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Search Results: 1 - 10 of 298949 matches for " Alison J Coffey "
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A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip? for Methylome Profiling
Christine Clark, Priit Palta, Christopher J. Joyce, Carol Scott, Elin Grundberg, Panos Deloukas, Aarno Palotie, Alison J. Coffey
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050233
Abstract: DNA methylation is one of the most studied epigenetic marks in the human genome, with the result that the desire to map the human methylome has driven the development of several methods to map DNA methylation on a genomic scale. Our study presents the first comparison of two of these techniques - the targeted approach of the Infinium HumanMethylation450 BeadChip? with the immunoprecipitation and sequencing-based method, MeDIP-seq. Both methods were initially validated with respect to bisulfite sequencing as the gold standard and then assessed in terms of coverage, resolution and accuracy. The regions of the methylome that can be assayed by both methods and those that can only be assayed by one method were determined and the discovery of differentially methylated regions (DMRs) by both techniques was examined. Our results show that the Infinium HumanMethylation450 BeadChip? and MeDIP-seq show a good positive correlation (Spearman correlation of 0.68) on a genome-wide scale and can both be used successfully to determine differentially methylated loci in RefSeq genes, CpG islands, shores and shelves. MeDIP-seq however, allows a wider interrogation of methylated regions of the human genome, including thousands of non-RefSeq genes and repetitive elements, all of which may be of importance in disease. In our study MeDIP-seq allowed the detection of 15,709 differentially methylated regions, nearly twice as many as the array-based method (8070), which may result in a more comprehensive study of the methylome.
An Evaluation of Different Target Enrichment Methods in Pooled Sequencing Designs for Complex Disease Association Studies
Aaron G. Day-Williams, Kirsten McLay, Eleanor Drury, Sarah Edkins, Alison J. Coffey, Aarno Palotie, Eleftheria Zeggini
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026279
Abstract: Pooled sequencing can be a cost-effective approach to disease variant discovery, but its applicability in association studies remains unclear. We compare sequence enrichment methods coupled to next-generation sequencing in non-indexed pools of 1, 2, 10, 20 and 50 individuals and assess their ability to discover variants and to estimate their allele frequencies. We find that pooled resequencing is most usefully applied as a variant discovery tool due to limitations in estimating allele frequency with high enough accuracy for association studies, and that in-solution hybrid-capture performs best among the enrichment methods examined regardless of pool size.
The word problem for 3-manifolds built from injective handlebodies
J. Coffey
Mathematics , 2006,
Abstract: This paper gives a proof that the fundamental group of a class of closed orientable 3-manifolds constructed from three injective handlebodies has a solvable word problem. This is done by giving an algorithm to decide if a closed curve in the manifold is null-homotopic. Non-Haken and non-Seifert fibered examples are constructed by performing Dehn surgery on a class of two-bridge knots.
Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencing
Johanna de Gruijter, Oscar Lao, Mark Vermeulen, Yali Xue, Cara Woodwark, Christopher J Gillson, Alison J Coffey, Qasim Ayub, S Qasim Mehdi, Manfred Kayser, Chris Tyler-Smith
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-24
Abstract: Applying all commonly used neutrality-test statistics for allele frequency distribution to the newly generated sequence data provided conflicting results regarding evidence for positive selection. Previous haplotype-based findings could not be clearly confirmed. Although some tests were marginally significant for some populations and genes, none of them were significant after multiple-testing correction. Combined P values for each gene-population pair did not improve these results. Application of Approximate Bayesian Computation Markov chain Monte Carlo based to these sequence data using a simple forward simulator revealed broad posterior distributions of the selective parameters for all four genes, providing no support for positive selection. However, when we applied this approach to published sequence data on SLC45A2, another human pigmentation candidate gene, we could readily confirm evidence for positive selection, as previously detected with sequence-based and some haplotype-based tests.Overall, our data indicate that even genes that are strong biological candidates for positive selection and show reproducible signatures of positive selection in SNP scans do not always show the same replicability of selection signals in other tests, which should be considered in future studies on detecting positive selection in genetic data.Large-scale genotyping projects using genome-wide single-nucleotide polymorphisms (SNPs) have provided large amounts of data describing the genetic diversity of human populations [1-6]. Several statistical methods have been developed and used for detection of signatures of selective processes from genome-wide SNP data, which we refer to as 'SNP scans' [7]. All these approaches try to recover fingerprints of selective sweeps by detecting signals in the haplotypic variation of a genomic region and/or the spectrum of the variation of the genetic diversity [8-15]. However, the results obtained with the different test statistics usually show limi
A Case Study of Water Education in Australia  [PDF]
Alison J. Sammel
Creative Education (CE) , 2014, DOI: 10.4236/ce.2014.513129
Abstract:

What does it mean to be scientifically literate in relation to water? Is this understanding the same for water literacy? And what implications do these two concepts have for water education in Australia? In addressing these questions, this paper provides a snapshot of the similar and competing educational ideologies that underpin the concepts of scientific literacy in relation to water, and water literacy. An investigation of the Australian Curriculum (Science), and a small case study of pre-service education students highlight the degree to which one concept is favored over the other. This bias ultimately raises questions for water education in Australia, as it is not about whether the ACS or [future] teachers should be addressing issues associated with water, but rather how and to what end goal. This necessitates exploring the partial and political nature of any approach to educating about water, and highlights that not all approaches are equally as politically neutral or challenging.

Science as a Human Endeavour: Outlining Scientific Literacy and Rethinking Why We Teach Science  [PDF]
Alison J. Sammel
Creative Education (CE) , 2014, DOI: 10.4236/ce.2014.510098
Abstract: What does it mean to be scientifically literate? Historically, dominant understandings of scientific literacy focus on science content acquisition. However, new understandings imply more genuine and authentic interactivity between science content knowledge/skills and understanding of the economic, sociocultural, religious, ecological, ideological, political and temporal connections upon which the science is based: this is the task of Science as a Human Endeavour. This paper presents a snapshot of what Science as a Human Endeavour is, its purpose and factors to consider. Science as a Human Endeavour doesn’t just necessitate that we change our teaching practices: it forces us to rethink the teaching and learning of science and the reason why we are doing it.


Closure properties of matrix operators with application to continuous-time Markov chains
J. J. Coffey
International Journal of Mathematical Analysis , 2012,
Abstract:
3-manifolds built from injective handlebodies
J. Coffey,H. Rubinstein
Mathematics , 2006,
Abstract: This paper looks at a class of closed orientable 3-manifolds constructed from a gluing of three handlebodies, such that the inclusion of each handlebody is $\pi_1$-injective. This construction is the generalisation to handlebodies of the condition for gluing three solid tori to produce non-Haken Seifert fibered 3-manifolds with infinite fundamental group. It is shown that there is an efficient algorithm to decide if a gluing of handlebodies meets the disk-condition. Also an outline for the construction of the characteristic variety (JSJ decomposition) in such manifolds is given. Some non-Haken and atoroidal examples are given.
Interdisciplinary Practice: Dialogue as Action to Resist Colonialism in Higher Education  [PDF]
Alison J. Sammel, Marcus Waters
Creative Education (CE) , 2014, DOI: 10.4236/ce.2014.514139
Abstract:


Two colleagues, one who is identified as a Kamilaroi First Nation of Australia man, and a woman who is identified as Australian, from European decent, come together through dialogue to explore interdisciplinary practices within their university setting. Focusing on their areas of expertise, they share the similarities and differences associated with the concepts of identity, identifying and binaries between the teaching and learning of Science Education and First Nations Knowledge production. Through emerging dialogue, they realize that even though their cultural backgrounds are completely different, both are subjected to the complexities of hegemonic binaries that impact and influence their teaching practice. In striving for equity, both authors aim to continually recognize and challenge the binaries that privilege some agendas and students, and marginalize others. By sharing assumptions, beliefs and practices, the article invites the possibility that something new can emerge from their encounter to generate innovative understandings that will inform future practice. Through their praxis and dialogues with students, both have come to understand that it is not only those students marginalized by the system that appreciate their actions, but those who are privileged also benefit as they become more aware of an ever changing world around them.


Microarray foray
Robert J Coffey, David Threadgill
Breast Cancer Research , 1999, DOI: 10.1186/bcr21
Abstract: The Brown and Botstein group selected the subset of genes from a 5500 complementary DNA chip that were differentially expressed in human breast tumors compared with cultured normal human mammary epithelial cells by threefold or greater in three out of 26 arrays. This subset of 1200 genes was then analyzed by gene-clustering analysis. Several problems have arisen. A minor one - that a gene that may change dramatically in only one array - is ignored. In addition, the criteria of a threefold change in gene expression may exclude biologically important genes with expression that falls into the 'noise' range. A more substantive problem that needs to be addressed by the microarray community is the choice of an appropriate reference sample. To quantify differences, a gene must be expressed in the reference sample. Diversity and reproducibility are two critical issues. It is unlikely that the Stanford control (human mammary epithelial cells) exhibits sufficiently diversified gene expression to measure quantitatively all of the genes that were not expressed in the mammary epithelial cells. The ideal 'generic' control would express all genes and would be a renewable source, thus providing reproducibility. In a perfect world, all users of microarray technology would utilize the same 'generic' reference sample, and results could then be compared across experiments and across different laboratories. The microarray community might settle on RNA from a pool of cell lines of different cell types, or, even better, from pools of primary cell cultures that exhibit broadly diverse gene expression patterns.Nevertheless, a wealth of data has been generated in the analysis of Perou et al [1]. Specific cell type signatures were identified. (The cynic will argue that a good pathologist can already provide this information at a fraction of the cost; however, consider that adequate diagnostic factors to identify the 30% of node-negative women with 1-2 cm breast tumors that will go on to devel
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