<?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%">Joanna Friesner</style></author><author><style face="normal" font="default" size="100%">Sarah M. Assmann</style></author><author><style face="normal" font="default" size="100%">Ruth Bastow</style></author><author><style face="normal" font="default" size="100%">Julia Bailey-Serres</style></author><author><style face="normal" font="default" size="100%">Jim Beynon</style></author><author><style face="normal" font="default" size="100%">Volker Brendel</style></author><author><style face="normal" font="default" size="100%">C. Robin Buell</style></author><author><style face="normal" font="default" size="100%">Alexander Bucksch</style></author><author><style face="normal" font="default" size="100%">Wolfgang Busch</style></author><author><style face="normal" font="default" size="100%">Taku Demura</style></author><author><style face="normal" font="default" size="100%">Jose R. Dinneny</style></author><author><style face="normal" font="default" size="100%">Colleen J. Doherty</style></author><author><style face="normal" font="default" size="100%">Andrea L. Eveland</style></author><author><style face="normal" font="default" size="100%">Pascal Falter-Braun</style></author><author><style face="normal" font="default" size="100%">Malia A. Gehan</style></author><author><style face="normal" font="default" size="100%">Michael Gonzales</style></author><author><style face="normal" font="default" size="100%">Erich Grotewold</style></author><author><style face="normal" font="default" size="100%">Rodrigo Gutierrez</style></author><author><style face="normal" font="default" size="100%">Ute Kramer</style></author><author><style face="normal" font="default" size="100%">Gabriel Krouk</style></author><author><style face="normal" font="default" size="100%">Shisong Ma</style></author><author><style face="normal" font="default" size="100%">R.J. Cody Markelz</style></author><author><style face="normal" font="default" size="100%">Molly Megraw</style></author><author><style face="normal" font="default" size="100%">Blake C. Meyers</style></author><author><style face="normal" font="default" size="100%">James A.H. Murray</style></author><author><style face="normal" font="default" size="100%">Nicholas J. Provart</style></author><author><style face="normal" font="default" size="100%">Sue Rhee</style></author><author><style face="normal" font="default" size="100%">Roger Smith</style></author><author><style face="normal" font="default" size="100%">Edgar P. Spalding</style></author><author><style face="normal" font="default" size="100%">Crispin Taylor</style></author><author><style face="normal" font="default" size="100%">Tracy K. Teal</style></author><author><style face="normal" font="default" size="100%">Keiko U. Torii</style></author><author><style face="normal" font="default" size="100%">Chris Town</style></author><author><style face="normal" font="default" size="100%">Matthew Vaughn</style></author><author><style face="normal" font="default" size="100%">Richard Vierstra</style></author><author><style face="normal" font="default" size="100%">Doreen Ware</style></author><author><style face="normal" font="default" size="100%">Olivia Wilkins</style></author><author><style face="normal" font="default" size="100%">Cranos Williams</style></author><author><style face="normal" font="default" size="100%">Siobhan M. Brady</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology</style></title><secondary-title><style face="normal" font="default" size="100%">Plant Physiology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2017</style></year><pub-dates><date><style  face="normal" font="default" size="100%">12/2017</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.plantphysiol.org/content/175/4/1499</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">175</style></volume><pages><style face="normal" font="default" size="100%">1499-1509</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;div&gt;It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges.&lt;/div&gt;</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%">Alexiou, Panagiotis</style></author><author><style face="normal" font="default" size="100%">Vergoulis, Thanasis</style></author><author><style face="normal" font="default" size="100%">Gleditzsch, Martin</style></author><author><style face="normal" font="default" size="100%">Prekas, George</style></author><author><style face="normal" font="default" size="100%">Dalamagas, Theodore</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Grosse, Ivo</style></author><author><style face="normal" font="default" size="100%">Sellis, Timos</style></author><author><style face="normal" font="default" size="100%">Hatzigeorgiou, Artemis G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">miRGen 2.0: a database of microRNA genomic information and regulation.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">3' Untranslated Regions</style></keyword><keyword><style  face="normal" font="default" size="100%">Algorithms</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Cell Line, Tumor</style></keyword><keyword><style  face="normal" font="default" size="100%">Computational Biology</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Databases, Nucleic Acid</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</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%">Mice</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Polymorphism, Single Nucleotide</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcription Factors</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">38</style></volume><pages><style face="normal" font="default" size="100%">D137-41</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;MicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding to the 3&amp;#39;UTR region of mRNAs. MicroRNAs are produced from longer transcripts which can code for more than one mature miRNAs. miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both predicted and experimentally supported data. Expression profiles of microRNAs in several tissues and cell lines, single nucleotide polymorphism locations, microRNA target prediction on protein coding genes and mapping of miRNA targets of co-regulated miRNAs on biological pathways are also integrated into the database and user interface. The miRGen database will be continuously maintained and freely available at http://www.microrna.gr/mirgen/.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Database issue</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%">Kawahara, Yukio</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly</style></author><author><style face="normal" font="default" size="100%">Kreider, Edward</style></author><author><style face="normal" font="default" size="100%">Iizasa, Hisashi</style></author><author><style face="normal" font="default" size="100%">Valente, Louis</style></author><author><style face="normal" font="default" size="100%">Hatzigeorgiou, Artemis G</style></author><author><style face="normal" font="default" size="100%">Nishikura, Kazuko</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Frequency and fate of microRNA editing in human brain.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Adenosine</style></keyword><keyword><style  face="normal" font="default" size="100%">Adenosine Deaminase</style></keyword><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Base Sequence</style></keyword><keyword><style  face="normal" font="default" size="100%">Brain</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Inosine</style></keyword><keyword><style  face="normal" font="default" size="100%">Mice</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Molecular Sequence Data</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA Editing</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA Precursors</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA Processing, Post-Transcriptional</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA-Binding Proteins</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 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">5270-80</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A--&amp;gt;I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT-PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that approximately 16% of human pri-miRNAs are subject to A--&amp;gt;I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">16</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%">Zhang, Lin</style></author><author><style face="normal" font="default" size="100%">Volinia, Stefano</style></author><author><style face="normal" font="default" size="100%">Bonome, Tomas</style></author><author><style face="normal" font="default" size="100%">Calin, George Adrian</style></author><author><style face="normal" font="default" size="100%">Greshock, Joel</style></author><author><style face="normal" font="default" size="100%">Yang, Nuo</style></author><author><style face="normal" font="default" size="100%">Liu, Chang-Gong</style></author><author><style face="normal" font="default" size="100%">Giannakakis, Antonis</style></author><author><style face="normal" font="default" size="100%">Alexiou, Pangiotis</style></author><author><style face="normal" font="default" size="100%">Hasegawa, Kosei</style></author><author><style face="normal" font="default" size="100%">Johnstone, Cameron N</style></author><author><style face="normal" font="default" size="100%">Megraw, Molly S</style></author><author><style face="normal" font="default" size="100%">Adams, Sarah</style></author><author><style face="normal" font="default" size="100%">Lassus, Heini</style></author><author><style face="normal" font="default" size="100%">Huang, Jia</style></author><author><style face="normal" font="default" size="100%">Kaur, Sippy</style></author><author><style face="normal" font="default" size="100%">Liang, Shun</style></author><author><style face="normal" font="default" size="100%">Sethupathy, Praveen</style></author><author><style face="normal" font="default" size="100%">Leminen, Arto</style></author><author><style face="normal" font="default" size="100%">Simossis, Victor A</style></author><author><style face="normal" font="default" size="100%">Sandaltzopoulos, Raphael</style></author><author><style face="normal" font="default" size="100%">Naomoto, Yoshio</style></author><author><style face="normal" font="default" size="100%">Katsaros, Dionyssios</style></author><author><style face="normal" font="default" size="100%">Gimotty, Phyllis A</style></author><author><style face="normal" font="default" size="100%">DeMichele, Angela</style></author><author><style face="normal" font="default" size="100%">Huang, Qihong</style></author><author><style face="normal" font="default" size="100%">Bützow, Ralf</style></author><author><style face="normal" font="default" size="100%">Rustgi, Anil K</style></author><author><style face="normal" font="default" size="100%">Weber, Barbara L</style></author><author><style face="normal" font="default" size="100%">Birrer, Michael J</style></author><author><style face="normal" font="default" size="100%">Hatzigeorgiou, Artemis G</style></author><author><style face="normal" font="default" size="100%">Croce, Carlo M</style></author><author><style face="normal" font="default" size="100%">Coukos, George</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.</style></title><secondary-title><style face="normal" font="default" size="100%">Proc Natl Acad Sci U S A</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">DNA, Neoplasm</style></keyword><keyword><style  face="normal" font="default" size="100%">Down-Regulation</style></keyword><keyword><style  face="normal" font="default" size="100%">Epigenesis, Genetic</style></keyword><keyword><style  face="normal" font="default" size="100%">Epithelial Cells</style></keyword><keyword><style  face="normal" font="default" size="100%">Female</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Profiling</style></keyword><keyword><style  face="normal" font="default" size="100%">Gene Expression Regulation, Neoplastic</style></keyword><keyword><style  face="normal" font="default" size="100%">Genome, Human</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">MicroRNAs</style></keyword><keyword><style  face="normal" font="default" size="100%">Neoplasm Staging</style></keyword><keyword><style  face="normal" font="default" size="100%">Ovarian Neoplasms</style></keyword><keyword><style  face="normal" font="default" size="100%">Ribonuclease III</style></keyword><keyword><style  face="normal" font="default" size="100%">RNA, Messenger</style></keyword><keyword><style  face="normal" font="default" size="100%">Survival Analysis</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 13</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">105</style></volume><pages><style face="normal" font="default" size="100%">7004-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;MicroRNAs (miRNAs) are an abundant class of small noncoding RNAs that function as negative gene regulators. miRNA deregulation is involved in the initiation and progression of human cancer; however, the underlying mechanism and its contributions to genome-wide transcriptional changes in cancer are still largely unknown. We studied miRNA deregulation in human epithelial ovarian cancer by integrative genomic approach, including miRNA microarray (n = 106), array-based comparative genomic hybridization (n = 109), cDNA microarray (n = 76), and tissue array (n = 504). miRNA expression is markedly down-regulated in malignant transformation and tumor progression. Genomic copy number loss and epigenetic silencing, respectively, may account for the down-regulation of approximately 15% and at least approximately 36% of miRNAs in advanced ovarian tumors and miRNA down-regulation contributes to a genome-wide transcriptional deregulation. Last, eight miRNAs located in the chromosome 14 miRNA cluster (Dlk1-Gtl2 domain) were identified as potential tumor suppressor genes. Therefore, our results suggest that miRNAs may offer new biomarkers and therapeutic targets in epithelial ovarian cancer.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">19</style></issue></record></records></xml>