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For: Mathelier A, Carbone A. MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. ACTA ACUST UNITED AC 2010;26:2226-34. [PMID: 20591903 DOI: 10.1093/bioinformatics/btq329] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
51
Backes C, Meder B, Hart M, Ludwig N, Leidinger P, Vogel B, Galata V, Roth P, Menegatti J, Grässer F, Ruprecht K, Kahraman M, Grossmann T, Haas J, Meese E, Keller A. Prioritizing and selecting likely novel miRNAs from NGS data. Nucleic Acids Res 2015;44:e53. [PMID: 26635395 PMCID: PMC4824081 DOI: 10.1093/nar/gkv1335] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022]  Open
52
Quek C, Jung CH, Bellingham SA, Lonie A, Hill AF. iSRAP - a one-touch research tool for rapid profiling of small RNA-seq data. J Extracell Vesicles 2015;4:29454. [PMID: 26561006 PMCID: PMC4641893 DOI: 10.3402/jev.v4.29454] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 12/23/2022]  Open
53
Evers M, Huttner M, Dueck A, Meister G, Engelmann JC. miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. BMC Bioinformatics 2015;16:370. [PMID: 26542525 PMCID: PMC4635600 DOI: 10.1186/s12859-015-0798-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/22/2015] [Indexed: 12/21/2022]  Open
54
Ku YS, Wong JWH, Mui Z, Liu X, Hui JHL, Chan TF, Lam HM. Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods. Int J Mol Sci 2015;16:24532-54. [PMID: 26501263 PMCID: PMC4632763 DOI: 10.3390/ijms161024532] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/31/2022]  Open
55
Nandety RS, Sharif A, Kamita SG, Ramasamy A, Falk BW. Identification of Novel and Conserved microRNAs in Homalodisca vitripennis, the Glassy-Winged Sharpshooter by Expression Profiling. PLoS One 2015;10:e0139771. [PMID: 26440407 PMCID: PMC4595010 DOI: 10.1371/journal.pone.0139771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/17/2015] [Indexed: 11/21/2022]  Open
56
Qin Q, Wang J, Dai J, Wang Y, Liu Y, Liu S. Induced All-Female Autotriploidy in the Allotetraploids of Carassius auratus red var. (♀) × Megalobrama amblycephala (♂). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2015;17:1-7. [PMID: 26242753 DOI: 10.1007/s10126-014-9593-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 07/15/2014] [Indexed: 05/27/2023]
57
Xue B. Improving MiRNA prediction accuracy by deep learning strategies. PROCEEDINGS OF THE 6TH ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND HEALTH INFORMATICS 2015. [DOI: 10.1145/2808719.2811417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
58
Peace RJ, Biggar KK, Storey KB, Green JR. A framework for improving microRNA prediction in non-human genomes. Nucleic Acids Res 2015;43:e138. [PMID: 26163062 PMCID: PMC4787757 DOI: 10.1093/nar/gkv698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 06/28/2015] [Indexed: 11/12/2022]  Open
59
Verdelli C, Forno I, Vaira V, Corbetta S. Epigenetic alterations in human parathyroid tumors. Endocrine 2015;49:324-32. [PMID: 25722013 DOI: 10.1007/s12020-015-0555-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/13/2015] [Indexed: 12/14/2022]
60
Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF. Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics 2015;16:179. [PMID: 26022464 PMCID: PMC4448272 DOI: 10.1186/s12859-015-0594-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 04/23/2015] [Indexed: 12/13/2022]  Open
61
Zhao F, Wang Z, Lang H, Liu X, Zhang D, Wang X, Zhang T, Wang R, Shi P, Pang X. Dynamic Expression of Novel MiRNA Candidates and MiRNA-34 Family Members in Early- to Mid-Gestational Fetal Keratinocytes Contributes to Scarless Wound Healing by Targeting the TGF-β Pathway. PLoS One 2015;10:e0126087. [PMID: 25978377 PMCID: PMC4433274 DOI: 10.1371/journal.pone.0126087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/30/2015] [Indexed: 12/21/2022]  Open
62
Karathanasis N, Tsamardinos I, Poirazi P. MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology. PLoS One 2015;10:e0126151. [PMID: 25961860 PMCID: PMC4427487 DOI: 10.1371/journal.pone.0126151] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/29/2015] [Indexed: 12/26/2022]  Open
63
Tran VDT, Tempel S, Zerath B, Zehraoui F, Tahi F. miRBoost: boosting support vector machines for microRNA precursor classification. RNA (NEW YORK, N.Y.) 2015;21:775-85. [PMID: 25795417 PMCID: PMC4408786 DOI: 10.1261/rna.043612.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 12/20/2014] [Indexed: 06/04/2023]
64
Kang W, Friedländer MR. Computational Prediction of miRNA Genes from Small RNA Sequencing Data. Front Bioeng Biotechnol 2015;3:7. [PMID: 25674563 PMCID: PMC4306309 DOI: 10.3389/fbioe.2015.00007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/07/2015] [Indexed: 01/19/2023]  Open
65
Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I. Prediction of miRNA targets. Methods Mol Biol 2015;1269:207-29. [PMID: 25577381 DOI: 10.1007/978-1-4939-2291-8_13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
66
Hattori H, Janky R, Nietfeld W, Aerts S, Madan Babu M, Venkitaraman AR. p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. Cell Cycle 2014;13:2572-86. [PMID: 25486198 PMCID: PMC4601526 DOI: 10.4161/15384101.2015.942209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
67
Etemadi M, Gutjahr C, Couzigou JM, Zouine M, Lauressergues D, Timmers A, Audran C, Bouzayen M, Bécard G, Combier JP. Auxin perception is required for arbuscule development in arbuscular mycorrhizal symbiosis. PLANT PHYSIOLOGY 2014;166:281-92. [PMID: 25096975 PMCID: PMC4149713 DOI: 10.1104/pp.114.246595] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/04/2014] [Indexed: 05/02/2023]
68
Rogato A, Richard H, Sarazin A, Voss B, Cheminant Navarro S, Champeimont R, Navarro L, Carbone A, Hess WR, Falciatore A. The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics 2014;15:698. [PMID: 25142710 PMCID: PMC4247016 DOI: 10.1186/1471-2164-15-698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/30/2014] [Indexed: 11/10/2022]  Open
69
Omer A, Singh P, Yadav NK, Singh RK. microRNAs: role in leukemia and their computational perspective. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014;6:65-78. [PMID: 25132152 DOI: 10.1002/wrna.1256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 06/19/2014] [Accepted: 06/26/2014] [Indexed: 12/22/2022]
70
Lei J, Sun Y. miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data. ACTA ACUST UNITED AC 2014;30:2837-9. [PMID: 24930140 DOI: 10.1093/bioinformatics/btu380] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
71
Sadeghi B, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A. BosFinder: a novell pre-microRNA gene prediction algorithm inBos taurus. Anim Genet 2014;45:479-84. [DOI: 10.1111/age.12170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2014] [Indexed: 01/27/2023]
72
Lopes IDON, Schliep A, de Carvalho ACPDLF. The discriminant power of RNA features for pre-miRNA recognition. BMC Bioinformatics 2014;15:124. [PMID: 24884650 PMCID: PMC4046174 DOI: 10.1186/1471-2105-15-124] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 04/08/2014] [Indexed: 12/26/2022]  Open
73
Zhang R, Murat F, Pont C, Langin T, Salse J. Paleo-evolutionary plasticity of plant disease resistance genes. BMC Genomics 2014;15:187. [PMID: 24617999 PMCID: PMC4234491 DOI: 10.1186/1471-2164-15-187] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 02/25/2014] [Indexed: 01/28/2023]  Open
74
Jin W, Ibeagha-Awemu EM, Liang G, Beaudoin F, Zhao X, Guan LL. Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics 2014. [PMID: 24606609 DOI: 10.1186/1471‐2164‐15‐181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
75
Jin W, Ibeagha-Awemu EM, Liang G, Beaudoin F, Zhao X, Guan LL. Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics 2014;15:181. [PMID: 24606609 PMCID: PMC4029070 DOI: 10.1186/1471-2164-15-181] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 02/25/2014] [Indexed: 01/23/2023]  Open
76
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L. eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing. BMC Genomics 2014;15:176. [PMID: 24593312 PMCID: PMC4029068 DOI: 10.1186/1471-2164-15-176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 02/26/2014] [Indexed: 01/19/2023]  Open
77
Chaturvedi A, Raeymaekers JAM, Volckaert FAM. Computational identification of miRNAs, their targets and functions in three-spined stickleback (Gasterosteus aculeatus). Mol Ecol Resour 2014;14:768-77. [DOI: 10.1111/1755-0998.12223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/27/2013] [Accepted: 01/03/2014] [Indexed: 12/12/2022]
78
Mehta JP. Sequencing small RNA: introduction and data analysis fundamentals. Methods Mol Biol 2014;1182:93-103. [PMID: 25055904 DOI: 10.1007/978-1-4939-1062-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
79
Billoud B, Nehr Z, Le Bail A, Charrier B. Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus. Nucleic Acids Res 2014;42:417-29. [PMID: 24078085 PMCID: PMC3874173 DOI: 10.1093/nar/gkt856] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 08/30/2013] [Accepted: 09/03/2013] [Indexed: 12/16/2022]  Open
80
Wei L, Liao M, Gao Y, Ji R, He Z, Zou Q. Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:192-201. [PMID: 26355518 DOI: 10.1109/tcbb.2013.146] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
81
Ballén-Taborda C, Plata G, Ayling S, Rodríguez-Zapata F, Becerra Lopez-Lavalle LA, Duitama J, Tohme J. Identification of Cassava MicroRNAs under Abiotic Stress. Int J Genomics 2013;2013:857986. [PMID: 24328029 PMCID: PMC3845235 DOI: 10.1155/2013/857986] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/11/2013] [Indexed: 11/18/2022]  Open
82
Leclercq M, Diallo AB, Blanchette M. Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res 2013;41:7200-11. [PMID: 23748953 PMCID: PMC3753617 DOI: 10.1093/nar/gkt466] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/30/2013] [Accepted: 05/05/2013] [Indexed: 12/19/2022]  Open
83
Zhong L, Wang JTL, Wen D, Aris V, Soteropoulos P, Shapiro BA. Effective classification of microRNA precursors using feature mining and AdaBoost algorithms. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013;17:486-93. [PMID: 23808606 DOI: 10.1089/omi.2013.0011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
84
Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q. mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing. RNA Biol 2013;10:1087-92. [PMID: 23778453 DOI: 10.4161/rna.25193] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
85
Mathelier A, Carbone A. Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Res 2013;41:4392-408. [PMID: 23444140 PMCID: PMC3632110 DOI: 10.1093/nar/gkt112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/08/2013] [Accepted: 02/03/2013] [Indexed: 02/06/2023]  Open
86
Kleftogiannis D, Korfiati A, Theofilatos K, Likothanassis S, Tsakalidis A, Mavroudi S. Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role. J Biomed Inform 2013;46:563-73. [PMID: 23501016 DOI: 10.1016/j.jbi.2013.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 01/08/2013] [Accepted: 02/12/2013] [Indexed: 12/19/2022]
87
Uva P, Da Sacco L, Del Cornò M, Baldassarre A, Sestili P, Orsini M, Palma A, Gessani S, Masotti A. Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters. RNA (NEW YORK, N.Y.) 2013;19:365-79. [PMID: 23329697 PMCID: PMC3677247 DOI: 10.1261/rna.035394.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
88
Shi Z, Montgomery TA, Qi Y, Ruvkun G. High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes. Genome Res 2013;23:497-508. [PMID: 23363624 PMCID: PMC3589538 DOI: 10.1101/gr.149112.112] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
89
Rossi S, Calin GA. Bioinformatics, non-coding RNAs and its possible application in personalized medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013;774:21-37. [PMID: 23377966 DOI: 10.1007/978-94-007-5590-1_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
90
An J, Lai J, Lehman ML, Nelson CC. miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res 2012;41:727-37. [PMID: 23221645 PMCID: PMC3553977 DOI: 10.1093/nar/gks1187] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
91
Cheng WC, Chung IF, Huang TS, Chang ST, Sun HJ, Tsai CF, Liang ML, Wong TT, Wang HW. YM500: a small RNA sequencing (smRNA-seq) database for microRNA research. Nucleic Acids Res 2012. [PMID: 23203880 PMCID: PMC3531161 DOI: 10.1093/nar/gks1238] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
92
miR-BAG: bagging based identification of microRNA precursors. PLoS One 2012;7:e45782. [PMID: 23049860 PMCID: PMC3458082 DOI: 10.1371/journal.pone.0045782] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 08/23/2012] [Indexed: 12/21/2022]  Open
93
Washietl S, Will S, Hendrix DA, Goff LA, Rinn JL, Berger B, Kellis M. Computational analysis of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012;3:759-78. [PMID: 22991327 DOI: 10.1002/wrna.1134] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
94
Krzyzanowski PM, Muro EM, Andrade-Navarro MA. Computational approaches to discovering noncoding RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012;3:567-79. [PMID: 22555938 DOI: 10.1002/wrna.1121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
95
Meng F, Hackenberg M, Li Z, Yan J, Chen T. Discovery of novel microRNAs in rat kidney using next generation sequencing and microarray validation. PLoS One 2012;7:e34394. [PMID: 22470567 PMCID: PMC3314633 DOI: 10.1371/journal.pone.0034394] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/27/2012] [Indexed: 01/12/2023]  Open
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Tempel S, Tahi F. A fast ab-initio method for predicting miRNA precursors in genomes. Nucleic Acids Res 2012;40:e80. [PMID: 22362754 PMCID: PMC3367186 DOI: 10.1093/nar/gks146] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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Xie F, Xiao P, Chen D, Xu L, Zhang B. miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. PLANT MOLECULAR BIOLOGY 2012;80:75-84. [PMID: 22290409 DOI: 10.1007/s11103-012-9885-2] [Citation(s) in RCA: 1010] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/12/2012] [Indexed: 05/19/2023]
98
Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B. Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res 2012;40:4298-305. [PMID: 22287634 PMCID: PMC3378883 DOI: 10.1093/nar/gks043] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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Mackowiak SD. Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2. ACTA ACUST UNITED AC 2011;Chapter 12:12.10.1-12.10.15. [DOI: 10.1002/0471250953.bi1210s36] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 2011;40:37-52. [PMID: 21911355 PMCID: PMC3245920 DOI: 10.1093/nar/gkr688] [Citation(s) in RCA: 2207] [Impact Index Per Article: 157.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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