BMC Genomics

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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* and The Students of Bioinformatics Computer Labs 2004 and 2005

BMC Genomics 2006, 7:25 doi:10.1186/1471-2164-7-25

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Research   Open Access

In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

Domenico Catalano, Domenico Pignone, Gabriella Sonnante, Mariella M Finetti-Sialer BMC Bioinformatics 2012, 13(Suppl 4):S12 (28 March 2012)

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Overexpression of microRNA-206 in the skeletal muscle from myotonic dystrophy type 1 patients

Stefano Gambardella, Fabrizio Rinaldi, Saverio M Lepore, Antonella Viola, Emanuele Loro, Corrado Angelini, Lodovica Vergani, Giuseppe Novelli, Annalisa Botta Journal of Translational Medicine 2010, 8:48 (20 May 2010)

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Genome-wide comparative analysis of microRNAs in three non-human primates

Markus Brameier BMC Research Notes 2010, 3:64 (9 March 2010)

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Identification and characterization of novel amphioxus microRNAs by Solexa sequencing

Xi Chen, Qibin Li, Jin Wang, Xing Guo, Xiangrui Jiang, Zhiji Ren, Chunyue Weng, Guoxun Sun, Xiuqiang Wang, Yaping Liu, Lijia Ma, Jun-Yuan Chen, Jun Wang, Ke Zen, Junfeng Zhang, Chen-Yu Zhang Genome Biology 2009, 10:R78 (17 July 2009)

An analysis of amphioxus miRNAs suggests an expansion of miRNAs played a key role in the evolution of chordates to vertebrates

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Clustered microRNAs' coordination in regulating protein-protein interaction network

Xiongying Yuan, Changning Liu, Pengcheng Yang, Shunmin He, Qi Liao, Shuli Kang, Yi Zhao BMC Systems Biology 2009, 3:65 (26 June 2009)

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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)

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Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust

Yuanyuan Wei, Shuang Chen, Pengcheng Yang, Zongyuan Ma, Le Kang Genome Biology 2009, 10:R6 (16 January 2009)

High-throughput sequencing of the small RNA transcriptome of locust reveals differences in post-transcriptional regulation between solitary and swarming phases and provides insights into the evolution of insect small RNAs.

Research   Open Access

Filtering of false positive microRNA candidates by a clustering-based approach

Wing-Sze Leung, Marie CM Lin, David W Cheung, SM Yiu BMC Bioinformatics 2008, 9(Suppl 12):S3 (12 December 2008)

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Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region

Martin Kircher, Christoph Bock, Martina Paulsen BMC Genomics 2008, 9:346 (23 July 2008)

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The evolution of core proteins involved in microRNA biogenesis

Dennis Murphy, Barry Dancis, James R Brown BMC Evolutionary Biology 2008, 8:92 (25 March 2008)

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miRNAminer: A tool for homologous microRNA gene search

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

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Progressive multiple sequence alignments from triplets

Matthias Kruspe, Peter F Stadler BMC Bioinformatics 2007, 8:254 (15 July 2007)

Progressive multiple sequence alignments using exact dynamic programming to achieve three-way alignment avoids the gap errors that are inevitable with pairwise alignments.

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Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution

Isam Fattash, Björn Voß, Ralf Reski, Wolfgang R Hess, Wolfgang Frank BMC Plant Biology 2007, 7:13 (14 March 2007)

The miRNA population in moss is surprisingly diverse and includes miRNAs with differential expression in protonema and gametophore tissue as well as many miRNAs involved in cell wall biosynthesis and defense.

Methodology article   Open Access

A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs

Yong Huang, Xun Gu BMC Genomics 2007, 8:66 (6 March 2007)