BMC Bioinformatics

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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 and Mihaela Zavolan*

BMC Bioinformatics 2005, 6:267 doi:10.1186/1471-2105-6-267

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Proceedings   Open Access

Discovery and characterization of medaka miRNA genes by next generation sequencing platform

Sung-Chou Li, Wen-Ching Chan, Meng-Ru Ho, Kuo-Wang Tsai, Ling-Yueh Hu, Chun-Hung Lai, Chun-Nan Hsu, Pung-Pung Hwang, Wen-chang Lin BMC Genomics 2010, 11(Suppl 4):S8 (2 December 2010)

Research   Open Access

Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm

Chih-Hung Hsieh, Darby Chang, Cheng-Hao Hsueh, Chi-Yeh Wu, Yen-Jen Oyang BMC Bioinformatics 2010, 11(Suppl 1):S52 (18 January 2010)

Research article   Open Access Highly Accessed

Alu-directed transcriptional regulation of some novel miRNAs

Tong J Gu, Xiang Yi, Xi W Zhao, Yi Zhao, James Q Yin BMC Genomics 2009, 10:563 (30 November 2009)

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

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing

Sanne Nygaard, Anders Jacobsen, Morten Lindow, Jens Eriksen, Eva Balslev, Henrik Flyger, Niels Tolstrup, Søren Møller, Anders Krogh, Thomas Litman BMC Medical Genomics 2009, 2:35 (9 June 2009)

Analysis of breast cancer and adjacent tissue using deep-sequencing technology and a novel computational pipeline identifies 5 new microRNAs, and indicates that sequence end variability may be used as a discriminatory feature to aid future microRNA discovery.

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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)

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

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)

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)

Research article   Open Access

Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

Guénola Ricard, Rob M de Graaf, Bas E Dutilh, I Duarte, Theo A van Alen, Angela HAM van Hoek, Brigitte Boxma, Georg WM van der Staay, Seung Moon-van der Staay, Wei-Jen Chang, Laura F Landweber, Johannes HP Hackstein, Martijn A Huynen BMC Genomics 2008, 9:587 (5 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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MicroRNA-encoding long non-coding RNAs

Shunmin He, Hua Su, Changning Liu, Geir Skogerbø, Housheng He, Dandan He, Xiaopeng Zhu, Tao Liu, Yi Zhao, Runsheng Chen BMC Genomics 2008, 9:236 (21 May 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)

Methodology article   Open Access Highly Accessed

Ab initio identification of human microRNAs based on structure motifs

Markus Brameier, Carsten Wiuf BMC Bioinformatics 2007, 8:478 (18 December 2007)

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)

Research article   Open Access Highly Accessed

SAGE detects microRNA precursors

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

Review   Open Access Highly Accessed

Host-virus interaction: a new role for microRNAs

Vinod Scaria, Manoj Hariharan, Souvik Maiti, Beena Pillai, Samir K Brahmachari Retrovirology 2006, 3:68 (11 October 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)

Research article   Open Access Highly Accessed

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.