was derived for three time points using real data...
2014: BMC Proceedings
Ake T Lu, Rita M Cantor
As the availability of cost-effective high-throughput sequencing technology increases, genetic research is beginning to focus on identifying the contributions of rare variants (RVs) to complex traits. Using RVs to detect associated genes requires statistical approaches that mitigate the lack of power with the analysis of single RVs. Here we report the development and application of an approach that aggregates and evaluates the transmissions of RVs in parent-child trios. An initial score that incorporates the distortion in transmission of the observed RVs from the parents to their offspring is calculated for each variant...
2014: BMC Proceedings
Jun Liu, Joseph Beyene
Many complex diseases are related to genetics, and it is of great interest to evaluate the association between single-nucleotide polymorphisms (SNPs) and disease outcome. The association of genetics with outcome can be modified by covariates such as age, sex, smoking status, and membership to the same pedigree. In this paper, we propose a block entropy method to separate two classes of SNPs, for which the association with hypertension is either sensitive or insensitive to the covariates. We also propose a consistency entropy method to further reduce the number of SNPs that might be associated with the outcome...
2014: BMC Proceedings
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