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SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system

Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph L. Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, Margaret Wrensch
2008 Nucleic Acids Research  
SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system  ...  Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information.  ...  INTRODUCTION Logical single nucleotide polymorphism (SNP) selection is a common challenge to designing a genotyping strategy for disease association studies.  ... 
doi:10.1093/nar/gkn756 pmid:18984625 pmcid:PMC2686434 fatcat:mgckpbqx5bbsbmycxcl66sxzb4

METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis

Gürkan Üstünkar, Yeşim Aydın Son
2011 Journal of Integrative Bioinformatics  
Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual's genetic variability in greatest detail.  ...  Here, we introduce and describe the system functionality and architecture of the METU-SNP.  ...  Acknowledgements We sincerely thank developers of SNPLogic for helping us with our integrated database structure.  ... 
doi:10.1515/jib-2011-187 fatcat:uniwvj4jkbgdvlzyb32vwfasb4

METU-SNP: an integrated software system for SNP-complex disease association analysis

Gürkan Ustünkar, Yeşim Aydın Son
2011 Journal of Integrative Bioinformatics  
Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual's genetic variability in greatest detail.  ...  Here, we introduce and describe the system functionality and architecture of the METU-SNP.  ...  Acknowledgements We sincerely thank developers of SNPLogic for helping us with our integrated database structure.  ... 
doi:10.2390/biecoll-jib-2011-187 pmid:22156365 fatcat:s4ngjm6ffzhndpmm7hrya2pc6u

regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions

Mingxiang Teng, Shoji Ichikawa, Leah R. Padgett, Yadong Wang, Matthew Mort, David N. Cooper, Daniel L. Koller, Tatiana Foroud, Howard J. Edenberg, Michael J. Econs, Yunlong Liu
2012 Computer applications in the biosciences : CABIOS  
Results: We present regSNPs, an informatics strategy that integrates several established bioinformatics tools, for prioritizing regulatory SNPs, i.e. the SNPs in the promoter regions that potentially affect  ...  Despite the technical advances, informatics methodologies need to be developed to prioritize thousands of variants for potential causative effects.  ...  ACKNOWLEDGEMENTS The authors thank the valuable discussion from Dr Lang Li in the Center for Computational Biology and Bioinformatics at Indiana University School of Medicine.  ... 
doi:10.1093/bioinformatics/bts275 pmid:22611130 pmcid:PMC3389767 fatcat:bikoa7y35jfcvilnytnhutrqpy

Identifying functional single nucleotide polymorphisms in the human CArGome

Craig C. Benson, Qian Zhou, Xiaochun Long, Joseph M. Miano
2011 Physiological Genomics  
Rob Fortuna and Brett Robbins from the University of Rochester Combined Internal Medicine-Pediatrics Residency Program for project support.  ...  SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) are the most common variant in the human genome.  ...  Fig. 1 . 1 Method of identifying functional single nucleotide polymorphism (SNPs) in the human CArGome.  ... 
doi:10.1152/physiolgenomics.00098.2011 pmid:21771879 pmcid:PMC3180741 fatcat:geotzcp22bg6zppsx7iu4xdrhy