BMC Bioinformatics

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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 and Xuegong Zhang*

BMC Bioinformatics 2005, 6:310 doi:10.1186/1471-2105-6-310

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MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features

Jiandong Ding, Shuigeng Zhou, Jihong Guan BMC Bioinformatics 2010, 11(Suppl 11):S11 (14 December 2010)

Research article   Open Access

In-silico prediction of blood-secretory human proteins using a ranking algorithm

Qi Liu, Juan Cui, Qiang Yang, Ying Xu BMC Bioinformatics 2010, 11:250 (14 May 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   Open Access

Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

Sumeet Agarwal, Candida Vaz, Alok Bhattacharya, Ashwin Srinivasan BMC Bioinformatics 2010, 11(Suppl 1):S29 (18 January 2010)

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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)

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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)

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Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis

Roberto T Arrial, Roberto C Togawa, Marcelo Brigido BMC Bioinformatics 2009, 10:239 (4 August 2009)

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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

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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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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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)

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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)

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New miRNAs cloned from neuroblastoma

Elena A Afanasyeva, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting, Frank Westermann BMC Genomics 2008, 9:52 (29 January 2008)

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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)

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Identification of novel homologous microRNA genes in the rhesus macaque genome

Junming Yue, Yi Sheng, Kyle E Orwig BMC Genomics 2008, 9:8 (10 January 2008)

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Ab initio identification of human microRNAs based on structure motifs

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

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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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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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miRAS: a data processing system for miRNA expression profiling study

Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yongjing Xia, Yiqing Wu, Xiangjun Liu BMC Bioinformatics 2007, 8:285 (4 August 2007)

Research article   Open Access

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

Andrew S Peek BMC Bioinformatics 2007, 8:182 (6 June 2007)

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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)