@article {939, title = {Select your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs.}, journal = {International journal of data mining and bioinformatics}, volume = {6}, year = {2012}, month = {2012}, pages = {324-34}, abstract = {Association studies are the choice approach in the discovery of the genomic basis of complex traits. To carry out such analysis, researchers frequently need to (1) select optimally informative sets of Single Nucleotide Polymorphisms (SNPs) in candidate regions and (2) annotate the results of associations found by means of genome-wide SNP arrays. These are complex tasks, since many criteria have to be considered, including the SNPs{\textquoteright} functional properties, technological information and haplotype frequencies in given populations. SYSNPs implements algorithms that allow for efficient and simultaneous consideration of all the relevant criteria to obtain sets of SNPs that properly cover arbitrarily large lists of genes or genomic regions. Complementarily, SYSNPs allows for comprehensive functional annotation of SNPs linked to any given marker SNP. SYSNPs dramatically reduces the effort needed for SNP selection from days of searching various databases to a few minutes using a simple browser.}, issn = {1748-5673}, url = {http://inderscience.metapress.com/content/f76740x8071u513n/}, author = {Lorente-Galdos, Bel{\'e}n and Medina, Ignacio and Morcillo-Suarez, Carlos and Heredia, Txema and Carre{\~n}o-Torres, Angel and Sangr{\'o}s, Ricardo and Alegre, Josep and Pita, Guillermo and Vellalta, Gemma and Malats, Nuria and Pisano, David G and Joaqu{\'\i}n Dopazo and Navarro, Arcadi} } @article {576, title = {Serial Expression Analysis: a web tool for the analysis of serial gene expression data.}, journal = {Nucleic Acids Res}, volume = {38}, year = {2010}, month = {2010 Jul}, pages = {W239-45}, abstract = {

Serial transcriptomics experiments investigate the dynamics of gene expression changes associated with a quantitative variable such as time or dosage. The statistical analysis of these data implies the study of global and gene-specific expression trends, the identification of significant serial changes, the comparison of expression profiles and the assessment of transcriptional changes in terms of cellular processes. We have created the SEA (Serial Expression Analysis) suite to provide a complete web-based resource for the analysis of serial transcriptomics data. SEA offers five different algorithms based on univariate, multivariate and functional profiling strategies framed within a user-friendly interface and a project-oriented architecture to facilitate the analysis of serial gene expression data sets from different perspectives. SEA is available at sea.bioinfo.cipf.es.

}, keywords = {Algorithms, Gene Expression Profiling, Internet, Kinetics, Linear Models, Oligonucleotide Array Sequence Analysis, Software}, issn = {1362-4962}, doi = {10.1093/nar/gkq488}, author = {Nueda, Maria Jos{\'e} and Carbonell, Jos{\'e} and Medina, Ignacio and Dopazo, Joaquin and Conesa, Ana} } @article {18443594, title = {SNP and haplotype mapping for genetic analysis in the rat}, journal = {Nat Genet}, volume = {40}, number = {5}, year = {2008}, note = {

STAR Consortium Saar, Kathrin Beck, Alfred Bihoreau, Marie-Therese Birney, Ewan Brocklebank, Denise Chen, Yuan Cuppen, Edwin Demonchy, Stephanie Dopazo, Joaquin Flicek, Paul Foglio, Mario Fujiyama, Asao Gut, Ivo G Gauguier, Dominique Guigo, Roderic Guryev, Victor Heinig, Matthias Hummel, Oliver Jahn, Niels Klages, Sven Kren, Vladimir Kube, Michael Kuhl, Heiner Kuramoto, Takashi Kuroki, Yoko Lechner, Doris Lee, Young-Ae Lopez-Bigas, Nuria Lathrop, G Mark Mashimo, Tomoji Medina, Ignacio Mott, Richard Patone, Giannino Perrier-Cornet, Jeanne-Antide Platzer, Matthias Pravenec, Michal Reinhardt, Richard Sakaki, Yoshiyuki Schilhabel, Markus Schulz, Herbert Serikawa, Tadao Shikhagaie, Medya Tatsumoto, Shouji Taudien, Stefan Toyoda, Atsushi Voigt, Birger Zelenika, Diana Zimdahl, Heike Hubner, Norbert 057733/Z/99/A/Wellcome Trust/United Kingdom 066780/Z/01/Z/Wellcome Trust/United Kingdom Research Support, Non-U.S. Gov{\textquoteright}t Technical Report United States Nature genetics Nat Genet. 2008 May;40(5):560-6.

}, pages = {560-6}, abstract = {

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81\% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

}, keywords = {Animals Chromosome Mapping *Databases, Genetic, Genetic Genome *Haplotypes Linkage Disequilibrium Phylogeny *Polymorphism, Inbred Strains/*genetics Recombination, Single Nucleotide *Quantitative Trait Loci Rats/*genetics Rats}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18443594}, author = {K. Saar and A. Beck and M. T. Bihoreau and E. Birney and D. Brocklebank and Y. Chen and E. Cuppen and S. Demonchy and Dopazo, J. and P. Flicek and M. Foglio and A. Fujiyama and I. G. Gut and D. Gauguier and R. Guigo and V. Guryev and M. Heinig and O. Hummel and N. Jahn and S. Klages and V. Kren and M. Kube and H. Kuhl and Kuramoto, T. and Kuroki, Y. and Lechner, D. and Lee, Y. A. and Lopez-Bigas, N. and Lathrop, G. M. and Mashimo, T. and Medina, Ignacio and Mott, R. and Patone, G. and Perrier-Cornet, J. A. and Platzer, M. and Pravenec, M. and Reinhardt, R. and Sakaki, Y. and Schilhabel, M. and Schulz, H. and Serikawa, T. and Shikhagaie, M. and Tatsumoto, S. and Taudien, S. and Toyoda, A. and Voigt, B. and Zelenika, D. and Zimdahl, H. and Hubner, N.} } @article {599, title = {SNP and haplotype mapping for genetic analysis in the rat.}, journal = {Nat Genet}, volume = {40}, year = {2008}, month = {2008 May}, pages = {560-6}, abstract = {

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81\% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.

}, keywords = {Animals, Chromosome Mapping, Databases, Genetic, Genome, Haplotypes, Linkage Disequilibrium, Phylogeny, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Rats, Rats, Inbred Strains, Recombination, Genetic}, issn = {1546-1718}, doi = {10.1038/ng.124}, author = {Saar, Kathrin and Beck, Alfred and Bihoreau, Marie-Th{\'e}r{\`e}se and Birney, Ewan and Brocklebank, Denise and Chen, Yuan and Cuppen, Edwin and Demonchy, Stephanie and Dopazo, Joaquin and Flicek, Paul and Foglio, Mario and Fujiyama, Asao and Gut, Ivo G and Gauguier, Dominique and Guig{\'o}, Roderic and Guryev, Victor and Heinig, Matthias and Hummel, Oliver and Jahn, Niels and Klages, Sven and Kren, Vladimir and Kube, Michael and Kuhl, Heiner and Kuramoto, Takashi and Kuroki, Yoko and Lechner, Doris and Lee, Young-Ae and Lopez-Bigas, Nuria and Lathrop, G Mark and Mashimo, Tomoji and Medina, Ignacio and Mott, Richard and Patone, Giannino and Perrier-Cornet, Jeanne-Antide and Platzer, Matthias and Pravenec, Michal and Reinhardt, Richard and Sakaki, Yoshiyuki and Schilhabel, Markus and Schulz, Herbert and Serikawa, Tadao and Shikhagaie, Medya and Tatsumoto, Shouji and Taudien, Stefan and Toyoda, Atsushi and Voigt, Birger and Zelenika, Diana and Zimdahl, Heike and Hubner, Norbert} }