@article {746, title = {The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology}, journal = {Plant Physiology}, volume = {175}, year = {2017}, month = {12/2017}, pages = {1499-1509}, abstract = {
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.
}, url = {http://www.plantphysiol.org/content/175/4/1499}, author = {Joanna Friesner and Sarah M. Assmann and Ruth Bastow and Julia Bailey-Serres and Jim Beynon and Volker Brendel and C. Robin Buell and Alexander Bucksch and Wolfgang Busch and Taku Demura and Jose R. Dinneny and Colleen J. Doherty and Andrea L. Eveland and Pascal Falter-Braun and Malia A. Gehan and Michael Gonzales and Erich Grotewold and Rodrigo Gutierrez and Ute Kramer and Gabriel Krouk and Shisong Ma and R.J. Cody Markelz and Molly Megraw and Blake C. Meyers and James A.H. Murray and Nicholas J. Provart and Sue Rhee and Roger Smith and Edgar P. Spalding and Crispin Taylor and Tracy K. Teal and Keiko U. Torii and Chris Town and Matthew Vaughn and Richard Vierstra and Doreen Ware and Olivia Wilkins and Cranos Williams and Siobhan M. Brady} } @article {324, title = {miRGen 2.0: a database of microRNA genomic information and regulation.}, journal = {Nucleic Acids Res}, volume = {38}, year = {2010}, month = {2010 Jan}, pages = {D137-41}, abstract = {

MicroRNAs are small, non-protein coding RNA molecules known to regulate the expression of genes by binding to the 3\&$\#$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/.

}, keywords = {3{\textquoteright} Untranslated Regions, Algorithms, Animals, Cell Line, Tumor, Computational Biology, Databases, Genetic, Databases, Nucleic Acid, Humans, Information Storage and Retrieval, Internet, Mice, MicroRNAs, Polymorphism, Single Nucleotide, Software, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gkp888}, author = {Alexiou, Panagiotis and Vergoulis, Thanasis and Gleditzsch, Martin and Prekas, George and Dalamagas, Theodore and Megraw, Molly and Grosse, Ivo and Sellis, Timos and Hatzigeorgiou, Artemis G} } @article {327, title = {Frequency and fate of microRNA editing in human brain.}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Sep}, pages = {5270-80}, abstract = {

Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A--\>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--\>I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.

}, keywords = {Adenosine, Adenosine Deaminase, Animals, Base Sequence, Brain, Humans, Inosine, Mice, MicroRNAs, Molecular Sequence Data, RNA Editing, RNA Precursors, RNA Processing, Post-Transcriptional, RNA-Binding Proteins}, issn = {1362-4962}, doi = {10.1093/nar/gkn479}, author = {Kawahara, Yukio and Megraw, Molly and Kreider, Edward and Iizasa, Hisashi and Valente, Louis and Hatzigeorgiou, Artemis G and Nishikura, Kazuko} } @article {328, title = {Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.}, journal = {Proc Natl Acad Sci U S A}, volume = {105}, year = {2008}, month = {2008 May 13}, pages = {7004-9}, abstract = {

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.

}, keywords = {DNA, Neoplasm, Down-Regulation, Epigenesis, Genetic, Epithelial Cells, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genome, Human, Humans, MicroRNAs, Neoplasm Staging, Ovarian Neoplasms, Ribonuclease III, RNA, Messenger, Survival Analysis}, issn = {1091-6490}, doi = {10.1073/pnas.0801615105}, author = {Zhang, Lin and Volinia, Stefano and Bonome, Tomas and Calin, George Adrian and Greshock, Joel and Yang, Nuo and Liu, Chang-Gong and Giannakakis, Antonis and Alexiou, Pangiotis and Hasegawa, Kosei and Johnstone, Cameron N and Megraw, Molly S and Adams, Sarah and Lassus, Heini and Huang, Jia and Kaur, Sippy and Liang, Shun and Sethupathy, Praveen and Leminen, Arto and Simossis, Victor A and Sandaltzopoulos, Raphael and Naomoto, Yoshio and Katsaros, Dionyssios and Gimotty, Phyllis A and DeMichele, Angela and Huang, Qihong and B{\"u}tzow, Ralf and Rustgi, Anil K and Weber, Barbara L and Birrer, Michael J and Hatzigeorgiou, Artemis G and Croce, Carlo M and Coukos, George} }