Genome Biology

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Computational identification of Drosophila microRNA genes

Eric C Lai*, Pavel Tomancak, Robert W Williams and Gerald M Rubin

Genome Biology 2003, 4:R42 doi:10.1186/gb-2003-4-7-r42

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BioMed Central: 33 citations

Research article   Open Access Highly Accessed

Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network

Jin Wang, Martin Haubrock, Kun-Ming Cao, Xu Hua, Chen-Yu Zhang, Edgar Wingender, Jie Li BMC Systems Biology 2011, 5:199 (16 December 2011)

Proceedings   Open Access

A framework for automated enrichment of functionally significant inverted repeats in whole genomes

Cyriac Kandoth, Fikret Ercal, Ronald L Frank BMC Bioinformatics 2010, 11(Suppl 6):S20 (7 October 2010)

Research article   Open Access Highly Accessed

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

Mingming Xin, Yu Wang, Yingyin Yao, Chaojie Xie, Huiru Peng, Zhongfu Ni, Qixin Sun BMC Plant Biology 2010, 10:123 (24 June 2010)

Method   Open Access Highly Accessed

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

David Hendrix, Michael Levine, Weiyang Shi Genome Biology 2010, 11:R39 (6 April 2010)

A novel method for prediction of miRs from deep sequencing data. Its utility is demonstrated when applied to Ciona data.

Research article   Open Access Highly Accessed

Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus

Rebecca L Skalsky, Dana L Vanlandingham, Frank Scholle, Stephen Higgs, Bryan R Cullen BMC Genomics 2010, 11:119 (18 February 2010)

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Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development

Guru Jagadeeswaran, Yun Zheng, Niranji Sumathipala, Haobo Jiang, Estela L Arrese, Jose L Soulages, Weixiong Zhang, Ramanjulu Sunkar BMC Genomics 2010, 11:52 (20 January 2010)

Research   Open Access

Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins

Francisco Merchan, Adnane Boualem, Martin Crespi, Florian Frugier Genome Biology 2009, 10:R136 (1 December 2009)

Functional homologous and non-homologous clusters of MIR genes that co-regulate target mRNA transcripts have been identified in plants

Short report   Open Access Highly Accessed

Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features

Shiva Kumar, Faraz A Ansari, Vinod Scaria Virology Journal 2009, 6:129 (20 August 2009)

Research article   Open Access Highly Accessed

In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity

Ate van der Burgt, Mark WJE Fiers, Jan-Peter Nap, Roeland CHJ van Ham BMC Genomics 2009, 10:204 (30 April 2009)

Research   Open Access

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

Sabah Kadri, Veronica Hinman, Panayiotis V Benos BMC Bioinformatics 2009, 10(Suppl 1):S35 (30 January 2009)

Research   Open Access

Finding microRNA regulatory modules in human genome using rule induction

Dang Tran, Kenji Satou, Tu Ho BMC Bioinformatics 2008, 9(Suppl 12):S5 (12 December 2008)

Research   Open Access

Using a kernel density estimation based classifier to predict species-specific microRNA precursors

Darby Chang, Chih-Ching Wang, Jian-Wei Chen BMC Bioinformatics 2008, 9(Suppl 12):S2 (12 December 2008)

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Identification and characteristics of microRNAs from Bombyx mori

Ping-an He, Zuoming Nie, Jianqing Chen, Jian Chen, Zhengbing Lv, Qing Sheng, Songping Zhou, Xiaolian Gao, Lingyin Kong, Xiangfu Wu, Yongfeng Jin, Yaozhou Zhang BMC Genomics 2008, 9:248 (28 May 2008)

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Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi

Edward Mead, Zhijian Tu BMC Genomics 2008, 9:244 (23 May 2008)

Methodology article   Open Access Highly Accessed

A novel representation of RNA secondary structure based on element-contact graphs

Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang BMC Bioinformatics 2008, 9:188 (11 April 2008)

Research   Open Access Highly Accessed

Learning from positive examples when the negative class is undetermined- microRNA gene identification

Malik Yousef, Segun Jung, Louise C Showe, Michael K Showe Algorithms for Molecular Biology 2008, 3:2 (28 January 2008)

Software   Open Access Highly Accessed

miRNAminer: A tool for homologous microRNA gene search

Shay Artzi, Adam Kiezun, Noam Shomron BMC Bioinformatics 2008, 9:39 (23 January 2008)

Research article   Open Access Highly Accessed

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)

Software   Open Access Highly Accessed

MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans

Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li, Shu-Hong Zhao BMC Bioinformatics 2007, 8:341 (17 September 2007)

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Cloning and characterization of microRNAs from wheat (Triticum aestivum L.)

Yingyin Yao, Ganggang Guo, Zhongfu Ni, Ramanjulu Sunkar, Jinkun Du, Jian-Kang Zhu, Qixin Sun Genome Biology 2007, 8:R96 (1 June 2007)

A small RNA library was used to identify 58 miRNAs from 43 miRNA families from wheat (Triticum aestivum L.), and 46 potential targets were predicted.

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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)

Research   Open Access

Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human

Zhaolei Zhang, Andy Pang, Mark Gerstein BMC Evolutionary Biology 2007, 7(Suppl 1):S14 (8 February 2007)

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SAGE detects microRNA precursors

Xijin Ge, Qingfa Wu, San Wang BMC Genomics 2006, 7:285 (7 November 2006)

Software   Open Access Highly Accessed

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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Bioinformatic discovery of microRNA precursors from human ESTs and introns

Sung-Chou Li, Chao-Yu Pan, Wen-chang Lin BMC Genomics 2006, 7:164 (3 July 2006)

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The expansion of the metazoan microRNA repertoire

Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L Hofacker, Peter F Stadler, BMC Genomics 2006, 7:25 (15 February 2006)

The first comprehensive analysis of miRNA phylogeny finds new homologs of known miRNAs and identifies episodes of rapid miRNA repertoire expansion that correspond to periods of developmental innovation and branching.

Methodology article   Open Access Highly Accessed

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine

Chenghai Xue, Fei Li, Tao He, Guo-Ping Liu, Yanda Li, Xuegong Zhang BMC Bioinformatics 2005, 6:310 (29 December 2005)

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Identification of clustered microRNAs using an ab initio prediction method

Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan BMC Bioinformatics 2005, 6:267 (7 November 2005)

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Comparative promoter region analysis powered by CORG

Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F Arndt, Peter F Stadler, Martin Vingron BMC Genomics 2005, 6:24 (21 February 2005)

Research   Open Access Highly Accessed

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 Arabidopsis miRNAs have been predicted. Putative target mRNAs have been identified for most of the candidate genes.

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Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation

Lorenzo F Sempere, Sarah Freemantle, Ian Pitha-Rowe, Eric Moss, Ethan Dmitrovsky, Victor Ambros Genome Biology 2004, 5:R13 (16 February 2004)

Northern blot analysis of 119 previously reported microRNAs in adult organs from mouse and human identified a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons, implicating these microRNAs in mammalian neuronal development or function

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MicroRNA targets in Drosophila

Anton J Enright, Bino John, Ulrike Gaul, Thomas Tuschl, Chris Sander, Debora S Marks Genome Biology 2003, 5:R1 (12 December 2003)

A computational method for whole-genome prediction of microRNA target genes is presented. Application of this method to the Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known microRNAs.

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Towards a complete description of the microRNA complement of animal genomes

Julius Brennecke, Stephen M Cohen Genome Biology 2003, 4:228 (21 August 2003)

Recent cloning and computational studies have sought to catalog all the microRNA genes encoded in animal genomes. Here, we highlight recent advances in identifying Caenorhabditis elegans and Drosophila melanogaster microRNAs.