MicroRNA targets in Drosophila
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* Corresponding authors: Chris Sander sanderc@mskcc.org - Debora S Marks Debbie@maple.bioc.columbia.edu
Genome Biology 2003, 5:R1 doi:10.1186/gb-2003-5-1-r1
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BioMed Central: 38 citations
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Database
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes Andrew E Bruno, Li Li, James L Kalabus, Yuzhuo Pan, Aiming Yu, Zihua Hu BMC Genomics 2012, 13:44 (25 January 2012) |
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Short report
Alzheimer-specific variants in the 3'UTR of Amyloid precursor protein affect microRNA function Charlotte Delay, Frédéric Calon, Paul Mathews, Sébastien S Hébert Molecular Neurodegeneration 2011, 6:70 (7 October 2011) |
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Research article
Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing Daniel Gonzalez-Ibeas, José Blanca, Livia Donaire, Montserrat Saladié, Albert Mascarell-Creus, Ana Cano-Delgado, Jordi Garcia-Mas, Cesar Llave, Miguel A Aranda BMC Genomics 2011, 12:393 (3 August 2011) |
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Research article
Henna Mattila, Martin Schindler, Jarkko Isotalo, Tarja Ikonen, Mauno Vihinen, Hannu Oja, Teuvo LJ Tammela, Tiina Wahlfors, Johanna Schleutker BMC Cancer 2011, 11:327 (2 August 2011) |
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Software
miRTar: an integrated system for identifying miRNA-target interactions in human Justin Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang BMC Bioinformatics 2011, 12:300 (26 July 2011) |
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Research
Coregulation of transcription factors and microRNAs in human transcriptional regulatory network Cho-Yi Chen, Shui-Tein Chen, Chiou-Shann Fuh, Hsueh-Fen Juan, Hsuan-Cheng Huang BMC Bioinformatics 2011, 12(Suppl 1):S41 (15 February 2011) |
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Method
Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie Genome Biology 2010, 11:R90 (27 August 2010) mirSVR is a method for miRNA target prediction that, unusually, takes into account non-canonical binding sequences and non-conserved sites
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Research article
Plant microRNAs and their role in defense against viruses: a bioinformatics approach Álvaro L Pérez-Quintero, Rafik Neme, Andrés Zapata, Camilo López BMC Plant Biology 2010, 10:138 (1 July 2010) |
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Research article
Detecting microRNA activity from gene expression data Stephen F Madden, Susan B Carpenter, Ian B Jeffery, Harry Björkbacka, Katherine A Fitzgerald, Luke A O'Neill, Desmond G Higgins BMC Bioinformatics 2010, 11:257 (18 May 2010) |
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Correspondence
Touring Ensembl: A practical guide to genome browsing Giulietta M Spudich, Xosé M Fernández-Suárez BMC Genomics 2010, 11:295 (11 May 2010) This article is part of a collection on Ensembl update 2010 |
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Research article
Huiqing Liu, Angela R Brannon, Anupama R Reddy, Gabriela Alexe, Michael W Seiler, Alexandra Arreola, Jay H Oza, Ming Yao, David Juan, Louis S Liou, Shridar Ganesan, Arnold J Levine, WK Rathmell, Gyan V Bhanot BMC Systems Biology 2010, 4:51 (27 April 2010) |
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Research article
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori Shiping Liu, Song Gao, Danyu Zhang, Jiyun Yin, Zhonghuai Xiang, Qingyou Xia BMC Genomics 2010, 11:85 (2 February 2010) |
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Research
MTar: a computational microRNA target prediction architecture for human transcriptome Vinod Chandra, Reshmi Girijadevi, Achuthsankar S Nair, Sreenadhan S Pillai, Radhakrishna M Pillai BMC Bioinformatics 2010, 11(Suppl 1):S2 (18 January 2010) |
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Research article
Ying Wang, Vinayak Brahmakshatriya, Huifeng Zhu, Blanca Lupiani, Sanjay M Reddy, Byung-Jun Yoon, Preethi H Gunaratne, Jong Kim, Rui Chen, Junjun Wang, Huaijun Zhou BMC Genomics 2009, 10:512 (5 November 2009) |
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Research article
Blanca M Herrera, Helen E Lockstone, Jennifer M Taylor, Quin F Wills, Pamela J Kaisaki, Amy Barrett, Carme Camps, Christina Fernandez, Jiannis Ragoussis, Dominique Gauguier, Mark I McCarthy, Cecilia M Lindgren BMC Medical Genomics 2009, 2:54 (18 August 2009) Combining global microRNA and mRNA expression data indicates MiR-125a is over-expressed in the liver of hyperglycaemic rats and is a putative modulator of glucose and lipid metabolism in a rat model of type 2 diabetes.
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Research article
Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data Yu-Ping Wang, Kuo-Bin Li BMC Genomics 2009, 10:218 (12 May 2009) |
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Database
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation Manoj Hariharan, Vinod Scaria, Samir K Brahmachari BMC Bioinformatics 2009, 10:108 (16 April 2009) |
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Research article
Jennifer S Guimbellot, Stephen W Erickson, Tapan Mehta, Hui Wen, Grier P Page, Eric J Sorscher, Jeong S Hong BMC Medical Genomics 2009, 2:15 (25 March 2009) |
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Research
HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression Zachary Klase, Rafael Winograd, Jeremiah Davis, Lawrence Carpio, Richard Hildreth, Mohammad Heydarian, Sidney Fu, Timothy McCaffrey, Eti Meiri, Mila Ayash-Rashkovsky, Shlomit Gilad, Zwi Bentwich, Fatah Kashanchi Retrovirology 2009, 6:18 (16 February 2009) |
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Research article
A large-scale survey of genetic copy number variations among Han Chinese residing in Taiwan Chien-Hsing Lin, Ling-Hui Li, Sheng-Feng Ho, Tzu-Po Chuang, Jer-Yuarn Wu, Yuan-Tsong Chen, Cathy SJ Fann BMC Genetics 2008, 9:92 (24 December 2008) |
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Research
HuMiTar: A sequence-based method for prediction of human microRNA targets Jishou Ruan, Hanzhe Chen, Lukasz Kurgan, Ke Chen, Chunsheng Kang, Peiyu Pu Algorithms for Molecular Biology 2008, 3:16 (22 December 2008) |
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Research
MiRTif: a support vector machine-based microRNA target interaction filter Yuchen Yang, Yu-Ping Wang, Kuo-Bin Li BMC Bioinformatics 2008, 9(Suppl 12):S4 (12 December 2008) |
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Research article
Martin Kircher, Christoph Bock, Martina Paulsen BMC Genomics 2008, 9:346 (23 July 2008) |
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Research
A scoring matrix approach to detecting miRNA target sites Simon Moxon, Vincent Moulton, Jan T Kim Algorithms for Molecular Biology 2008, 3:3 (31 March 2008) |
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Research article
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li BMC Bioinformatics 2007, 8:432 (8 November 2007) |
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Methodology article
Gene expression trees in lymphoid development Ivan G Costa, Stefan Roepcke, Alexander Schliep BMC Immunology 2007, 8:25 (9 October 2007) |
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Research
Lawrence S Hon, Zemin Zhang Genome Biology 2007, 8:R166 (14 August 2007) A genome wide analysis of factors affecting repression of mRNAs by microRNAs reveals roles for 3'UTR length, the number of target sites on the mRNA and the distance between pairs of binding sites. |
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Research article
Inference of miRNA targets using evolutionary conservation and pathway analysis Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan BMC Bioinformatics 2007, 8:69 (1 March 2007) |
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Research
Diana O Perkins, Clark D Jeffries, L Fredrik Jarskog, J Michael Thomson, Keith Woods, Martin A Newman, Joel S Parker, Jianping Jin, Scott M Hammond Genome Biology 2007, 8:R27 (27 February 2007) Transcriptional profiling reveals a possible association between schizophrenia and altered miRNA expression |
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Review
Carlo Presutti, Jessica Rosati, Sara Vincenti, Sergio Nasi BMC Neuroscience 2006, 7(Suppl 1):S5 (30 October 2006) |
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Software
Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT Tom Cheung, Yin Kwan, Micah Hamady, Xuedong Liu Genome Biology 2006, 7:R97 (25 October 2006) GENEACT, a new software suite for the detection of evolutionarily conserved transcription factor binding sites or microRNAs from differentially expressed genes from DNA microarray data, is described. |
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Software
miTarget: microRNA target gene prediction using a support vector machine Sung-Kyu Kim, Jin-Wu Nam, Je-Keun Rhee, Wha-Jin Lee, Byoung-Tak Zhang BMC Bioinformatics 2006, 7:411 (18 September 2006) |
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Research article
Computational evidence for hundreds of non-conserved plant microRNAs Morten Lindow, Anders Krogh BMC Genomics 2005, 6:119 (13 September 2005) A computational approach that identifies genomic sequences that are complementary to known mRNA sequences indicates that the number of plant miRNAs has been greatly underestimated and points to the existence of recently evolved miRNAs.
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Software
Craig Burgler, Paul M Macdonald BMC Genomics 2005, 6:88 (8 June 2005) |
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Method
Identification of co-regulated transcripts affecting male body size in Drosophila Cynthia J Coffman, Marta L Wayne, Sergey V Nuzhdin, Laura A Higgins, Lauren M McIntyre Genome Biology 2005, 6:R53 (1 June 2005) Factor analysis is applied to microarray data in order to relate gene networks to complex traits and identifies a factor associated with body size in |
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Research article
Neil R Smalheiser, Vetle I Torvik BMC Bioinformatics 2004, 5:139 (28 September 2004) |
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Opinion
Predicting and validating microRNA targets Eric C Lai Genome Biology 2004, 5:115 (31 August 2004) There has been considerable progress in finding microRNA targets computationally, but assessing success and biological significance requires a move into the 'wet' lab. |
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Research
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets Xiu-Jie Wang, José L Reyes, Nam-Hai Chua, Terry Gaasterland Genome Biology 2004, 5:R65 (31 August 2004) Using bioinformatic methods, 83 novel |