Literature DB >> 12007398

Computational genomics of noncoding RNA genes.

Sean R Eddy1.   

Abstract

The number of known noncoding RNA genes is expanding rapidly. Computational analysis of genome sequences, which has been revolutionary for protein gene analysis, should also be able to address questions of the number and diversity of noncoding RNA genes. However, noncoding RNAs present computational genomics with a new set of challenges.

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Year:  2002        PMID： 12007398     DOI： 10.1016/s0092-8674(02)00727-4

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  75 in total

1.  Dendritic BC1 RNA: functional role in regulation of translation initiation.

Authors:  Huidong Wang; Anna Iacoangeli; Susanna Popp; Ilham A Muslimov; Hiroaki Imataka; Nahum Sonenberg; Ivan B Lomakin; Henri Tiedge
Journal:  J Neurosci       Date:  2002-12-01       Impact factor: 6.167

2.  Identification and characterization of multi-species conserved sequences.

Authors:  Elliott H Margulies; Mathieu Blanchette; David Haussler; Eric D Green
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

3.  Rfam: an RNA family database.

Authors:  Sam Griffiths-Jones; Alex Bateman; Mhairi Marshall; Ajay Khanna; Sean R Eddy
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Over 20% of human transcripts might form sense-antisense pairs.

Authors:  Jianjun Chen; Miao Sun; W James Kent; Xiaoqiu Huang; Hanqing Xie; Wenquan Wang; Guolin Zhou; Run Zhang Shi; Janet D Rowley
Journal:  Nucleic Acids Res       Date:  2004-09-08       Impact factor: 16.971

5.  Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula.

Authors:  Anna Campalans; Adam Kondorosi; Martin Crespi
Journal:  Plant Cell       Date:  2004-03-22       Impact factor: 11.277

6.  Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency.

Authors:  Peter Clote; Fabrizio Ferré; Evangelos Kranakis; Danny Krizanc
Journal:  RNA       Date:  2005-05       Impact factor: 4.942

Review 7.  Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum.

Authors:  Andrea Hinas; Fredrik Söderbom
Journal:  Curr Genet       Date:  2007-03       Impact factor: 3.886

8.  The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator.

Authors:  Jianchi Feng; Chunming Bi; Brian S Clark; Rina Mady; Palak Shah; Jhumku D Kohtz
Journal:  Genes Dev       Date:  2006-05-16       Impact factor: 11.361

9.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Authors:  Alexander Stark; Michael F Lin; Pouya Kheradpour; Jakob S Pedersen; Leopold Parts; Joseph W Carlson; Madeline A Crosby; Matthew D Rasmussen; Sushmita Roy; Ameya N Deoras; J Graham Ruby; Julius Brennecke; Emily Hodges; Angie S Hinrichs; Anat Caspi; Benedict Paten; Seung-Won Park; Mira V Han; Morgan L Maeder; Benjamin J Polansky; Bryanne E Robson; Stein Aerts; Jacques van Helden; Bassem Hassan; Donald G Gilbert; Deborah A Eastman; Michael Rice; Michael Weir; Matthew W Hahn; Yongkyu Park; Colin N Dewey; Lior Pachter; W James Kent; David Haussler; Eric C Lai; David P Bartel; Gregory J Hannon; Thomas C Kaufman; Michael B Eisen; Andrew G Clark; Douglas Smith; Susan E Celniker; William M Gelbart; Manolis Kellis
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

10.  The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

Authors:  Helena Brentani; Otávia L Caballero; Anamaria A Camargo; Aline M da Silva; Wilson Araújo da Silva; Emmanuel Dias Neto; Marco Grivet; Arthur Gruber; Pedro Edson Moreira Guimaraes; Winston Hide; Christian Iseli; C Victor Jongeneel; Janet Kelso; Maria Aparecida Nagai; Elida Paula Benquique Ojopi; Elisson C Osorio; Eduardo M R Reis; Gregory J Riggins; Andrew John George Simpson; Sandro de Souza; Brian J Stevenson; Robert L Strausberg; Eloiza H Tajara; Sergio Verjovski-Almeida; Marcio Luis Acencio; Mário Henrique Bengtson; Fabiana Bettoni; Walter F Bodmer; Marcelo R S Briones; Luiz Paulo Camargo; Webster Cavenee; Janete M Cerutti; Luis Eduardo Coelho Andrade; Paulo César Costa dos Santos; Maria Cristina Ramos Costa; Israel Tojal da Silva; Marcos Roberto H Estécio; Karine Sa Ferreira; Frank B Furnari; Milton Faria; Pedro A F Galante; Gustavo S Guimaraes; Adriano Jesus Holanda; Edna Teruko Kimura; Maarten R Leerkes; Xin Lu; Rui M B Maciel; Elizabeth A L Martins; Katlin Brauer Massirer; Analy S A Melo; Carlos Alberto Mestriner; Elisabete Cristina Miracca; Leandro Lorenco Miranda; Francisco G Nobrega; Paulo S Oliveira; Apua C M Paquola; José Rodrigo C Pandolfi; Maria Ines de Moura Campos Pardini; Fabio Passetti; John Quackenbush; Beatriz Schnabel; Mari Cleide Sogayar; Jorge E Souza; Sandro R Valentini; Andre C Zaiats; Elisabete Jorge Amaral; Liliane A T Arnaldi; Amelia Goes de Araújo; Simone Aparecida de Bessa; David C Bicknell; Maria Eugenia Ribeiro de Camaro; Dirce Maria Carraro; Helaine Carrer; Alex F Carvalho; Christian Colin; Fernando Costa; Cyntia Curcio; Ismael Dale Cotrim Guerreiro da Silva; Neusa Pereira da Silva; Márcia Dellamano; Hamza El-Dorry; Enilza Maria Espreafico; Ari José Scattone Ferreira; Cristiane Ayres Ferreira; Maria Angela H Z Fortes; Angelita Habr Gama; Daniel Giannella-Neto; Maria Lúcia C C Giannella; Ricardo R Giorgi; Gustavo Henrique Goldman; Maria Helena S Goldman; Christine Hackel; Paulo Lee Ho; Elza Myiuki Kimura; Luiz Paulo Kowalski; Jose E Krieger; Luciana C C Leite; Ademar Lopes; Ana Mercedes S C Luna; Alan Mackay; Suely Kazue Nagahashi Mari; Adriana Aparecida Marques; Waleska K Martins; André Montagnini; Mario Mourão Neto; Ana Lucia T O Nascimento; A Munro Neville; Marina P Nobrega; Mike J O'Hare; Audrey Yumi Otsuka; Anna Izabel Ruas de Melo; Maria Luisa Paco-Larson; Gonçalo Guimarães Pereira; Neusa Pereira da Silva; Joao Bosco Pesquero; Juliana Gilbert Pessoa; Paula Rahal; Claudia Aparecida Rainho; Vanderlei Rodrigues; Silvia Regina Rogatto; Camila Malta Romano; Janaina Gusmao Romeiro; Benedito Mauro Rossi; Monica Rusticci; Renata Guerra de Sá; Simone Cristina Sant' Anna; Miriam L Sarmazo; Teresa Cristina de Lima E Silva; Fernando Augusto Soares; Maria de Fátima Sonati; Josane de Freitas Sousa; Diana Queiroz; Valéria Valente; André Luiz Vettore; Fabiola Elizabeth Villanova; Marco Antonio Zago; Heloisa Zalcberg
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-30       Impact factor: 11.205
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