Genomes and Genes
rna sequence analysis
Summary: A multistage process that includes RNA cloning, physical mapping, subcloning, sequencing, and information analysis.
Publications254 found, 100 shown here
- The transcriptional landscape of the yeast genome defined by RNA sequencingUgrappa Nagalakshmi
Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
Science 320:1344-9. 2008..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
- Mapping and quantifying mammalian transcriptomes by RNA-SeqAli Mortazavi
Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
Nat Methods 5:621-8. 2008..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
- RNA-seq: an assessment of technical reproducibility and comparison with gene expression arraysJohn C Marioni
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
Genome Res 18:1509-17. 2008..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
- RNA-Seq: a revolutionary tool for transcriptomicsZhong Wang
Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
Nat Rev Genet 10:57-63. 2009..This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes...
- Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cellsRyan D Morin
Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
Genome Res 18:610-21. 2008..Included among the high-ranked predicted gene targets are those implicated in differentiation, cell cycle control, programmed cell death, and transcriptional regulation...
- Discovering microRNAs from deep sequencing data using miRDeepMarc R Friedländer
Max Delbruck Centrum fur Molekulare Medizin, Robert Rossle Strasse 10, D 13125 Berlin Buch, Germany
Nat Biotechnol 26:407-15. 2008..miRDeep reports altogether approximately 230 previously unannotated miRNAs, of which four novel C. elegans miRNAs are validated by northern blot analysis...
- Vienna RNA secondary structure serverIvo L Hofacker
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
Nucleic Acids Res 31:3429-31. 2003..All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/...
- Statistical inferences for isoform expression in RNA-SeqHui Jiang
Institute for Computational and Mathematical Engineering and Department of Statistics, Stanford University, Stanford, CA 94305, USA
Bioinformatics 25:1026-32. 2009..Our results show that isoform expression inference in RNA-Seq is possible by employing appropriate statistical methods...
- Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencingQun Pan
Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
Nat Genet 40:1413-5. 2008..From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels...
- A global view of gene activity and alternative splicing by deep sequencing of the human transcriptomeMarc Sultan
Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
Science 321:956-60. 2008..A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing...
- Criteria for annotation of plant MicroRNAsBlake C Meyers
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Plant Cell 20:3186-90. 2008..Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature...
- A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thalianaRamya Rajagopalan
Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Genes Dev 20:3407-25. 2006....
- High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genesNoah Fahlgren
Center for Genome Research and Biocomputing, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
PLoS ONE 2:e219. 2007..We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks...
- ARB: a software environment for sequence dataWolfgang Ludwig
Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 853530 Freising, Germany
Nucleic Acids Res 32:1363-71. 2004..Currently, the package is used by numerous working groups worldwide...
- A diverse set of microRNAs and microRNA-like small RNAs in developing rice grainsQian Hao Zhu
CSIRO Plant Industry, Canberra, ACT 2601, Australia
Genome Res 18:1456-65. 2008..Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner...
- Stem cell transcriptome profiling via massive-scale mRNA sequencingNicole Cloonan
Expression Genomics Laboratory, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Queensland, 4072, Australia
Nat Methods 5:613-9. 2008....
- miRU: an automated plant miRNA target prediction serverYuanji Zhang
Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
Nucleic Acids Res 33:W701-4. 2005..The miRU web server is available at http://bioinfo3.noble.org/miRU.htm...
- ESEfinder: A web resource to identify exonic splicing enhancersLuca Cartegni
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
Nucleic Acids Res 31:3568-71. 2003....
- GMAP: a genomic mapping and alignment program for mRNA and EST sequencesThomas D Wu
Department of Bioinformatics Genentech, Inc, South San Francisco, CA 94080, USA
Bioinformatics 21:1859-75. 2005....
- Global identification of microRNA-target RNA pairs by parallel analysis of RNA endsMarcelo A German
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Nat Biotechnol 26:941-6. 2008..This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs...
- Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promotersLeighton J Core
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
Science 322:1845-8. 2008..These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription...
- Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradomeCharles Addo-Quaye
Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
Curr Biol 18:758-62. 2008..This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions...
- MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA librariesMerav Bar
Divisions of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Stem Cells 26:2496-505. 2008..Disclosure of potential conflicts of interest is found at the end of this article...
- NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsKim D Pruitt
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
Nucleic Acids Res 33:D501-4. 2005....
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
- Local RNA base pairing probabilities in large sequencesStephan H Bernhart
Institut fur Theoretische Chemie, Universitat Wien, Währingerstr 17, A 1090 Wien, Austria
Bioinformatics 22:614-5. 2006..Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window...
- microPred: effective classification of pre-miRNAs for human miRNA gene predictionRukshan Batuwita
Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Oxford, UK
Bioinformatics 25:989-95. 2009....
- Conservation and divergence of microRNAs in PopulusAbdelali Barakat
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, 403 Life Sciences Building, The Pennsylvania State University, University Park, PA 16802, USA
BMC Genomics 8:481. 2007..In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing...
- Identification of microRNAs of the herpesvirus familySebastien Pfeffer
Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
Nat Methods 2:269-76. 2005..Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses...
- Using expression profiling data to identify human microRNA targetsJim C Huang
Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
Nat Methods 4:1045-9. 2007..Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels...
- RNA cytosine methylation analysis by bisulfite sequencingMatthias Schaefer
Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
Nucleic Acids Res 37:e12. 2009..These results establish a versatile method for the identification and characterization of RNA methylation patterns, which will be useful for defining the biological function of RNA methylation...
- Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimizationDavid H Mathews
Center for Human Genetics and Molecular Pediatric Disease, Aab Institute of Biomedical Sciences, University of Rochester Medical Center, 601 Elmwood Avenue, Box 703, NY 14642, USA
RNA 10:1178-90. 2004..Predicted secondary structures can be color annotated to demonstrate pairs with high probability that are therefore well determined as compared to base pairs with lower probability of pairing...
- RegRNA: an integrated web server for identifying regulatory RNA motifs and elementsHsi Yuan Huang
Institute of Bioinformatics, National Chiao Tung University, Hsin Chu 300, Taiwan
Nucleic Acids Res 34:W429-34. 2006..An intuitive user interface is designed to facilitate the comprehensive annotation of user-submitted mRNA sequences. The RegRNA web server is now available at http://RegRNA.mbc.NCTU.edu.tw/...
- miRExpress: analyzing high-throughput sequencing data for profiling microRNA expressionWei Chi Wang
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin Chu 300, Taiwan, Republic of China
BMC Bioinformatics 10:328. 2009..Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs...
- Prediction of RNA secondary structure using generalized centroid estimatorsMichiaki Hamada
Mizuho Information and Research Institute, Inc, 2 3 Kanda Nishikicho, Chiyoda ku, Tokyo 101 8443, Japan
Bioinformatics 25:465-73. 2009..However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures...
- A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhiTimothy T Perkins
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
PLoS Genet 5:e1000569. 2009..Typhi OmpR regulon and identify novel OmpR regulated transcripts. Thus, ssRNA-seq provides a novel and powerful approach to the characterization of the bacterial transcriptome...
- Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methodsRobert A Ach
Agilent Laboratories, Agilent Technologies, Santa Clara, CA 95051, USA
BMC Biotechnol 8:69. 2008..Since both methods use total RNA as a starting material, it is also critical to understand how measurement of miRNAs might be affected by the particular method of total RNA preparation used...
- Elucidation of the small RNA component of the transcriptomeCheng Lu
Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Science 309:1567-9. 2005..Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs...
- Rfam: updates to the RNA families databasePaul P Gardner
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Nucleic Acids Res 37:D136-40. 2009..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/...
- Construction of small RNA cDNA libraries for deep sequencingCheng Lu
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Methods 43:110-7. 2007..Here, we describe the methods used in our laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS...
- Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequencesEric Bonnet
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052 Ghent, Belgium
Bioinformatics 20:2911-7. 2004..Statistical biases are assessed by a randomization test, in which the predicted minimum free energy of folding is compared with values obtained for structures inferred from randomly shuffling the original sequences...
- Massively parallel sequencing of the polyadenylated transcriptome of C. elegansLadeana W Hillier
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195 5065, USA
Genome Res 19:657-66. 2009..Although most sequences align with protein-coding genes, a small fraction falls in introns and intergenic regions. One notable region on the X chromosome encodes a noncoding transcript of >10 kb localized to somatic nuclei...
- Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativaRyan D Morin
Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
Genome Res 18:571-84. 2008..Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/...
- The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAsToutai Mituyama
National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center, Tokyo 135 0064, Japan
Nucleic Acids Res 37:D89-92. 2009..The current version of UCSC GenomeBrowser for Functional RNA features a larger number of tracks and richer features than the former version. The databases are available at http://www.ncrna.org/...
- A comparative method for finding and folding RNA secondary structures within protein-coding regionsJakob Skou Pedersen
Bioinformatics Research Center, Department of Ecology and Genetics, The Institute of Biological Sciences, University of Aarhus, Ny Munkegade, Building 550, 8000 Aarhus C, Denmark
Nucleic Acids Res 32:4925-36. 2004..When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD...
- The ERPIN server: an interface to profile-based RNA motif identificationAndré Lambert
CNRS UMR 6207, Universite de la Mediterranee, Luminy Case 906, 13288 Marseille, Cedex 09, France
Nucleic Acids Res 32:W160-5. 2004..An example of a complete genome scan is provided, as well as an evaluation of run times and specificity/sensitivity information for all available motifs...
- Estimating accuracy of RNA-Seq and microarrays with proteomicsXing Fu
Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, China Academy of Sciences, Shanghai, 200031, PR China
BMC Genomics 10:161. 2009..At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed by microarray design, its potential to estimate absolute transcript levels is unknown...
- NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteinsKim D Pruitt
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Rm 6An 12J, 45 Center Drive, Bethesda, MD 20892 6510, USA
Nucleic Acids Res 35:D61-5. 2007..The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence...
- RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencingBrian T Wilhelm
Laboratory of Molecular Genetics of Stem Cells, C P 6128 Succursale Centre Ville, Montreal, Que H3C3J7, Canada
Methods 48:249-57. 2009..This article discusses the experimental approach for both sample preparation and data analysis for the technique of RNA-seq...
- Mapping the Burkholderia cenocepacia niche response via high-throughput sequencingD R Yoder-Himes
Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
Proc Natl Acad Sci U S A 106:3976-81. 2009..Compared with the CF strain, the soil strain shows a stronger global gene expression response to its environment, which is consistent with the need for a more dynamic reaction to the heterogeneous conditions of soil...
- Rational siRNA design for RNA interferenceAngela Reynolds
Dharmacon, Inc, 2650 Crescent Drive, Suite 100, Lafayette, Colorado 80026, USA
Nat Biotechnol 22:326-30. 2004..This highlights the utility of rational design for selecting potent siRNAs and facilitating functional gene knockdown studies...
- Poly A- transcripts expressed in HeLa cellsQingfa Wu
Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
PLoS ONE 3:e2803. 2008..Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown...
- CMfinder--a covariance model based RNA motif finding algorithmZizhen Yao
Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
Bioinformatics 22:445-52. 2006..Previous tools fall short of this goal...
- Prediction of regulatory modules comprising microRNAs and target genesSungroh Yoon
Computer Systems Laboratory, Stanford University, Stanford, CA 94305, USA
Bioinformatics 21:ii93-100. 2005..We propose a computational method to predict miRNA regulatory modules (MRMs) or groups of miRNAs and target genes that are believed to participate cooperatively in post-transcriptional gene regulation...
- AceView: a comprehensive cDNA-supported gene and transcripts annotationDanielle Thierry-Mieg
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
Genome Biol 7:S12.1-14. 2006..The organizers evaluated the protein predictions in depth. We present a complementary analysis of the mRNAs, including alternative transcript variants...
- Bacterial phylogeny based on comparative sequence analysisW Ludwig
Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Germany
Electrophoresis 19:554-68. 1998....
- The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functionsA G Balakin
Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst 01003, USA
Cell 86:823-34. 1996..Binding of this or another common small nucleolar ribonucleoprotein particle protein is predicted to be a critical entry point to snoRNA posttranscriptional life, including precise formation of the snoRNA 3' end...
- An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cellsGene W Yeo
Crick Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
Nat Struct Mol Biol 16:130-7. 2009..These findings suggest that FOX2 functions as a critical regulator of a splicing network, and we further show that FOX2 is important for the survival of human embryonic stem cells...
- Identification of novel small RNAs using comparative genomics and microarraysK M Wassarman
Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
Genes Dev 15:1637-51. 2001..The approaches used here should allow identification of small RNAs in other organisms...
- A universal framework for regulatory element discovery across all genomes and data typesOlivier Elemento
Lewis Sigler Institute for Integrative Genomics, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Mol Cell 28:337-50. 2007....
- RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesignEckart Bindewald
Basic Research Program, SAIC Frederick and Center for Cancer Research Nanobiology Program, NCI Frederick, Frederick, MD 21702, USA
Nucleic Acids Res 36:D392-7. 2008..This database is useful for analyzing RNA structures as well as for designing novel RNA structures on a nanoscale. The database can be accessed at: http://rnajunction.abcc.ncifcrf.gov/..
- Evolution of vault RNAsPeter F Stadler
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
Mol Biol Evol 26:1975-91. 2009..In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction...
- Codon usage bias amongst plant virusesM J Adams
Plant Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts, UK
Arch Virol 149:113-35. 2004..Mutational bias, rather than translational selection appears to account for the majority of the variation detected. The software is available at http://www.dpvweb.net/analysis/codons.php...
- Computational analysis of mouse piRNA sequence and biogenesisDoron Betel
Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
PLoS Comput Biol 3:e222. 2007....
- Memory efficient folding algorithms for circular RNA secondary structuresIvo L Hofacker
Institute for Theoretical Chemistry, University of Vienna Währingerstr 17, A 1090 Vienna, Austria
Bioinformatics 22:1172-6. 2006..This is incompatible, however, with the memory-saving approach of the Vienna RNA Package which builds a linear RNA structure from shorter (internal) structures only...
- Prediction of mRNA polyadenylation sites by support vector machineYiming Cheng
Department of Mathematical Sciences, New Jersey Institute of Technology Newark, NJ 07102, USA
Bioinformatics 22:2320-5. 2006....
- Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcriptsJudith Hirsch
Institut des Sciences du Vegetal, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
Plant Physiol 140:1192-204. 2006..Our results provide new insights into Arabidopsis npcRNA biology and the potential roles of these genes...
- Identification and classification of conserved RNA secondary structures in the human genomeJakob Skou Pedersen
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA
PLoS Comput Biol 2:e33. 2006....
- A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genesJörg Peplies
Ribocon GmbH, D 28359 Bremen, Germany
Syst Appl Microbiol 31:251-7. 2008..Feedback and suggestions from the scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi...
- Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) BeauvBo Wei
National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences CAAS, Beijing, PR China
Funct Integr Genomics 9:499-511. 2009..Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon...
- Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcriptsJeremy R Sanford
Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 19:381-94. 2009..This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts...
- The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomyJ R Cole
Center for Microbial Ecology, 2225A Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
Nucleic Acids Res 31:442-3. 2003..The RDP-II email address for questions or comments is email@example.com...
- MicroRNA identification based on sequence and structure alignmentXiaowo Wang
MOE Key Laboratory of Bioinformatics, Department of Automation, Tsinghua University, Beijing 100084, China
Bioinformatics 21:3610-4. 2005..Therefore, secondary structural features should be more fully exploited in the homologue search for new miRNA genes...
- The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public dataJ R Cole
Center for Microbial Ecology, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824 4320, USA
Nucleic Acids Res 35:D169-72. 2007..In addition, new video tutorials describe how to use RDP features. Details about RDP data and analytical functions can be found at the RDP-II website (http://rdp.cme.msu.edu/)...
- High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis viniferaErica Mica
Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, Milano, Italy
BMC Genomics 10:558. 2009..The recent annotation of the genome of the grapevine (Vitis vinifera L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families...
- A tetracycline-binding RNA aptamerC Berens
Institute of Microbiology and Genetics, Vienna Biocenter Dr. Bohrgasse 9/4, A-1030, Vienna, Austria
Bioorg Med Chem 9:2549-56. 2001..The mode of binding of tetracycline to the cb28 aptamer resembles its interaction with the primary binding site on the small ribosomal subunit...
- Inferring noncoding RNA families and classes by means of genome-scale structure-based clusteringSebastian Will
Bioinformatics Group, Institute of Computer Science, University of Freiburg, Freiburg, Germany
PLoS Comput Biol 3:e65. 2007....
- The impact of target site accessibility on the design of effective siRNAsHakim Tafer
Institute of Theoretical Biochemistry TBI, University of Vienna, Austria
Nat Biotechnol 26:578-83. 2008..Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs...
- Hidden layers of human small RNAsHideya Kawaji
Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
BMC Genomics 9:157. 2008....
- A fast structural multiple alignment method for long RNA sequencesYasuo Tabei
Graduate School of Frontier Science, University of Tokyo, CB04 Kiban tou 5 1 5 Kashiwanoha, Kashiwa, Chiba, 277 8561, Japan
BMC Bioinformatics 9:33. 2008..Faster methods with reasonable accuracies are required for genome-scale analyses...
- The Vienna RNA websuiteAndreas R Gruber
Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
Nucleic Acids Res 36:W70-4. 2008..The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/...
- Conserved RNA secondary structures in viral genomes: a surveyI L Hofacker
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, Vienna, A 1090, Austria
Bioinformatics 20:1495-9. 2004..Here we present results from pilot studies on a variety of viral families performed during bioinformatics computer lab courses in past years...
- Sweating the small stuff: microRNA discovery in plantsBlake C Meyers
Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
Curr Opin Biotechnol 17:139-46. 2006....
- Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1Andreas S Richter
Bioinformatics Group, University of Freiburg, Georges Köhler Allee 106, Freiburg D 79110, Germany
Bioinformatics 26:1-5. 2010..The compact genome size of Prochlorococcus offers an ideal system to search for targets of small RNAs (sRNAs) and to refine existing target prediction algorithms...
- Novel micro-RNAs and intermediates of micro-RNA biogenesis from mossMali Talmor-Neiman
Department of Ornamental Horticulture, Agricultural Research Organization, The Volcani Center, PO Box 6, Bet Dagan 50250, Israel
Plant J 47:25-37. 2006..Our findings suggest that miRNAs are common in mosses and set the stage for the elucidation of their varied biological functions...
- Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomesBenjamin J Blencowe
Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
Genes Dev 23:1379-86. 2009..We also consider how future advances in HTS technology are likely to transform our understanding of integrated cellular networks operating at the RNA level...
- Identification and characterization of new plant microRNAs using EST analysisBao Hong Zhang
The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
Cell Res 15:336-60. 2005..Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized...
- EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic Guigo
Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
Genome Biol 7:S2.1-31. 2006..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
- Sampling the Arabidopsis transcriptome with massively parallel pyrosequencingAndreas P M Weber
Department of Plant Biology, Michigan State University, East Lansing, MI 48824 1312, USA
Plant Physiol 144:32-42. 2007..EST sequence accession numbers in GenBank are EH 795234 through EH 995233 and EL 000001 through EL 341852...
- The beginning of the end for microarrays?Jay Shendure
Nat Methods 5:585-7. 2008
- Inference of miRNA targets using evolutionary conservation and pathway analysisDimos Gaidatzis
Biozentrum, University of Basel, Basel, Switzerland
BMC Bioinformatics 8:69. 2007..In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially...
- MicroRNA target prediction by expression analysis of host genesVincenzo Alessandro Gennarino
Telethon Institute of Genetics and Medicine TIGEM, 80131 Naples, Italy
Genome Res 19:481-90. 2009..Finally, our data further confirm that miRNAs have a significant impact on the mRNA levels of most of their targets...
- RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequencesGiulio Pavesi
Department of Computer Science and Communication D I Co, University of Milan, Via Comelico 39, 20135 Milan, Italy
Nucleic Acids Res 32:3258-69. 2004..We also show how it can be applied to corrupted datasets in which a motif does not appear in all the input sequences, as well as to the discovery of more complex motifs in the non-coding RNA...
- Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNAMayumi Nakano
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
Nucleic Acids Res 34:D731-5. 2006..Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu...
- RNAshapes: an integrated RNA analysis package based on abstract shapesPeter Steffen
Faculty of Technology and, Bielefeld University, 33594 Bielefeld, Germany
Bioinformatics 22:500-3. 2006..Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach...
- jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequencesYoon Seong Jeon
Interdisciplinary Program in Bioinformatics, Seoul National University Shilim dong, Kwanak gu, Seoul, Republic of Korea
Bioinformatics 21:3171-3. 2005....
- Tissue-dependent paired expression of miRNAsSeungil Ro
Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
Nucleic Acids Res 35:5944-53. 2007....
- Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencingXinwei Han
Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
Proc Natl Acad Sci U S A 106:12741-6. 2009..Our transcriptome analysis may serve as a blueprint for gene expression pattern and provide functional clues of previously unknown genes and disease-related genes during early brain development...
- DIANA-mirPath: Integrating human and mouse microRNAs in pathwaysG L Papadopoulos
Institute of Molecular Oncology, Biomedical Sciences Research Center Alexander Fleming, 16602 Varkiza, Greece
Bioinformatics 25:1991-3. 2009..The graphical output of the program provides an overview of the parts of the pathway modulated by microRNAs, facilitating the interpretation and presentation of the analysis results...
- Thermodynamics of RNA-RNA bindingUlrike Mückstein
Institute for Theoretical Chemistry, University of Vienna Währingerstrasse 17, A 1090 Vienna, Austria
Bioinformatics 22:1177-82. 2006..The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization...
- Comparative sequence analysis of tmRNAC Zwieb
Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708 3154, USA
Nucleic Acids Res 27:2063-71. 1999..Described are the conserved and variable features of the tmRNAs from a wide phylogenetic spectrum, the structural properties specific to the bacterial subgroups and preliminary 3-dimensional models from the pseudoknotted regions...
- Regulatory and functional RNAs: computational approachesElena Rivas; Fiscal Year: 2003..Inference of RNA function. (3) RNA structural alignments and homology searches. How to improve RNA similarity searches by taking into account the structure as well as the sequence information. ..
- High Fidelity Transcriptome Sequencing ToolsMICHAEL JOSEPH LODES; Fiscal Year: 2011..has discovered and developed a unique enzyme called PyroScript RT that promises to improve the accuracy of RNA sequence analysis by two orders of magnitude compared to conventional enzymes and greatly reduce the frequency of ..
- MicroRNAs in lobular involution and breast cancerE Aubrey Thompson; Fiscal Year: 2012..To this end we will use next generation small RNA sequence analysis to identify all miRNA species (mature miRNAs, polymorphisms, and isomiRs) that are differentially ..
- MOLECULAR DETERMINANTS OF THE CYTOTOXIC T CELL RESPONSEMaria Salvato; Fiscal Year: 1992..Viral genetic variations will be determined by direct RNA sequence analysis, while such factors as host genetics, age and route of infection will be held constant...
- Comparison of US and European Babesia divergens IsolatesPatricia Holman; Fiscal Year: 2004..The molecular aspects may provide information that will be useful in future efforts to devise diagnostic tests. ..
- Probabilistic methods to identify noncoding RNA genesElena Rivas; Fiscal Year: 2003..elegans and E. coli. ..
- Computational methods to identify noncoding RNA genesElena Rivas; Fiscal Year: 2006..abstract_text> ..
- Computational approaches to noncoding RNAsElena Rivas; Fiscal Year: 2006..How to improve RNA similarity searches by taking into account the structure as well as the sequence information. (5) RNA-based phylogenetic methods. (6) ncRNA families and RNA databases. [unreadable] [unreadable]..
- Discovery of Novel RNA Genes in Genomic DNA SequencesSTEPHEN HOLBROOK; Fiscal Year: 2005....
- Beacon Aptamers for the Detection of Small MoleculesDaniel Morse; Fiscal Year: 2006..Current ADAR assays are difficult and time consuming. An inosine beacon aptamer will greatly simplify studies of ADAR mechanisms, substrate specificity and regulation. [unreadable] [unreadable]..
- RATIONAL DESIGN TOOLS FOR ANTISENSE NUCLEIC ACIDSYe Ding; Fiscal Year: 2007..In the post-genomic era, the availability of the software and the Web server will substantially facilitate applications of antisense nucleic acids in high throughput functional genomics. ..
- Genomic analysis of RNA binding protein target specificityJEREMY ROBERT SANFORD; Fiscal Year: 2010..2) Determine the genomic landscape of cis-acting RNA elements recognized by SR proteins. (3) Functionally validate SR protein cis-acting RNA elements. ..
- GENETIC ANALYSIS OF RNA VIRUS-HOST INTERACTIONJAMES CARRINGTON; Fiscal Year: 2007..Interactions between several viral silencing suppressors and cellular complexes and regulatory RNAs, and the interactions between suppressors and microRNA-controlled developmental pathways, will be examined. ..
- Allosteric RNA-based regulators of gene expressionChristina Smolke; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Rapid Microbial Identification by MALDI-TOF Mass Spectrometry of Ribosomal RNAGeorge Jackson; Fiscal Year: 2007..This project focuses on developing a total system for microbial identification using predictive software, novel molecular techniques, and mass spectral analysis of ribosomal RNA fragments. [unreadable] [unreadable] [unreadable]..
- In vivo Selection of Ribosomal Aptamers for Improved BioremediationGeorge Jackson; Fiscal Year: 2008..Additionally, the developed strains are expected to have considerable commercial value for bioremediation at industrial, government, and military clean-up sites. [unreadable] [unreadable] [unreadable]..
- Evolutionary Modeling/Prediction of ncRNA Genes in FliesIan H Holmes; Fiscal Year: 2010..All our software will be freely available online. ..
- Red Cell Band 4.1 - Developmental Changes in RNA SplicingJohn G Conboy; Fiscal Year: 2010..These studies should also provide insights into disease mechanisms caused by aberrant splicing, ultimately leading to splicing therapeutics to correct such defects. ..
- MOLECULAR STUDIES OF CORONAVIRUS REPLICATIONShinji Makino; Fiscal Year: 2006..Any N domain(s) affecting viral RNA packaging will be investigated. Finally, we will study whether homotypic interaction of N exists in the viral nucleocapsid, and if it does, we will look at whether the PS or M protein triggers this. ..
- Splicing, Folding, and Stretching Nucleic AcidsDANIEL AALBERTS; Fiscal Year: 2003..Calculations are straightforward for this two-state model and preliminary results suggest they compare well with recent stretched DNA experiments. The SFJC is also handy for modeling single-stranded loop sections of RNA. ..
- ACTIVITY AND TRANSPORT OF TOBACCO ETCH VIRUS PROTEINASEJAMES CARRINGTON; Fiscal Year: 2003..Identification of these host mutants will provide the starting point for isolation of genes involved in NIa-interacting reactions and pathways. ..
- Zeiss LSM 510 META Confocal MicroscopeJAMES CARRINGTON; Fiscal Year: 2003....
- SUBCLINICAL CMV INFECTION AFTER MARROW TRANSPLANTATIONWilliam Nichols; Fiscal Year: 2004..This award will support my first step towards obtaining my long-term career goal, which is to be a proficient clinical investigator for infections in the immunocompromised host. ..
- Redox mechanism of cancer prevention by seleniumVADIM GLADYSHEV; Fiscal Year: 2002..These approaches should yield insight into the mechanism of the anticancer effect of selenium and may lead to the identification of human cancers most susceptible to selenium chemoprevention. ..
- A Structural Classification of RNASTEPHEN HOLBROOK; Fiscal Year: 2005..The database will also provide a convenient and logical means for experts and neophytes alike to access and interpret the growing wealth of RNA sequence and structural data. ..
- Searching Genomes for Non-Coding RNAs by Their StructureLiming Cai; Fiscal Year: 2009..Our proposed research will help biologists find RNA molecules of interest in the mass of genome sequence data being generated. ..
- Molecular sensors for real-time metabolite detection and dynamic network controlChristina Smolke; Fiscal Year: 2008..Due to the flexibility of the sensor platform and the ability of these molecules to 'sense' specific concentrations, these sensors will be powerful research tools in a variety of other applications. ..
- AUTOMATED PROTEIN FOLD MODEL GENERATIONTemple Smith; Fiscal Year: 2003..In addition, these libraries and their associated analysis tools will provide valuable data to aid in the experimental design to test predictions about the cellular roles of such proteins. ..
- Temperature Gradient Hybridizer and Real-time Imager for DNA MicroarraysGeorge Jackson; Fiscal Year: 2008..unreadable] [unreadable] [unreadable]..
- Application of genomic approaches to classify retinoblastoma tumorsArupa Ganguly; Fiscal Year: 2008..This will allow us to identify molecular signatures associated with risk of RB recurrence. [unreadable] [unreadable] [unreadable] [unreadable]..
- Red Cell Band 4.1 - Developmental Changes in RNA SplicingJOHN CONBOY; Fiscal Year: 2008..These studies should also provide insights into disease mechanisms caused by aberrant splicing, ultimately leading to splicing therapeutics to correct such defects. ..
- ENHANCING THE INTRACELLULAR FUNCTIONING OF HIV RIBOZYMESJohn Rossi; Fiscal Year: 2001..The results from this program will greatly facilitate the effective use of ribozyme treatment for HIV-1 infection in a gene therapy setting. ..
- COMPUTATIONAL ANALYSIS OF GENOME EXPRESSION DATAMichael Zhang; Fiscal Year: 2002..abstract_text> ..
- ALGORITHMS, THERMODYNAMICS AND STATISTICS FOR RNA FOLDINMichael Zuker; Fiscal Year: 2003..Partition function computations will be extended to allow folding constraints and to compute probabilities of foldings similar to a given one. ..
- Developing Efficient HCV Replication Cell Culture SystemShinji Makino; Fiscal Year: 2003..abstract_text> ..
- Programmed Changes in Alternative Splicing Within the Erythroid TranscriptomeJOHN CONBOY; Fiscal Year: 2007..Ultimately, methods for therapeutic correction of splicing defects, under development in model systems, may allow correction of such defects in erythroid cells as well. [unreadable] [unreadable] [unreadable]..
- GABA Receptor Regulation by Splicing TruncationDavid Burt; Fiscal Year: 2005..These studies may establish a novel and important mechanism of regulation of GABAA receptors responsive to alcohol. ..
- Structure and function of SRP RNAChristian Zwieb; Fiscal Year: 2006..These studies will focus on the specific features of two critical interactions and define their dynamic relationship to SRP function. [unreadable] [unreadable]..
- Workshop on Methods for Macromolecular ModelingTamar Schlick; Fiscal Year: 2004....
- 2006 Thiol-based Redox Regulation and Signaling Gordon Research ConferenceVADIM GLADYSHEV; Fiscal Year: 2006..A diverse mix of established and emerging leaders in the field, and of junior and senior investigators will be included in the program. [unreadable] [unreadable] [unreadable]..
- Methods for characterizing noncoding RNAs in bacteriaBrian Tjaden; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- Alternative Splicing Technologies in Cancer ImagingChristina Smolke; Fiscal Year: 2006..The research design in this phase uses the constructs developed in the previous phase as novel probes for BLI applications and develops their utility for simultaneous detection and treatment strategies. ..
- HEPATITIS DELTA VIRUS RNA EDITINGJohn Casey; Fiscal Year: 2007..unreadable] [unreadable] [unreadable]..
- Support Vector Machine modeling software for improving RNAi efficacy predictionANDREW PEEK; Fiscal Year: 2006..unreadable] [unreadable] [unreadable]..
- Genes Controlling the Renal Handling of PhosphateRalph Meyer; Fiscal Year: 2004..Such intervention may improve the skeletal symptoms of patients with hypophosphatemic bone disease and improve their quality of life. ..
- Mechanisms of DNA PolymerasesTamar Schlick; Fiscal Year: 2007..Such studies have immediate applications to the diagnostics, and eventually treatment via polymerase inhibitors, of human diseases caused by defective repair of DNA, like various cancers and premature aging. ..
- PROBABILISTIC MODELS OF PROTEIN AND RNA STRUCTURESean Eddy; Fiscal Year: 2006..A final aim proposes a method for identifying the mRNA targets of regulatory RNAs (such as the newly discovered micro RNAs) by comparative genome analysis. ..