<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ferreira, Pedro G</style></author><author><style face="normal" font="default" size="100%">Muñoz-Aguirre, Manuel</style></author><author><style face="normal" font="default" size="100%">Reverter, Ferran</style></author><author><style face="normal" font="default" size="100%">Sá Godinho, Caio P</style></author><author><style face="normal" font="default" size="100%">Sousa, Abel</style></author><author><style face="normal" font="default" size="100%">Amadoz, Alicia</style></author><author><style face="normal" font="default" size="100%">Sodaei, Reza</style></author><author><style face="normal" font="default" size="100%">Hidalgo, Marta R</style></author><author><style face="normal" font="default" size="100%">Pervouchine, Dmitri</style></author><author><style face="normal" font="default" size="100%">Carbonell-Caballero, José</style></author><author><style face="normal" font="default" size="100%">Nurtdinov, Ramil</style></author><author><style face="normal" font="default" size="100%">Breschi, Alessandra</style></author><author><style face="normal" font="default" size="100%">Amador, Raziel</style></author><author><style face="normal" font="default" size="100%">Oliveira, Patrícia</style></author><author><style face="normal" font="default" size="100%">Cubuk, Cankut</style></author><author><style face="normal" font="default" size="100%">Curado, João</style></author><author><style face="normal" font="default" size="100%">Aguet, François</style></author><author><style face="normal" font="default" size="100%">Oliveira, Carla</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Sammeth, Michael</style></author><author><style face="normal" font="default" size="100%">Ardlie, Kristin G</style></author><author><style face="normal" font="default" size="100%">Guigó, Roderic</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The effects of death and post-mortem cold ischemia on human tissue transcriptomes.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Commun</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Commun</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Blood</style></keyword><keyword><style  face="normal" font="default" size="100%">Cold Ischemia</style></keyword><keyword><style  face="normal" font="default" size="100%">Death</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">gene expression</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Biological</style></keyword><keyword><style  face="normal" font="default" size="100%">Postmortem Changes</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Stochastic Processes</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2018</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2018 Feb 13</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">490</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/29440659?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lagarde, Julien</style></author><author><style face="normal" font="default" size="100%">Uszczynska-Ratajczak, Barbara</style></author><author><style face="normal" font="default" size="100%">Santoyo-López, Javier</style></author><author><style face="normal" font="default" size="100%">Gonzalez, Jose Manuel</style></author><author><style face="normal" font="default" size="100%">Tapanari, Electra</style></author><author><style face="normal" font="default" size="100%">Mudge, Jonathan M.</style></author><author><style face="normal" font="default" size="100%">Steward, Charles A.</style></author><author><style face="normal" font="default" size="100%">Wilming, Laurens</style></author><author><style face="normal" font="default" size="100%">Tanzer, Andrea</style></author><author><style face="normal" font="default" size="100%">Howald, Cédric</style></author><author><style face="normal" font="default" size="100%">Chrast, Jacqueline</style></author><author><style face="normal" font="default" size="100%">Vela-Boza, Alicia</style></author><author><style face="normal" font="default" size="100%">Rueda, Antonio</style></author><author><style face="normal" font="default" size="100%">Lopez-Domingo, Francisco J.</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Reymond, Alexandre</style></author><author><style face="normal" font="default" size="100%">Guigó, Roderic</style></author><author><style face="normal" font="default" size="100%">Harrow, Jennifer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)</style></title><secondary-title><style face="normal" font="default" size="100%">Nature Communications</style></secondary-title><short-title><style face="normal" font="default" size="100%">Nat Commun</style></short-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">Jan-11-2016</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.nature.com/articles/ncomms12339http://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339.pdfhttp://www.nature.com/articles/ncomms12339</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">7</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><issue><style face="normal" font="default" size="100%">1</style></issue></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lagarde, Julien</style></author><author><style face="normal" font="default" size="100%">Uszczynska-Ratajczak, Barbara</style></author><author><style face="normal" font="default" size="100%">Santoyo-López, Javier</style></author><author><style face="normal" font="default" size="100%">Gonzalez, Jose Manuel</style></author><author><style face="normal" font="default" size="100%">Tapanari, Electra</style></author><author><style face="normal" font="default" size="100%">Mudge, Jonathan M</style></author><author><style face="normal" font="default" size="100%">Steward, Charles A</style></author><author><style face="normal" font="default" size="100%">Wilming, Laurens</style></author><author><style face="normal" font="default" size="100%">Tanzer, Andrea</style></author><author><style face="normal" font="default" size="100%">Howald, Cédric</style></author><author><style face="normal" font="default" size="100%">Chrast, Jacqueline</style></author><author><style face="normal" font="default" size="100%">Vela-Boza, Alicia</style></author><author><style face="normal" font="default" size="100%">Antonio Rueda</style></author><author><style face="normal" font="default" size="100%">López-Domingo, Francisco J</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Reymond, Alexandre</style></author><author><style face="normal" font="default" size="100%">Guigó, Roderic</style></author><author><style face="normal" font="default" size="100%">Harrow, Jennifer</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).</style></title><secondary-title><style face="normal" font="default" size="100%">Nature communications</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.nature.com/articles/ncomms12339</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">12339</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Long non-coding RNAs (lncRNAs) constitute a large, yet mostly uncharacterized fraction of the mammalian transcriptome. Such characterization requires a comprehensive, high-quality annotation of their gene structure and boundaries, which is currently lacking. Here we describe RACE-Seq, an experimental workflow designed to address this based on RACE (rapid amplification of cDNA ends) and long-read RNA sequencing. We apply RACE-Seq to 398 human lncRNA genes in seven tissues, leading to the discovery of 2,556 on-target, novel transcripts. About 60% of the targeted loci are extended in either 5’ or 3’, often reaching genomic hallmarks of gene boundaries. Analysis of the novel transcripts suggests that lncRNAs are as long, have as many exons and undergo as much alternative splicing as protein-coding genes, contrary to current assumptions. Overall, we show that RACE-Seq is an effective tool to annotate an organism’s deep transcriptome, and compares favourably to other targeted sequencing techniques.</style></abstract></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wilkinson, Mark D</style></author><author><style face="normal" font="default" size="100%">Senger, Martin</style></author><author><style face="normal" font="default" size="100%">Kawas, Edward</style></author><author><style face="normal" font="default" size="100%">Bruskiewich, Richard</style></author><author><style face="normal" font="default" size="100%">Gouzy, Jerome</style></author><author><style face="normal" font="default" size="100%">Noirot, Celine</style></author><author><style face="normal" font="default" size="100%">Bardou, Philippe</style></author><author><style face="normal" font="default" size="100%">Ng, Ambrose</style></author><author><style face="normal" font="default" size="100%">Haase, Dirk</style></author><author><style face="normal" font="default" size="100%">Saiz, Enrique de Andres</style></author><author><style face="normal" font="default" size="100%">Wang, Dennis</style></author><author><style face="normal" font="default" size="100%">Gibbons, Frank</style></author><author><style face="normal" font="default" size="100%">Gordon, Paul M K</style></author><author><style face="normal" font="default" size="100%">Sensen, Christoph W</style></author><author><style face="normal" font="default" size="100%">Carrasco, Jose Manuel Rodriguez</style></author><author><style face="normal" font="default" size="100%">Fernández, José M</style></author><author><style face="normal" font="default" size="100%">Shen, Lixin</style></author><author><style face="normal" font="default" size="100%">Links, Matthew</style></author><author><style face="normal" font="default" size="100%">Ng, Michael</style></author><author><style face="normal" font="default" size="100%">Opushneva, Nina</style></author><author><style face="normal" font="default" size="100%">Neerincx, Pieter B T</style></author><author><style face="normal" font="default" size="100%">Leunissen, Jack A M</style></author><author><style face="normal" font="default" size="100%">Ernst, Rebecca</style></author><author><style face="normal" font="default" size="100%">Twigger, Simon</style></author><author><style face="normal" font="default" size="100%">Usadel, Bjorn</style></author><author><style face="normal" font="default" size="100%">Good, Benjamin</style></author><author><style face="normal" font="default" size="100%">Wong, Yan</style></author><author><style face="normal" font="default" size="100%">Stein, Lincoln</style></author><author><style face="normal" font="default" size="100%">Crosby, William</style></author><author><style face="normal" font="default" size="100%">Karlsson, Johan</style></author><author><style face="normal" font="default" size="100%">Royo, Romina</style></author><author><style face="normal" font="default" size="100%">Párraga, Iván</style></author><author><style face="normal" font="default" size="100%">Ramírez, Sergio</style></author><author><style face="normal" font="default" size="100%">Gelpi, Josep Lluis</style></author><author><style face="normal" font="default" size="100%">Trelles, Oswaldo</style></author><author><style face="normal" font="default" size="100%">Pisano, David G</style></author><author><style face="normal" font="default" size="100%">Jimenez, Natalia</style></author><author><style face="normal" font="default" size="100%">Kerhornou, Arnaud</style></author><author><style face="normal" font="default" size="100%">Rosset, Roman</style></author><author><style face="normal" font="default" size="100%">Zamacola, Leire</style></author><author><style face="normal" font="default" size="100%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Huerta-Cepas, Jaime</style></author><author><style face="normal" font="default" size="100%">Carazo, Jose María</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Guigó, Roderic</style></author><author><style face="normal" font="default" size="100%">Navarro, Arcadi</style></author><author><style face="normal" font="default" size="100%">Orozco, Modesto</style></author><author><style face="normal" font="default" size="100%">Valencia, Alfonso</style></author><author><style face="normal" font="default" size="100%">Claros, M Gonzalo</style></author><author><style face="normal" font="default" size="100%">Pérez, Antonio J</style></author><author><style face="normal" font="default" size="100%">Aldana, Jose</style></author><author><style face="normal" font="default" size="100%">Rojano, M  Mar</style></author><author><style face="normal" font="default" size="100%">Fernandez-Santa Cruz, Raul</style></author><author><style face="normal" font="default" size="100%">Navas, Ismael</style></author><author><style face="normal" font="default" size="100%">Schiltz, Gary</style></author><author><style face="normal" font="default" size="100%">Farmer, Andrew</style></author><author><style face="normal" font="default" size="100%">Gessler, Damian</style></author><author><style face="normal" font="default" size="100%">Schoof, Heiko</style></author><author><style face="normal" font="default" size="100%">Groscurth, Andreas</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">BioMoby Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Interoperability with Moby 1.0--it's better than sharing your toothbrush!</style></title><secondary-title><style face="normal" font="default" size="100%">Brief Bioinform</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Brief Bioinform</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Database Management Systems</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Factual</style></keyword><keyword><style  face="normal" font="default" size="100%">Information Storage and Retrieval</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Programming Languages</style></keyword><keyword><style  face="normal" font="default" size="100%">Systems Integration</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">220-31</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/18238804?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Saar, Kathrin</style></author><author><style face="normal" font="default" size="100%">Beck, Alfred</style></author><author><style face="normal" font="default" size="100%">Bihoreau, Marie-Thérèse</style></author><author><style face="normal" font="default" size="100%">Birney, Ewan</style></author><author><style face="normal" font="default" size="100%">Brocklebank, Denise</style></author><author><style face="normal" font="default" size="100%">Chen, Yuan</style></author><author><style face="normal" font="default" size="100%">Cuppen, Edwin</style></author><author><style face="normal" font="default" size="100%">Demonchy, Stephanie</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Flicek, Paul</style></author><author><style face="normal" font="default" size="100%">Foglio, Mario</style></author><author><style face="normal" font="default" size="100%">Fujiyama, Asao</style></author><author><style face="normal" font="default" size="100%">Gut, Ivo G</style></author><author><style face="normal" font="default" size="100%">Gauguier, Dominique</style></author><author><style face="normal" font="default" size="100%">Guigó, Roderic</style></author><author><style face="normal" font="default" size="100%">Guryev, Victor</style></author><author><style face="normal" font="default" size="100%">Heinig, Matthias</style></author><author><style face="normal" font="default" size="100%">Hummel, Oliver</style></author><author><style face="normal" font="default" size="100%">Jahn, Niels</style></author><author><style face="normal" font="default" size="100%">Klages, Sven</style></author><author><style face="normal" font="default" size="100%">Kren, Vladimir</style></author><author><style face="normal" font="default" size="100%">Kube, Michael</style></author><author><style face="normal" font="default" size="100%">Kuhl, Heiner</style></author><author><style face="normal" font="default" size="100%">Kuramoto, Takashi</style></author><author><style face="normal" font="default" size="100%">Kuroki, Yoko</style></author><author><style face="normal" font="default" size="100%">Lechner, Doris</style></author><author><style face="normal" font="default" size="100%">Lee, Young-Ae</style></author><author><style face="normal" font="default" size="100%">Lopez-Bigas, Nuria</style></author><author><style face="normal" font="default" size="100%">Lathrop, G Mark</style></author><author><style face="normal" font="default" size="100%">Mashimo, Tomoji</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Mott, Richard</style></author><author><style face="normal" font="default" size="100%">Patone, Giannino</style></author><author><style face="normal" font="default" size="100%">Perrier-Cornet, Jeanne-Antide</style></author><author><style face="normal" font="default" size="100%">Platzer, Matthias</style></author><author><style face="normal" font="default" size="100%">Pravenec, Michal</style></author><author><style face="normal" font="default" size="100%">Reinhardt, Richard</style></author><author><style face="normal" font="default" size="100%">Sakaki, Yoshiyuki</style></author><author><style face="normal" font="default" size="100%">Schilhabel, Markus</style></author><author><style face="normal" font="default" size="100%">Schulz, Herbert</style></author><author><style face="normal" font="default" size="100%">Serikawa, Tadao</style></author><author><style face="normal" font="default" size="100%">Shikhagaie, Medya</style></author><author><style face="normal" font="default" size="100%">Tatsumoto, Shouji</style></author><author><style face="normal" font="default" size="100%">Taudien, Stefan</style></author><author><style face="normal" font="default" size="100%">Toyoda, Atsushi</style></author><author><style face="normal" font="default" size="100%">Voigt, Birger</style></author><author><style face="normal" font="default" size="100%">Zelenika, Diana</style></author><author><style face="normal" font="default" size="100%">Zimdahl, Heike</style></author><author><style face="normal" font="default" size="100%">Hubner, Norbert</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">STAR Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">SNP and haplotype mapping for genetic analysis in the rat.</style></title><secondary-title><style face="normal" font="default" size="100%">Nat Genet</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat Genet</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Chromosome Mapping</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Haplotypes</style></keyword><keyword><style  face="normal" font="default" size="100%">Linkage Disequilibrium</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword><keyword><style  face="normal" font="default" size="100%">Quantitative Trait Loci</style></keyword><keyword><style  face="normal" font="default" size="100%">Rats</style></keyword><keyword><style  face="normal" font="default" size="100%">Rats, Inbred Strains</style></keyword><keyword><style  face="normal" font="default" size="100%">Recombination, Genetic</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">40</style></volume><pages><style face="normal" font="default" size="100%">560-6</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;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.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/18443594?dopt=Abstract</style></custom1></record></records></xml>