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A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms

Stephen B. Montgomery, Obi L. Griffith, Johanna M. Schuetz, Angela Brooks-Wilson, Steven J. M. Jones
2007 PLoS Computational Biology  
Citation: Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJM (2007) A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol 3(6): e106.  ...  We further used the entire set of properties to evaluate their collective performance in detecting regulatory polymorphisms.  ...  Wasserman for support and feedback during the development of this work. Author contributions. SBM and SJMJ conceived and designed the experiments, performed the experiments, and wrote the paper.  ... 
doi:10.1371/journal.pcbi.0030106 pmid:17559298 pmcid:PMC1892352 fatcat:5r54oipzsneunljq6sd2xyouyq

A Survey Of Genomic Properties For The Detection Of Regulatory Polymorphisms

Stephen B Montgomery, Obi Lee Griffith, Johanna M Schuetz, Angela Brooks Wilson, Steven JM Jones
2005 PLoS Computational Biology  
Citation: Montgomery SB, Griffith OL, Schuetz JM, Brooks-Wilson A, Jones SJM (2007) A survey of genomic properties for the detection of regulatory polymorphisms. PLoS Comput Biol 3(6): e106.  ...  We further used the entire set of properties to evaluate their collective performance in detecting regulatory polymorphisms.  ...  Wasserman for support and feedback during the development of this work. Author contributions. SBM and SJMJ conceived and designed the experiments, performed the experiments, and wrote the paper.  ... 
doi:10.1371/journal.pcbi.0030106.eor fatcat:zdnxwjg4ifcfbmtww5ghpw5j4y

Quantitative genetics in the age of omics

Joost JB Keurentjes, Maarten Koornneef, Dick Vreugdenhil
2008 Current opinion in plant biology  
The use of natural variation in the genetic dissection of quantitative traits has a long-standing tradition.  ...  The progress made in analytical and statistical techniques now allows the construction of regulatory networks that integrate the different levels of the biological information flow from gene-to-function  ...  We acknowledge support from the Netherlands Organization for Scientific Research, Program Genomics (050-10-029) and the Centre for Biosystems Genomics (CBSG, Netherlands Genomics Initiative).  ... 
doi:10.1016/j.pbi.2008.01.006 pmid:18325828 fatcat:hvmyriqb6bdbbhgh2doec3f25m

Characterizing natural variation using next-generation sequencing technologies

Yoav Gilad, Jonathan K. Pritchard, Kevin Thornton
2009 Trends in Genetics  
Marioni for helpful discussion and/or comments on the manuscript.  ...  Y.G. is supported by the Sloan foundation and NIH grants HL092206 and GM077959; K.T. is supported by the Sloan Foundation and by NIH grant GM085183; J.K.P. is supported by the HHMI and by NIH grant MH084703  ...  Thus, for the most part, it has been challenging to study the evolution of regulatory elements at a genomic level (but see Refs [57] [58] [59] ).  ... 
doi:10.1016/j.tig.2009.09.003 pmid:19801172 pmcid:PMC3994700 fatcat:5zkgv2ghnnhxjgck6zvl72dxiu

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae

Joseph Schacherer, Joshua A. Shapiro, Douglas M. Ruderfer, Leonid Kruglyak
2009 Nature  
We detected a total of 1,896,131 single nucleotide polymorphisms (SNPs) in non-repetitive regions of the genome (Supplementary Table 1 ).  ...  With their small and compact genomes, the hemiascomycetes (the group of fungi that includes S. cerevisiae) represent a powerful model for comparative genomics and studies of genome evolution 4-6 .  ...  Gresham for comments on the manuscript. The authors acknowledge discussions with members of the Kruglyak and Botstein laboratories. This work was supported by NIH grant R37 MH059520 and a James S.  ... 
doi:10.1038/nature07670 pmid:19212320 pmcid:PMC2782482 fatcat:osconlxhhne3xjjxldh6gl6ofe

Abundant Raw Material for Cis-Regulatory Evolution in Humans

Matthew V. Rockman, Gregory A. Wray
2002 Molecular biology and evolution  
We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed.  ...  We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism.  ...  Acknowledgments We thank the National Science Foundation and NASA for support and E. Davidson  ... 
doi:10.1093/oxfordjournals.molbev.a004023 pmid:12411608 fatcat:p4mtgongtzfczodz6j35yenkli

GENETIC MAPPING OF GENE EXPRESSION LEVELS: EXPRESSION LEVEL POLYMORPHISM ANALYSIS FOR DISSECTING REGULATORY NETWORKS OF PLANT DISEASE RESISTANCE

Kyunga Kim, Marilyn A. L. West, Richard W. Michelmore, Dina A. St. Clair, R. W. Doerge
2004 Conference on Applied Statistics in Agriculture  
This approach allows comprehensive dissection of regulatory networks for complex traits at a systems biology level.  ...  We introduce a novel functional genomics approach that integrates two areas, genetics and genomics, by applying QTL analysis to quantitative differences in the mRNA abundance of trait-related genes.  ...  As such, we propose a linear genetic model for the dissection of a regulatory pathway of a single structural gene with a regulatory locus.  ... 
doi:10.4148/2475-7772.1153 fatcat:ogpwygcrszh3rnylwcbydrnsqe

Probing functional polymorphisms in the dengue vector, Aedes aegypti

Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William Dunn, Joseph Fass, Anthony A James
2013 BMC Genomics  
Additionally, data supporting NTU discovery emphasizes the need for continuous amendments of the reference genome annotation.  ...  In contrast, a number of peroxidases, serpins and Clip-domain serine proteases exhibited conservation of putative UTR regulatory sequences while displaying diversification of the ORFs.  ...  This work was supported by the National Institutes of Health (U54AI065359 to AAJ).  ... 
doi:10.1186/1471-2164-14-739 pmid:24168143 pmcid:PMC4007706 fatcat:ztsvasudzvhj5mbmvgxfw62fxm

Page 668 of Genetics Vol. 181, Issue 2 [page]

2009 Genetics  
Many out- standing questions exist for this field. How many sites, when mutated, affect cis-regulatory properties? What fraction of such sites is polymorphic in populations?  ...  Gruber and A. D. Long genetic diversity at a majority of surveyed genes.  ... 

Genomics and conservation genetics

Michael H. Kohn, William J. Murphy, Elaine A. Ostrander, Robert K. Wayne
2006 Trends in Ecology & Evolution  
Acknowledgements We thank Phil Hedrick, Jay Storz and two additional reviewers for providing insightful comments; Phil Morin for his reading of an earlier version of the article, and John Pollinger for  ...  computing genetic distances of the canids.  ...  A comparative genomics perspective can enhance the value of SNP surveys for conservation.  ... 
doi:10.1016/j.tree.2006.08.001 pmid:16908089 fatcat:pmtbpzwtgbc55kymy64ltin76y

Phylogenetic Analysis of Polyomavirus Simian Virus 40 from Monkeys and Humans Reveals Genetic Variation

Z. H. Forsman, J. A. Lednicky, G. E. Fox, R. C. Willson, Z. S. White, S. J. Halvorson, C. Wong, A. M. Lewis, J. S. Butel
2004 Journal of Virology  
Four other polymorphic regions in the genome were also identified.  ...  Thus, adaptation is not essential for SV40 survival in humans. The C terminus of the T-antigen (T-ag-C) gene contains the highest proportion of variable sites in the SV40 genome.  ...  ACKNOWLEDGMENTS This work was supported in part by a grant from the Center for Biologics Evaluation and Research, Food and Drug Administration, to J.S.B.; by grant CA096951 from the National Cancer Institute  ... 
doi:10.1128/jvi.78.17.9306-9316.2004 pmid:15308725 pmcid:PMC506915 fatcat:2yih5adjmjbn7o6ruinyr2qd7q

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

S. Mooney
2005 Briefings in Bioinformatics  
Predicting and understanding the downstream effects of genetic variation using computational methods are becoming increasingly important for single nucleotide polymorphism (SNP) selection in genetics studies  ...  Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals.  ...  INTRODUCTION Single nucleotide polymorphisms (SNPs; Table 1 provides a glossary of terms) are the most common form of genetic variation in humans comprising nearly 1/1,000th of the average human genome  ... 
doi:10.1093/bib/6.1.44 pmid:15826356 fatcat:okbeyyns6nda7ogkiqxiynuk24

Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: Current and developing technologies

B CHORLEY, X WANG, M CAMPBELL, G PITTMAN, M NOUREDDINE, D BELL
2008 Mutation research. Reviews in mutation research  
It is well known that SNPs within regulatory regions of the genome can result in disregulation of gene transcription.  ...  However, the impact of SNPs located in putative regulatory regions, or rSNPs, is harder to predict for two primary reasons.  ...  Conclusions A key challenge in identifying functional polymorphisms in gene regulatory regions is the shear amount of genomic data and the undefined nature of these regions.  ... 
doi:10.1016/j.mrrev.2008.05.001 pmid:18565787 pmcid:PMC2676583 fatcat:uebs3444wnc2fomouieohae3jm

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions

Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardeux, Jianrong Li, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S Ramos, Ian Foster, Joshua C Denny (+2 others)
2016 npj Genomic Medicine  
We additionally confirmed synergistic and antagonistic genetic interactions for a subset of prioritised SNP pairs in independent studies of Alzheimer's disease (entropy P = 0.046), bladder cancer (entropy  ...  Using computational modelling of 2 million pairs of disease-associated SNPs drawn from genome-wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology  ...  Maienschein-Cline for his assistance with the data preparation and Colleen Kenost for her assistance with proofreading the manuscript.  ... 
doi:10.1038/npjgenmed.2016.6 pmid:27482468 pmcid:PMC4966659 fatcat:gemhabka3bcxfcwfn4rzzvzotm

Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA

Yves A. Lussier, Joanne Berghout, Francesca Vitali, Kenneth S. Ramos, Maricel Kann, Jason H. Moore
2017 Biocomputing 2018  
Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements.  ...  This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology.  ...  Introduction The majority of the human genome is comprised of noncoding DNA.  ... 
doi:10.1142/9789813235533_0046 fatcat:fplkzrvi3fh23f3rebifh6t42a
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