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bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila

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The BRCA1/2-directed miRNA signature predicts a good prognosis in ovarian cancer patients with wild-type BRCA1/2

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Large-Scale Integration of MicroRNA and Gene Expression Data for Identification of Enriched MicroRNA–mRNA Associations in Biological Systems

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The DNA-Damage Response to γ-Radiation Is Affected by miR-27a in A549 Cells

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Ornithine decarboxylase mRNA is stabilized in an mTORC1-dependent manner in Ras-transformed cells

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Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data

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A 3′UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1

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MicroRNA Screening and the Quest for Biologically Relevant Targets

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MicroRNA-494, Upregulated by Tumor Necrosis Factor-α, Desensitizes Insulin Effect in C2C12 Muscle Cells

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miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis

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Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

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A compilation of Web-based research tools for miRNA analysis

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Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases

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MicroRNA‐142 controls thymocyte proliferation

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Overexpression of Chromosome 21 miRNAs May Affect Mitochondrial Function in the Hearts of Down Syndrome Fetuses

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Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases

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MicroRNAs regulate key cell survival pathways and mediate chemosensitivity during progression of diffuse large B-cell lymphoma

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microRNA regulation in an ancient obligate endosymbiosis

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miRNA-135b Contributes to Triple Negative Breast Cancer Molecular Heterogeneity: Different Expression Profile in Basal-like Versus non-Basal-like Phenotypes

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miARma-Seq, a comprehensive pipeline for the simultaneous study and integration of miRNA and mRNA expression data

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An alternative miRISC targets a cancer‐associated coding sequence mutation in FOXL2

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MiR-182-5p promotes the Metastasis and Epithelial-mesenchymal Transition in Non-small Cell Lung Cancer by Targeting EPAS1

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A discovery of novel microRNAs in the silkworm (Bombyx mori) genome

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Targetome profiling and functional genetics implicate miR-618 in lymphomagenesis

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Rhythmic expression of miR‐27b‐3p targets the clock gene Bmal1 at the posttranscriptional level in the mouse liver

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Combined miRNA profiling and proteomics demonstrates that different miRNAs target a common set of proteins to promote colorectal cancer metastasis

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Computational Biology in microRNA

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MicroRNA-29a regulates the benzo[a]pyrene dihydrodiol epoxide-induced DNA damage response through Cdc7 kinase in lung cancer cells

Barkley, L. R., & Santocanale, C. (2013) · Oncogenesis · doi:10.1038/oncsis.2013.20 · Cited by 37

Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay

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A study of neural-related microRNAs in the developing amphioxus

Candiani, S., Moronti, L., Tonelli, D. D. P., Garbarino, G., & Pestarino, M. (2011) · EvoDevo · doi:10.1186/2041-9139-2-15 · Cited by 36

Association between XPF Polymorphisms and Cancer Risk: A Meta-Analysis

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Cooperation meets competition in microRNA-mediated DMPK transcript regulation

Kościańska, E., Witkos, T. M., Kozłowska, E., Wojciechowska, M., & Krzyżosiak, W. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv849 · Cited by 40

Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression

Ben‐Hamo, R., & Efroni, S. (2011) · Genome Medicine · doi:10.1186/gm293 · Cited by 36

An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

Catalán, A., Glaser‐Schmitt, A., Argyridou, E., Duchen, P., & Parsch, J. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005987 · Cited by 38

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction

Pirro, S., Minutolo, A., Galgani, A., Potestà, M., Colizzi, V., & Montesano, C. (2016) · Journal of Computational Biology · doi:10.1089/cmb.2016.0059 · Cited by 37

Pervasive Behavioral Effects of MicroRNA Regulation in Drosophila

Picão-Osório, J., Lago‐Baldaia, I., Patraquim, P., & Alonso, C. R. (2017) · Genetics · doi:10.1534/genetics.116.195776 · Cited by 35

Intestinal and Circulating MicroRNAs in Coeliac Disease

Felli, C., Baldassarre, A., & Masotti, A. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18091907 · Cited by 36

Regulatory network analysis of high expressed long non-coding RNA LINC00941 in gastric cancer

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Identification and characterization of differentially expressed Phaseolus vulgaris miRNAs and their targets during mungbean yellow mosaic India virus infection reveals new insight into Phaseolus-MYMIV interaction

Patwa, N., Nithin, C., Bahadur, R. P., & Basak, J. (2018) · Genomics · doi:10.1016/j.ygeno.2018.09.005 · Cited by 36

Characterization and expression profiling of microRNAs in response to plant feeding in two host-plant strains of the lepidopteran pest Spodoptera frugiperda

Moné, Y., Nhim, S., Gimenez, S., Legeai, F., Séninet, I., Parrinello, H., Negre, N. N., & d’Alençon, E. (2018) · BMC Genomics · doi:10.1186/s12864-018-5119-6 · Cited by 36

The enemy within: intronic miR-26b represses its host gene,ctdsp2, to regulate neurogenesisPreprint

Han, J., Denli, A. M., & Gage, F. H. (2012) · Genes & Development · doi:10.1101/gad.184416.111 · Cited by 35

Inflammatory gene networks in term human decidual cells define a potential signature for cytokine-mediated parturition

Ibrahim, S. A., Ackerman, W. E., Summerfield, T. L. S., Lockwood, C. J., Schatz, F., & Kniss, D. A. (2015) · American Journal of Obstetrics and Gynecology · doi:10.1016/j.ajog.2015.08.075 · Cited by 35

Predicting kissing interactions in microRNA–target complex and assessment of microRNA activity

Cao, S., & Chen, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks052 · Cited by 35

MicroRNA-665 is involved in the regulation of the expression of the cardioprotective cannabinoid receptor CB2 in patients with severe heart failure

Möhnle, P., Schütz, S. V., Schmidt, M. T., Hinske, L. C., Hübner, M., Heyn, J., Beiras-Fernández, A., & Kreth, S. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.08.008 · Cited by 35

An NTD-Associated Polymorphism in the 3′ UTR of MTHFD1L can Affect Disease Risk by Altering miRNA Binding

Minguzzi, S., Selçuklu, S. D., Spillane, C., & Parle‐McDermott, A. (2013) · Human Mutation · doi:10.1002/humu.22459 · Cited by 33

Preferential regulation of miRNA targets by environmental chemicals in the human genome

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Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers

Lee, E., Ito, K., Zhao, Y. B., Schadt, E. E., Irie, H. Y., & Zhu, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv531 · Cited by 35

MicroRNAs Expressed during Viral Infection: Biomarker Potential and Therapeutic Considerations

Louten, J., Beach, M., Palermino, K., Weeks, M., & Holenstein, G. (2015) · Biomarker Insights · doi:10.4137/bmi.s29512 · Cited by 36

SePIA: RNA and small RNA sequence processing, integration, and analysis

Icay, K., Chen, P., Cervera, A., Rantanen, V., Lehtonen, R., & Hautaniemi, S. (2016) · BioData Mining · doi:10.1186/s13040-016-0099-z · Cited by 30

The genetic variants in 3’ untranslated region of voltage-gated sodium channel alpha 1 subunit gene affect the mRNA-microRNA interactions and associate with epilepsy

Li, T., Kuang, Y., & Li, B. (2016) · BMC Genetics · doi:10.1186/s12863-016-0417-y · Cited by 35

Integrated network analysis reveals distinct regulatory roles of transcription factors and microRNAs

Guo, Y., Alexander, K. A., Clark, A. G., Grimson, A., & Yu, H. (2016) · RNA · doi:10.1261/rna.048025.114 · Cited by 35

Down‐regulation of miR‐146a‐5p and its potential targets in hepatocellular carcinoma validated by a TCGA ‐ and GEO ‐based study

Zhang, X., Ye, Z., Liang, H., Ren, F., Li, P., Dang, Y., & Chen, G. (2017) · FEBS Open Bio · doi:10.1002/2211-5463.12198 · Cited by 35

Interplay between TETs and microRNAs in the adult brain for memory formation

Kremer, E. A., Gaur, N., Lee, M. A., Engmann, O., Bohacek, J., & Mansuy, I. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-19806-z · Cited by 35

Genes and microRNAs associated with mouse cleft palate: A systematic review and bioinformatics analysis

Suzuki, A., Abdallah, N., Gajera, M. V., Jun, G., Jia, P., Zhao, Z., & Iwata, J. (2018) · Mechanisms of Development · doi:10.1016/j.mod.2018.02.003 · Cited by 35

miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer

Tong, Y., Ru, B., & Zhang, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty320 · Cited by 35

Unveiling ncRNA regulatory axes in atherosclerosis progression

Navarro, E., Mallén, A., Cruzado, J. M., Torrás, J., & Hueso, M. (2020) · Clinical and Translational Medicine · doi:10.1186/s40169-020-0256-3 · Cited by 35

Multi-Omics Data Fusion for Cancer Molecular Subtyping Using Sparse Canonical Correlation Analysis

Lin, Q., Wang, W., Wu, T., Zhu, L., He, L., & Wang, X. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.607817 · Cited by 36

Controlling Gene Expression in Mammalian Cells Using Multiplexed Conditional Guide RNAs for Cas12a**

Oesinghaus, L., & Simmel, F. C. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202107258 · Cited by 35

Insect MicroRNAs

Bellés, X., Cristino, A. S., Tanaka, É. D., Rubio, M., & Piulachs, M. (2011) · Elsevier eBooks · doi:10.1016/b978-0-12-384747-8.10002-9 · Cited by 35

Mutation in the 3’untranslated region of APP as a genetic determinant of cerebral amyloid angiopathy

Nicolas, G., Wallon, D., Goupil, C., Richard, A., Pottier, C. P., Dorval, V., Sarov-Rivière, M., Riant, F., Hervé, D., Amouyel, P., et al. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2015.61 · Cited by 35

Employing machine learning for reliable miRNA target identification in plants

Jha, A., & Shankar, R. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-636 · Cited by 36

MicroRNA-33b downregulates the differentiation and development of porcine preadipocytes

Taniguchi, M., Nakajima, I., CHIKUNI, K., Kojima, M., Awata, T., & Mikawa, S. (2014) · Molecular Biology Reports · doi:10.1007/s11033-013-2954-z · Cited by 35

Systems Biology Reveals MicroRNA-Mediated Gene Regulation

Watanabe, Y., & Kanai, A. (2011) · Frontiers in Genetics · doi:10.3389/fgene.2011.00029 · Cited by 37

The Influence of 3′UTRs on MicroRNA Function Inferred from Human SNP Data

Hu, Z., & Bruno, A. E. (2011) · Comparative and Functional Genomics · doi:10.1155/2011/910769 · Cited by 34

MicroRNA 497 modulates interleukin 1 signalling via the MAPK/ERK pathway

Zheng, D., Radziszewska, A., & Woo, P. M. (2012) · FEBS Letters · doi:10.1016/j.febslet.2012.10.014 · Cited by 34

Refining microRNA target predictions: Sorting the wheat from the chaff

Ritchie, W., & Rasko, J. E. J. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.01.181 · Cited by 34

Bicc1 Polymerization Regulates the Localization and Silencing of Bound mRNA

Rothé, B., Leal-Esteban, L. C., Bernet, F., Urfer, S., Doerr, N., Weimbs, T., Iwaszkiewicz, J., & Constam, D. B. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00341-15 · Cited by 34

Human Long Noncoding RNAs Are Substantially Less Folded than Messenger RNAs

Yang, J., & Zhang, J. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu402 · Cited by 32

Evaluation of online miRNA resources for biomedical applications

Gana, N. H. T., Victoriano, A. F. B., & Okamoto, T. (2011) · Genes to Cells · doi:10.1111/j.1365-2443.2011.01564.x · Cited by 34

The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery

Hoffman, Y., Dahary, D., Bublik, D. R., Oren, M., & Pilpel, Y. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt044 · Cited by 34

Unveiling MYCN regulatory networks in neuroblastoma via integrative analysis of heterogeneous genomics data

Hsu, C., Chang, H., Chang, J.-Y., Hsu, W., Huang, H., & Juan, H. (2016) · Oncotarget · doi:10.18632/oncotarget.9202 · Cited by 34

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

West, S. M., Mecenas, D., Gutwein, M. R., Aristizábal-Corrales, D., Piano, F., & Gunsalus, K. C. (2018) · Genome biology · doi:10.1186/s13059-017-1369-x · Cited by 32

Alternative polyadenylation confers PtenmRNAs stability and resistance to microRNAs

Thivierge, C., Tseng, H.-W., Mayya, V. K., Lussier, C. R., Gravel, S., & Duchaîne, T. F. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky666 · Cited by 34

Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells

Zhang, F., Zhang, Y., Lv, X., Xu, B., Zhang, H., Yan, J., Li, H., & Wu, L. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz001 · Cited by 30

Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

Lau, A. Y. T., Cheng, X., Cheng, C. K., Nong, W., Cheung, M. K., Chan, R. H.-F., Hui, J. H. L., & Kwan, H. S. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198234 · Cited by 32

Hypoxic naked mole–rat brains use microRNA to coordinate hypometabolic fuels and neuroprotective defenses

Hadj‐Moussa, H., Pamenter, M. E., & Storey, K. B. (2020) · Journal of Cellular Physiology · doi:10.1002/jcp.30216 · Cited by 36

MicroRNAs as predictive biomarkers and therapeutic targets in prostate cancer.

Wen, X., Deng, F., & Wang, J. (2014) · PubMed Central · Cited by 34

miR‐26a‐5p alleviates CFA‐induced chronic inflammatory hyperalgesia through Wnt5a/CaMKII/NFAT signaling in mice

Lu, Y., Liu, M., Guo, X., Wang, P., Zeng, F., Wang, H., Tang, J. Y., Qin, Z., & Tao, T. (2023) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.14099 · Cited by 33

Human microRNAs co-silence in well-separated groups and have different predicted essentialities

Boross, G. Z., Orosz, K., & Farkas, I. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp018 · Cited by 34

miR-802 regulates human angiotensin II type 1 receptor expression in intestinal epithelial C2BBe1 cells

Sansom, S. E., Nuovo, G. J., Martin, M. M., Kotha, S. R., Parinandi, N. L., & Elton, T. S. (2010) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00120.2010 · Cited by 34

Correction: Tissue and Process Specific microRNA–mRNA Co-Expression in Mammalian Development and Malignancy

Liu, H., & Kohane, I. S. (2009) · PLoS ONE · doi:10.1371/annotation/1cdc7975-50d7-40a5-99ca-83580df2982f · Cited by 34

Genome-wide search for miRNA-target interactions in Arabidopsis thaliana with an integrated approach

Ding, J., Li, D., Ohler, U., Guan, J., & Zhou, S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s3-s3 · Cited by 33

Post-transcriptional control of candidate risk genes for type 1 diabetes by rare genetic variants

de Jong, V. M., Zaldumbide, A., van der Slik, A. R., Persengiev, S. P., Roep, B. O., & Koeleman, B. P. C. (2012) · Genes and Immunity · doi:10.1038/gene.2012.38 · Cited by 33

Structural Map of a MicroRNA-122:Hepatitis C Virus Complex

Pang, P. S., Pham, E. A., Elazar, M., Patel, S., Eckart, M. R., & Glenn, J. S. (2011) · Journal of Virology · doi:10.1128/jvi.06367-11 · Cited by 33

Transcriptome-Wide Analysis of UTRs in Non-Small Cell Lung Cancer Reveals Cancer-Related Genes with SNV-Induced Changes on RNA Secondary Structure and miRNA Target Sites

Sabarinathan, R., Wenzel, A., Novotny, P., Tang, X., Kalari, K. R., & Gorodkin, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0082699 · Cited by 33

A possible role for miRNA silencing in disease phenotype variation in Swedish transthyretin V30M carriers

Olsson, M. B., Norgren, N., Obayashi, K., Planté‐Bordeneuve, V., Suhr, O. B., Cederquist, K., & Jonasson, J. (2010) · BMC Medical Genetics · doi:10.1186/1471-2350-11-130 · Cited by 33

MicroRNAs in the Host Response to Viral Infections of Veterinary Importance

Samir, M., Vaas, L. A. I., & Peßler, F. (2016) · Frontiers in Veterinary Science · doi:10.3389/fvets.2016.00086 · Cited by 33

T-cell acute lymphoblastic leukemia from miRNA perspective: Basic concepts, experimental approaches, and potential biomarkers

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ncRNA Editing: Functional Characterization and Computational Resources

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