Trends in the development of miRNA bioinformatics tools
Abstract MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structu...
Saved in:
| Published in | Briefings in bioinformatics Vol. 20; no. 5; pp. 1836 - 1852 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
27.09.2019
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. |
|---|---|
| AbstractList | MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. Abstract MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools. |
| Author | Heikkinen, Liisa Sun, Huiyan Wang, Changliang Chen, Liang Yang, Yang Wong, Garry |
| AuthorAffiliation | 2 Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, China 1 Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R, China |
| AuthorAffiliation_xml | – name: 1 Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R, China – name: 2 Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, China |
| Author_xml | – sequence: 1 givenname: Liang surname: Chen fullname: Chen, Liang organization: Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China – sequence: 2 givenname: Liisa surname: Heikkinen fullname: Heikkinen, Liisa organization: Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China – sequence: 3 givenname: Changliang surname: Wang fullname: Wang, Changliang organization: Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China – sequence: 4 givenname: Yang surname: Yang fullname: Yang, Yang organization: Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China – sequence: 5 givenname: Huiyan surname: Sun fullname: Sun, Huiyan organization: Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China – sequence: 6 givenname: Garry surname: Wong fullname: Wong, Garry email: GarryGWong@umac.mo organization: Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29982332$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9kd1KAzEQRoMoVqs3PoAsiCDCapLNdrI3goh_IApSr0OSZm1kN6nJrtC3N6VWtIhXGciZjzMzu2jTeWcQOiD4jOCqOFdWnSs1xyXbQDuEAeQs1ZuLegR5yUbFAO3G-IYxxcDJNhrQquK0KOgOgnEwbhIz67JuarKJ-TCNn7XGdZmvs9Y-P15mynrrah9a2Vkds877Ju6hrVo20ex_vUP0cnM9vrrLH55u768uH3JdYtrlhutScVXJQhFOKS-AgKqVMYQZQlWyAeAADGM8YVyrkkjCa8YYB4lBV8UQXSxzZ71qzUQnsSAbMQu2lWEuvLTi94-zU_HqPwQwwkrKUsDJV0Dw772JnWht1KZppDO-j4LiERCaHCChR2vom--DS-MJWpUl5RhGC-rwp9G3ymqnCcBLQAcfYzC10LZLq_MLQdsIgsXibCKdTSzPllpO11pWqX_Cx0vY97P_uE9O7KTy |
| CitedBy_id | crossref_primary_10_3390_ijms242216453 crossref_primary_10_1007_s12033_021_00436_2 crossref_primary_10_3892_ol_2021_13077 crossref_primary_10_3390_ijms25147743 crossref_primary_10_1007_s11064_022_03585_1 crossref_primary_10_1007_s11738_020_3013_8 crossref_primary_10_1152_physrev_00032_2022 crossref_primary_10_3390_ijms25031673 crossref_primary_10_1093_bib_bbac217 crossref_primary_10_1093_humupd_dmz039 crossref_primary_10_1016_j_pharmthera_2022_108215 crossref_primary_10_1016_j_virusres_2021_198567 crossref_primary_10_1007_s00432_023_04986_7 crossref_primary_10_1089_omi_2021_0087 crossref_primary_10_3390_cimb44120413 crossref_primary_10_1080_21655979_2022_2068923 crossref_primary_10_1016_j_clinsp_2022_100115 crossref_primary_10_1016_j_prp_2024_155482 crossref_primary_10_32604_biocell_2024_055505 crossref_primary_10_1016_j_bcp_2024_116411 crossref_primary_10_1093_bib_bbad418 crossref_primary_10_54005_geneltip_1431670 crossref_primary_10_3389_fonc_2022_839508 crossref_primary_10_1093_database_baad014 crossref_primary_10_1002_cam4_5382 crossref_primary_10_1016_j_heliyon_2024_e35663 crossref_primary_10_2139_ssrn_4142087 crossref_primary_10_1111_odi_14351 crossref_primary_10_31083_j_rcm2304148 crossref_primary_10_3390_plants12173070 crossref_primary_10_1007_s12672_025_02048_7 crossref_primary_10_1093_bib_bbac365 crossref_primary_10_1016_j_aquaculture_2021_737450 crossref_primary_10_1016_j_acthis_2024_152133 crossref_primary_10_3389_fonc_2022_918778 crossref_primary_10_1007_s12033_024_01094_w crossref_primary_10_1002_jcp_29023 crossref_primary_10_1016_j_neulet_2020_135482 crossref_primary_10_1186_s13052_024_01795_7 crossref_primary_10_1093_bioinformatics_btz940 crossref_primary_10_1016_j_compbiomed_2021_104448 crossref_primary_10_1155_2021_6034413 crossref_primary_10_1021_acsomega_1c00154 crossref_primary_10_18632_aging_203873 crossref_primary_10_1016_j_jhazmat_2022_130276 crossref_primary_10_1093_bib_bbz079 crossref_primary_10_3390_ijms252212454 crossref_primary_10_1002_cbin_11774 crossref_primary_10_1093_bib_bbaa001 crossref_primary_10_1111_gcbb_12909 crossref_primary_10_1007_s10528_022_10257_w crossref_primary_10_1016_j_intimp_2021_108508 crossref_primary_10_1016_j_mrfmmm_2024_111872 crossref_primary_10_1093_bib_bbaa117 crossref_primary_10_1093_bib_bbab448 crossref_primary_10_2174_0929866529666220721090209 crossref_primary_10_1109_JBHI_2024_3397003 crossref_primary_10_1016_j_gendis_2022_07_016 crossref_primary_10_1016_j_gpb_2021_02_010 crossref_primary_10_62347_JVBV7887 crossref_primary_10_1002_mog2_93 crossref_primary_10_31083_j_fbl2709275 crossref_primary_10_1093_bib_bbac411 crossref_primary_10_1038_s41420_024_01977_6 crossref_primary_10_1007_s12033_021_00324_9 crossref_primary_10_1007_s10142_022_00915_y crossref_primary_10_1093_bib_bbaa346 crossref_primary_10_1186_s12957_021_02463_4 crossref_primary_10_2174_0929866530666230104155209 crossref_primary_10_3390_genes13071143 crossref_primary_10_3390_curroncol29080427 crossref_primary_10_1016_j_phymed_2022_154516 crossref_primary_10_1016_j_jot_2024_12_006 crossref_primary_10_1038_s41598_024_56786_9 crossref_primary_10_1038_s41598_024_76095_5 crossref_primary_10_1016_j_omtn_2023_04_031 crossref_primary_10_1016_j_tranon_2024_102000 crossref_primary_10_1007_s00221_022_06305_x crossref_primary_10_1186_s12868_022_00747_3 crossref_primary_10_1007_s00705_024_06086_4 crossref_primary_10_1016_j_humgen_2025_201380 crossref_primary_10_2174_1570159X21666221129122932 crossref_primary_10_3389_fendo_2025_1557797 crossref_primary_10_1002_kjm2_12432 crossref_primary_10_1016_j_vetmic_2022_109430 crossref_primary_10_1080_16078454_2024_2428482 crossref_primary_10_3389_fonc_2021_683725 crossref_primary_10_1089_omi_2024_0047 crossref_primary_10_1186_s13018_022_03000_z crossref_primary_10_1186_s12864_023_09923_z crossref_primary_10_1007_s11010_023_04876_z crossref_primary_10_1080_21655979_2022_2063537 crossref_primary_10_3390_molecules28020818 crossref_primary_10_1002_glia_23846 crossref_primary_10_1155_2024_4887984 crossref_primary_10_7717_peerj_17662 crossref_primary_10_1021_acs_jafc_2c05103 crossref_primary_10_1088_1757_899X_1129_1_012047 crossref_primary_10_3390_ijms241914892 crossref_primary_10_1016_j_fsi_2023_109124 crossref_primary_10_1021_acs_jafc_2c03049 crossref_primary_10_1097_SHK_0000000000002229 crossref_primary_10_1007_s00604_024_06401_5 crossref_primary_10_5604_01_3001_0014_6578 crossref_primary_10_3390_ijms241814025 crossref_primary_10_3389_fimmu_2022_990571 crossref_primary_10_1016_j_csbj_2021_01_029 crossref_primary_10_1093_gigascience_giac093 crossref_primary_10_1080_21655979_2022_2033409 crossref_primary_10_3390_metabo14080403 crossref_primary_10_3389_fmed_2023_1158907 crossref_primary_10_3390_agronomy12010011 crossref_primary_10_1007_s10072_025_08051_8 crossref_primary_10_3390_biom12121774 crossref_primary_10_1111_jch_70033 crossref_primary_10_3390_ani15020226 crossref_primary_10_1155_2021_8870353 crossref_primary_10_1177_03000605251317476 crossref_primary_10_3389_fmolb_2022_888624 crossref_primary_10_1186_s12876_022_02622_1 crossref_primary_10_3389_fcell_2021_732415 crossref_primary_10_2174_0109298665245603231106050224 crossref_primary_10_3390_biomedicines11113087 crossref_primary_10_1080_08916934_2024_2304826 crossref_primary_10_1016_j_ygeno_2022_110442 crossref_primary_10_3389_fimmu_2022_1059947 crossref_primary_10_1016_j_jep_2023_116967 crossref_primary_10_1039_D1RA00539A crossref_primary_10_3390_biomedicines11041230 crossref_primary_10_3390_diagnostics12020369 crossref_primary_10_1007_s12017_021_08685_9 crossref_primary_10_1016_j_biopha_2024_117513 crossref_primary_10_1007_s11011_022_00910_z crossref_primary_10_1093_bib_bbab428 crossref_primary_10_31089_1026_9428_2021_61_11_734_739 crossref_primary_10_2147_OTT_S289241 crossref_primary_10_3390_genes14061202 crossref_primary_10_1007_s12015_020_10082_x crossref_primary_10_1016_j_prp_2022_154216 crossref_primary_10_1007_s00403_024_03669_8 crossref_primary_10_1007_s12672_023_00687_2 crossref_primary_10_2174_0929866530666230511115213 crossref_primary_10_1093_jambio_lxad104 crossref_primary_10_1038_s41598_022_12681_9 crossref_primary_10_1186_s13287_024_04116_1 crossref_primary_10_1007_s12672_025_01993_7 crossref_primary_10_1016_j_intimp_2022_109643 crossref_primary_10_1002_aps3_11414 crossref_primary_10_3892_ol_2024_14842 crossref_primary_10_1080_0886022X_2024_2322688 crossref_primary_10_1080_21655979_2021_2017588 crossref_primary_10_1093_nar_gkab499 crossref_primary_10_1186_s12885_023_10714_8 crossref_primary_10_1001_jamanetworkopen_2021_36913 crossref_primary_10_1007_s12010_024_04951_1 crossref_primary_10_1371_journal_pone_0311055 crossref_primary_10_1007_s10528_024_10998_w crossref_primary_10_1002_cam4_5869 crossref_primary_10_1186_s40662_023_00370_1 crossref_primary_10_1093_nar_gkab268 crossref_primary_10_1186_s12943_023_01877_w crossref_primary_10_3389_fbinf_2024_1487292 crossref_primary_10_1016_j_exer_2025_110306 crossref_primary_10_1002_tox_24103 crossref_primary_10_1007_s13721_021_00297_4 crossref_primary_10_3390_cells11030572 crossref_primary_10_1002_bit_27821 crossref_primary_10_3390_ijms24108899 crossref_primary_10_1016_j_biopha_2021_112544 crossref_primary_10_2147_DMSO_S359759 crossref_primary_10_3390_ijms242116010 crossref_primary_10_3390_insects12020186 crossref_primary_10_1016_j_lungcan_2024_107902 crossref_primary_10_1080_15384047_2024_2373497 crossref_primary_10_1007_s11302_024_10002_5 crossref_primary_10_1007_s12033_023_00835_7 crossref_primary_10_2147_DMSO_S349528 crossref_primary_10_1002_chem_202101171 crossref_primary_10_1111_rda_14529 crossref_primary_10_1016_j_phymed_2022_153973 crossref_primary_10_3390_ijms22116067 crossref_primary_10_3390_biom10111576 crossref_primary_10_1186_s12879_024_09232_0 crossref_primary_10_1210_endocr_bqac071 crossref_primary_10_1016_j_yexcr_2023_113828 crossref_primary_10_1055_a_1735_3318 crossref_primary_10_1080_08941939_2023_2216756 crossref_primary_10_1016_j_acthis_2024_152211 crossref_primary_10_3389_fgene_2022_1003964 crossref_primary_10_3389_fphar_2023_1103971 crossref_primary_10_1007_s12539_020_00387_3 crossref_primary_10_1016_j_bcp_2023_115914 crossref_primary_10_1002_jbt_23767 crossref_primary_10_1016_j_ijbiomac_2025_141392 crossref_primary_10_1016_j_bios_2022_114236 crossref_primary_10_1007_s11010_022_04375_7 crossref_primary_10_2147_JIR_S422114 crossref_primary_10_1111_1744_7917_13512 crossref_primary_10_3390_genes13050761 crossref_primary_10_3389_fgene_2024_1480431 crossref_primary_10_5466_ijoms_23_111 crossref_primary_10_1016_j_ijpharm_2024_125140 crossref_primary_10_1038_s41420_022_01005_5 crossref_primary_10_1007_s13577_023_00899_2 crossref_primary_10_1080_07366205_2024_2368394 crossref_primary_10_1080_14622416_2024_2355864 crossref_primary_10_3389_fimmu_2022_924667 crossref_primary_10_1016_j_biopha_2023_114264 crossref_primary_10_3389_fonc_2022_783079 crossref_primary_10_1002_jbt_23134 crossref_primary_10_3390_life10060095 crossref_primary_10_1155_2022_2691997 crossref_primary_10_1007_s11864_024_01203_6 crossref_primary_10_1111_jcmm_15114 crossref_primary_10_5808_gi_21067 crossref_primary_10_3390_ijms232214318 crossref_primary_10_3390_genes13030468 crossref_primary_10_1155_2022_2322565 crossref_primary_10_1155_2022_7538025 crossref_primary_10_1007_s12094_023_03180_y crossref_primary_10_3389_fphar_2023_1178310 crossref_primary_10_1016_j_ijbiomac_2024_133688 crossref_primary_10_1186_s12872_024_03966_0 crossref_primary_10_1007_s10528_023_10458_x crossref_primary_10_3390_biomedicines10040915 crossref_primary_10_1002_cbin_11902 crossref_primary_10_21467_exr_3_1_5147 crossref_primary_10_1002_jgm_3372 crossref_primary_10_2485_jhtb_30_239 crossref_primary_10_3892_or_2023_8648 crossref_primary_10_1007_s10616_025_00708_8 crossref_primary_10_1016_j_phrs_2024_107345 crossref_primary_10_1016_j_brainresbull_2022_03_002 crossref_primary_10_1186_s12886_024_03396_8 crossref_primary_10_1021_acschemneuro_4c00429 crossref_primary_10_1007_s12264_022_00950_6 crossref_primary_10_1038_s41405_024_00278_5 crossref_primary_10_1002_jsfa_13718 crossref_primary_10_1111_jcmm_17999 crossref_primary_10_1016_j_jplph_2021_153451 crossref_primary_10_1186_s12935_020_01342_4 crossref_primary_10_1186_s13027_023_00492_0 crossref_primary_10_3390_diagnostics12112872 crossref_primary_10_1186_s12890_023_02818_5 crossref_primary_10_3390_ncrna10020017 crossref_primary_10_2174_0122115366296148240530072346 crossref_primary_10_1002_mc_23879 crossref_primary_10_1016_j_phrs_2024_107469 crossref_primary_10_1016_j_aca_2024_343603 crossref_primary_10_4103_1673_5374_382255 crossref_primary_10_1016_j_ecoenv_2022_113999 crossref_primary_10_1002_advs_202414625 crossref_primary_10_3390_biom14101259 crossref_primary_10_1080_15257770_2022_2052314 crossref_primary_10_3389_fgene_2022_857507 crossref_primary_10_1016_j_bone_2022_116503 crossref_primary_10_1620_tjem_2024_J075 crossref_primary_10_1080_15384101_2021_1919820 crossref_primary_10_2217_fon_2021_1130 crossref_primary_10_1096_fj_202101023R crossref_primary_10_1002_jssc_202300123 crossref_primary_10_1007_s12033_021_00375_y crossref_primary_10_1097_MD_0000000000031928 crossref_primary_10_1016_j_ijbiomac_2024_133650 crossref_primary_10_1007_s11010_025_05214_1 crossref_primary_10_1002_ps_5957 crossref_primary_10_1007_s12013_024_01528_x crossref_primary_10_3389_fcvm_2022_1094388 crossref_primary_10_3389_fonc_2022_889658 crossref_primary_10_1016_j_semcancer_2022_03_024 crossref_primary_10_1016_j_heliyon_2024_e27019 crossref_primary_10_1371_journal_pone_0254854 crossref_primary_10_1016_j_biopha_2020_111115 crossref_primary_10_3390_ijms242417224 crossref_primary_10_2174_0122115366261005231018070640 crossref_primary_10_1007_s13555_023_00931_1 crossref_primary_10_1093_nar_gkac1070 crossref_primary_10_1111_1759_7714_15460 crossref_primary_10_1002_cbdv_202403263 crossref_primary_10_1536_ihj_23_379 crossref_primary_10_1080_15384101_2022_2154549 crossref_primary_10_3390_diagnostics11060964 crossref_primary_10_1111_jcmm_15133 crossref_primary_10_3390_ijms25137006 crossref_primary_10_1038_s41526_024_00441_0 crossref_primary_10_18632_aging_204474 crossref_primary_10_1016_j_phrs_2021_106018 crossref_primary_10_3389_fcvm_2021_773083 crossref_primary_10_1016_j_phymed_2021_153821 crossref_primary_10_1007_s10528_023_10435_4 crossref_primary_10_1186_s12859_023_05629_x crossref_primary_10_3390_cells13171459 crossref_primary_10_1016_j_bbadis_2024_167642 crossref_primary_10_1016_j_ijpharm_2022_122352 crossref_primary_10_18632_aging_203036 crossref_primary_10_1080_00071668_2024_2319779 crossref_primary_10_1186_s12935_023_02974_y crossref_primary_10_1002_jcb_30453 crossref_primary_10_1080_21655979_2021_1926195 crossref_primary_10_3390_cancers15123140 crossref_primary_10_3389_fgene_2023_1145769 crossref_primary_10_1186_s12964_023_01092_6 crossref_primary_10_1515_med_2022_0424 crossref_primary_10_1093_femspd_ftae011 crossref_primary_10_1111_cpr_13624 crossref_primary_10_3390_ijms23158057 crossref_primary_10_3389_fcvm_2024_1356286 crossref_primary_10_3389_fgene_2023_1147222 crossref_primary_10_1089_cbr_2021_0339 crossref_primary_10_3389_fonc_2024_1380448 crossref_primary_10_1007_s12011_023_03691_3 crossref_primary_10_3389_fmed_2022_840030 crossref_primary_10_1016_j_bbi_2024_02_016 crossref_primary_10_1002_jbt_70080 crossref_primary_10_1096_fj_202402443R crossref_primary_10_3390_ijms22105317 crossref_primary_10_1007_s10495_022_01787_0 crossref_primary_10_1016_j_intimp_2022_109066 crossref_primary_10_3390_ncrna9020018 crossref_primary_10_3389_fimmu_2024_1419660 crossref_primary_10_3892_etm_2021_10480 crossref_primary_10_1002_bies_202100256 crossref_primary_10_1002_hsr2_2079 crossref_primary_10_3390_ijms24087307 crossref_primary_10_1097_MD_0000000000040289 crossref_primary_10_1007_s11064_021_03492_x crossref_primary_10_2174_1568009623666230202155440 crossref_primary_10_1002_jcla_24422 crossref_primary_10_1007_s00210_024_02960_9 crossref_primary_10_3390_nano11030691 crossref_primary_10_1016_j_jds_2021_08_017 crossref_primary_10_3390_ncrna7010019 crossref_primary_10_1080_13510002_2025_2466142 crossref_primary_10_3389_phrs_2024_1606879 crossref_primary_10_2217_epi_2023_0207 crossref_primary_10_3389_fcell_2021_660853 crossref_primary_10_3390_genes15070911 crossref_primary_10_1007_s12013_024_01452_0 crossref_primary_10_1016_j_tice_2024_102669 crossref_primary_10_1016_j_mce_2023_111996 crossref_primary_10_3390_biomedicines10061305 crossref_primary_10_1111_jcmm_18219 crossref_primary_10_1155_2022_3032407 crossref_primary_10_1097_MD_0000000000038061 crossref_primary_10_3389_fendo_2022_916469 crossref_primary_10_3390_jof7070561 crossref_primary_10_1016_j_bbrc_2023_149335 crossref_primary_10_1016_j_compbiolchem_2022_107729 crossref_primary_10_1016_j_snb_2022_133003 crossref_primary_10_1016_j_cej_2024_150706 crossref_primary_10_2174_1386207325666220819194249 crossref_primary_10_1002_jcp_27486 crossref_primary_10_1016_j_compbiomed_2021_104603 crossref_primary_10_1016_j_ijbiomac_2024_132732 crossref_primary_10_1152_physiolgenomics_00041_2020 crossref_primary_10_2174_0113816128310724240730072626 crossref_primary_10_1080_00071668_2022_2102891 crossref_primary_10_1080_21655979_2021_1997244 crossref_primary_10_3390_ijms24021214 crossref_primary_10_1016_j_prp_2022_153912 crossref_primary_10_1038_s41390_022_02206_5 crossref_primary_10_2147_JIR_S359887 crossref_primary_10_1016_j_biopha_2023_114463 crossref_primary_10_1002_wrna_1768 crossref_primary_10_1016_j_bbadis_2021_166166 crossref_primary_10_1016_j_labinv_2024_102044 crossref_primary_10_12677_ACM_2023_134905 crossref_primary_10_3389_fgene_2022_953580 crossref_primary_10_1016_j_canlet_2022_01_019 crossref_primary_10_26508_lsa_202101203 crossref_primary_10_3389_fpls_2025_1535384 crossref_primary_10_1002_jbt_70160 crossref_primary_10_1016_j_bcp_2024_116503 crossref_primary_10_1007_s10495_023_01890_w crossref_primary_10_1155_2022_9413562 crossref_primary_10_1007_s11033_022_07603_x crossref_primary_10_1016_j_compbiolchem_2021_107448 crossref_primary_10_1016_j_ijbiomac_2024_131628 crossref_primary_10_1111_1759_7714_15092 crossref_primary_10_3390_ncrna10060062 crossref_primary_10_1615_CritRevEukaryotGeneExpr_v33_i5_60 crossref_primary_10_3390_cancers14215384 crossref_primary_10_4081_ejh_2022_3505 crossref_primary_10_1186_s12905_022_02056_7 crossref_primary_10_1038_s41598_019_47399_8 crossref_primary_10_2147_IJN_S440619 crossref_primary_10_1016_j_ijcrp_2024_200355 crossref_primary_10_1002_mco2_657 crossref_primary_10_1016_j_fitote_2024_106353 crossref_primary_10_3390_ijms24076423 crossref_primary_10_1186_s12885_024_12007_0 crossref_primary_10_1186_s12987_023_00484_7 crossref_primary_10_1186_s13046_023_02693_2 crossref_primary_10_1097_CAD_0000000000001381 crossref_primary_10_1093_bib_bbac044 crossref_primary_10_3389_fphar_2024_1410479 crossref_primary_10_1166_jbt_2022_2970 crossref_primary_10_1097_CAD_0000000000001257 crossref_primary_10_1016_j_vetmic_2023_109676 crossref_primary_10_1186_s13059_019_1629_z crossref_primary_10_3390_biomedicines9091181 crossref_primary_10_1186_s12890_021_01617_0 crossref_primary_10_1007_s10142_024_01305_2 crossref_primary_10_1093_bib_bbac397 crossref_primary_10_3389_fendo_2023_1210627 crossref_primary_10_17235_reed_2024_10882_2024 crossref_primary_10_1155_2022_1544648 crossref_primary_10_2174_0929867328666210804090224 crossref_primary_10_1016_j_imu_2023_101272 crossref_primary_10_3389_fgene_2022_895629 crossref_primary_10_1016_j_bioactmat_2021_01_031 |
| Cites_doi | 10.1093/nar/gkw1185 10.1016/j.febslet.2013.06.047 10.1186/1471-2105-12-107 10.1016/0092-8674(93)90529-Y 10.1093/bioinformatics/btw660 10.1186/1471-2164-14-S1-S2 10.1146/annurev-genet-120213-092023 10.1186/1748-7188-6-26 10.1038/nmeth1130 10.1093/nar/gks1187 10.1002/jez.b.22483 10.1007/7651_2015_237 10.1038/nmeth.3485 10.1093/nar/gkv403 10.1093/database/bau080 10.1371/journal.pone.0066857 10.1186/1471-2229-13-33 10.1186/1471-2105-14-S14-S9 10.1093/nar/gkt1181 10.1105/tpc.113.113159 10.1093/nar/gkm1012 10.1016/j.molmed.2011.05.005 10.1093/nar/gkm368 10.1016/j.cell.2009.01.002 10.1073/pnas.0307969100 10.1038/ng.2764 10.1007/BF00337288 10.1126/science.1062961 10.1371/journal.pone.0011843 10.1093/nar/gkp803 10.1093/bioinformatics/btw070 10.1007/978-1-61779-427-8_2 10.1093/nar/gkx1141 10.1093/nar/gkt251 10.1109/5.726791 10.1186/1471-2105-10-328 10.1093/bioinformatics/btr144 10.1145/2975167.2975212 10.1093/nar/gkw1084 10.1371/journal.pone.0051673 10.1093/bioinformatics/btx210 10.1093/nar/gkw1008 10.3389/fgene.2014.00023 10.1016/S0092-8674(04)00045-5 10.1093/nar/gkx836 10.1093/bioinformatics/btw002 10.1093/nar/gkl243 10.1093/nar/gku598 10.1186/gb-2010-11-8-r90 10.1186/1471-2164-13-661 10.1080/15476286.2015.1068496 10.1371/journal.pone.0042390 10.1371/journal.pone.0151771 10.1093/bioinformatics/btv187 10.5772/60489 10.1371/journal.pbio.0000060 10.1186/gb-2009-10-3-r25 10.1093/nar/gkr604 10.1093/nar/gkv1221 10.1016/j.gpb.2015.07.001 10.1109/TCBB.2015.2510002 10.1093/nar/gkw1079 10.1152/physrev.00006.2010 10.1007/s00018-017-2469-1 10.1126/science.1073827 10.1016/S0092-8674(03)00759-1 10.1038/srep39684 10.1016/j.stem.2012.01.017 10.3390/genes8090234 10.1371/journal.pone.0174999 10.1155/2017/6037168 10.1371/journal.pone.0168392 10.1007/978-1-60327-005-2_4 10.1080/15476286.2016.1234658 10.1016/j.cell.2013.03.043 10.1534/genetics.116.196774 10.1007/978-1-62703-514-9_9 10.1093/nar/gkl321 10.1016/j.cub.2006.01.050 10.1038/ng2135 10.1093/nar/gki567 10.1038/35040556 10.1093/database/bay004 10.1109/TCBB.2016.2576459 10.1038/emboj.2011.3 10.3390/genes7120113 10.1093/bioinformatics/btw189 10.1016/j.cell.2007.06.028 10.1016/j.bbrc.2008.05.134 10.1104/pp.105.062943 10.1093/nar/gkx851 10.1093/nar/gkt1248 10.1186/1471-2164-10-366 10.1093/bioinformatics/btq329 10.1093/bioinformatics/btr430 10.1093/nar/gkq1019 10.1373/clinchem.2010.147405 10.1093/nar/gkt1156 10.1093/bioinformatics/btv380 10.1186/s12859-017-1772-z 10.1016/S0092-8674(01)00431-7 10.1093/nar/gkt1023 10.1093/nar/gkx318 10.1016/j.tplants.2016.09.003 10.1002/minf.201600141 10.1093/nar/gkn851 10.1093/nar/gks1168 10.1016/j.ygeno.2012.04.002 10.1093/nar/gkv1258 10.1016/j.jmb.2015.09.019 10.2174/138920209789177575 10.1093/nar/gkt290 10.1093/database/bau099 10.1093/nar/gkn714 10.1093/bioinformatics/btt014 10.1016/j.cell.2006.10.040 10.1093/bioinformatics/btp324 10.1261/rna.1560209 10.1093/bib/bbv033 10.1093/bioinformatics/bts615 10.1038/nature08170 10.1093/nar/gku1063 10.1101/gad.1074403 10.1093/bioinformatics/btx627 10.1126/science.1107130 10.1093/nar/gkw459 10.1016/j.ejca.2010.11.005 10.1261/rna.2387911 10.1038/nature12986 10.1093/nar/gkr319 10.1093/nar/gkw916 10.7554/eLife.05005 10.1186/s12859-016-1353-6 10.1038/ncomms6700 10.1186/1471-2164-12-507 10.1038/nature01957 10.1038/nature11928 10.1016/j.cell.2011.09.028 10.1073/pnas.242606799 10.1371/journal.pcbi.0040020 10.1186/1471-2105-15-275 10.1093/nar/gkt1028 10.1016/j.cell.2011.07.014 10.1007/BF00994018 10.1186/s12859-017-1561-8 10.1016/j.celrep.2015.02.047 10.1073/pnas.0403293101 10.1093/bioinformatics/btv632 10.1101/gr.7179508 10.1093/bioinformatics/btp336 10.1038/nrg2843 10.1093/nar/gkr247 10.1093/nar/gks1193 10.1038/onc.2010.487 10.1093/nar/gkx854 10.1186/1471-2105-11-476 10.1093/nar/gkr688 10.1186/1471-2105-10-S1-S35 10.1007/s00018-015-1922-2 10.1186/1471-2105-6-310 10.1186/s12859-017-1601-4 10.1093/nar/gkx1144 10.1093/nar/gkw965 10.1038/cr.2008.282 10.1093/nar/gkx1067 10.1073/pnas.0804549105 10.1093/bioinformatics/bts698 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2018. Published by Oxford University Press. 2018 The Author(s) 2018. Published by Oxford University Press. |
| Copyright_xml | – notice: The Author(s) 2018. Published by Oxford University Press. 2018 – notice: The Author(s) 2018. Published by Oxford University Press. |
| DBID | TOX AAYXX CITATION CGR CUY CVF ECM EIF NPM 7QO 7SC 8FD FR3 JQ2 K9. L7M L~C L~D P64 RC3 7X8 5PM |
| DOI | 10.1093/bib/bby054 |
| DatabaseName | Oxford Journals Open Access Collection CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed Biotechnology Research Abstracts Computer and Information Systems Abstracts Technology Research Database Engineering Research Database ProQuest Computer Science Collection ProQuest Health & Medical Complete (Alumni) Advanced Technologies Database with Aerospace Computer and Information Systems Abstracts Academic Computer and Information Systems Abstracts Professional Biotechnology and BioEngineering Abstracts Genetics Abstracts MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) Genetics Abstracts Biotechnology Research Abstracts Technology Research Database Computer and Information Systems Abstracts – Academic ProQuest Computer Science Collection Computer and Information Systems Abstracts ProQuest Health & Medical Complete (Alumni) Engineering Research Database Advanced Technologies Database with Aerospace Biotechnology and BioEngineering Abstracts Computer and Information Systems Abstracts Professional MEDLINE - Academic |
| DatabaseTitleList | Genetics Abstracts MEDLINE MEDLINE - Academic CrossRef |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 3 dbid: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1477-4054 |
| EndPage | 1852 |
| ExternalDocumentID | PMC7414524 29982332 10_1093_bib_bby054 10.1093/bib/bby054 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Review |
| GrantInformation_xml | – fundername: University of Macau Faculty of Health Sciences grantid: MYRG2016-00101-FHS – fundername: National Natural Science Foundation of China grantid: 61472158; 61572228; 61602207 funderid: 10.13039/501100001809 – fundername: Academy of Finland grantid: #62340 funderid: 10.13039/501100002341 – fundername: ; ; grantid: #62340 – fundername: ; grantid: MYRG2016-00101-FHS – fundername: ; ; grantid: 61472158; 61572228; 61602207 |
| GroupedDBID | --- -E4 .2P .I3 0R~ 1TH 23N 2WC 36B 4.4 48X 53G 5GY 5VS 6J9 70D 8VB AAGQS AAHBH AAIJN AAIMJ AAJKP AAJQQ AAMDB AAMVS AAOGV AAPQZ AAPXW AARHZ AAUQX AAVAP AAVLN ABDBF ABEJV ABEUO ABGNP ABIXL ABNKS ABPQP ABPTD ABQLI ABQTQ ABWST ABXVV ABXZS ABZBJ ACGFO ACGFS ACGOD ACIWK ACPRK ACUFI ACUHS ACUXJ ACYTK ADBBV ADEYI ADFTL ADGKP ADGZP ADHKW ADHZD ADOCK ADPDF ADQBN ADRDM ADRTK ADVEK ADYVW ADZTZ ADZXQ AECKG AEGPL AEGXH AEJOX AEKKA AEKSI AELWJ AEMDU AEMOZ AENEX AENZO AEPUE AETBJ AEWNT AFFZL AFGWE AFIYH AFOFC AFRAH AGINJ AGKEF AGQXC AGSYK AHMBA AHQJS AHXPO AIAGR AIJHB AJEEA AJEUX AKHUL AKVCP AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC ALXQX AMNDL ANAKG APIBT APWMN ARIXL AXUDD AYOIW AZVOD BAWUL BAYMD BEYMZ BHONS BQDIO BQUQU BSWAC BTQHN C1A C45 CAG CDBKE COF CS3 CZ4 DAKXR DIK DILTD DU5 D~K E3Z EAD EAP EAS EBA EBC EBD EBR EBS EBU EE~ EJD EMB EMK EMOBN EST ESX F5P F9B FHSFR FLIZI FLUFQ FOEOM FQBLK GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HW0 HZ~ IOX J21 JXSIZ K1G KBUDW KOP KSI KSN M-Z M49 MK~ ML0 N9A NGC NLBLG NMDNZ NOMLY NU- O0~ O9- OAWHX ODMLO OJQWA OK1 OVD OVEED P2P PAFKI PEELM PQQKQ Q1. Q5Y QWB RD5 RPM RUSNO RW1 RXO SV3 TEORI TH9 TJP TLC TOX TR2 TUS W8F WOQ X7H YAYTL YKOAZ YXANX ZKX ZL0 ~91 AAYXX AHGBF CITATION CGR CUY CVF ECM EIF NPM 7QO 7SC 8FD FR3 JQ2 K9. L7M L~C L~D P64 RC3 7X8 5PM |
| ID | FETCH-LOGICAL-c502t-e8c5b8b9a3b182283717bfbee14e12b781778774000d48cb51a18f44487a07c93 |
| IEDL.DBID | TOX |
| ISSN | 1467-5463 1477-4054 |
| IngestDate | Thu Aug 21 18:29:45 EDT 2025 Fri Jul 11 08:44:16 EDT 2025 Mon Jul 21 01:49:48 EDT 2025 Mon Jul 21 05:58:04 EDT 2025 Tue Jul 01 03:39:27 EDT 2025 Thu Apr 24 22:52:15 EDT 2025 Wed Apr 02 06:55:43 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 5 |
| Keywords | bibliometric miRNA text mining ranking bioinformatics tools |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com http://creativecommons.org/licenses/by-nc/4.0 The Author(s) 2018. Published by Oxford University Press. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c502t-e8c5b8b9a3b182283717bfbee14e12b781778774000d48cb51a18f44487a07c93 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Literature Review-3 ObjectType-Review-3 content type line 23 |
| OpenAccessLink | https://dx.doi.org/10.1093/bib/bby054 |
| PMID | 29982332 |
| PQID | 2955280767 |
| PQPubID | 26846 |
| PageCount | 17 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_7414524 proquest_miscellaneous_2067128777 proquest_journals_2955280767 pubmed_primary_29982332 crossref_citationtrail_10_1093_bib_bby054 crossref_primary_10_1093_bib_bby054 oup_primary_10_1093_bib_bby054 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2019-09-27 |
| PublicationDateYYYYMMDD | 2019-09-27 |
| PublicationDate_xml | – month: 09 year: 2019 text: 2019-09-27 day: 27 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England – name: Oxford |
| PublicationTitle | Briefings in bioinformatics |
| PublicationTitleAlternate | Brief Bioinform |
| PublicationYear | 2019 |
| Publisher | Oxford University Press Oxford Publishing Limited (England) |
| Publisher_xml | – name: Oxford University Press – name: Oxford Publishing Limited (England) |
| References | Yuan (2020080807563881500_bby054-B74) 2017; 45 An (2020080807563881500_bby054-B95) 2014; 15 Lall (2020080807563881500_bby054-B64) 2006; 16 Chou (2020080807563881500_bby054-B114) 2018; 46 Singh (2020080807563881500_bby054-B145) 2017; 74 Hinske (2020080807563881500_bby054-B47) 2014; 2014 Bortoluzzi (2020080807563881500_bby054-B177) 2011; 17 Kruger (2020080807563881500_bby054-B65) 2006; 34 Schwarz (2020080807563881500_bby054-B30) 2003; 115 Lorenz (2020080807563881500_bby054-B51) 2011; 6 Zeng (2020080807563881500_bby054-B175) 2016; 17 Cohen (2020080807563881500_bby054-B41) 2008; 4 Hackenberg (2020080807563881500_bby054-B56) 2011; 39 Bhattacharya (2020080807563881500_bby054-B108) 2014; 42 Weinstein (2020080807563881500_bby054-B79) 2013; 45 Wang (2020080807563881500_bby054-B109) 2016; 32 Dweep (2020080807563881500_bby054-B112) 2015; 12 Betel (2020080807563881500_bby054-B62) 2010; 11 Abbas (2020080807563881500_bby054-B133) 2016; 7 Salmena (2020080807563881500_bby054-B17) 2011; 146 Ahadi (2020080807563881500_bby054-B61) 2017; 45 Stark (2020080807563881500_bby054-B166) 2003; 1 Chou (2020080807563881500_bby054-B116) 2013; 14 Russo (2020080807563881500_bby054-B75) 2018; 46 Cesana (2020080807563881500_bby054-B72) 2011; 147 Shuang (2020080807563881500_bby054-B117) 2016; 13 Kohonen (2020080807563881500_bby054-B43) 1982; 43 Wang (2020080807563881500_bby054-B103) 2010; 38 Tay (2020080807563881500_bby054-B16) 2014; 505 Wu (2020080807563881500_bby054-B169) 2011; 12 Preusse (2020080807563881500_bby054-B158) 2015; 12 Lu (2020080807563881500_bby054-B124) 2012; 7 Wang (2020080807563881500_bby054-B98) 2009; 10 Zhang (2020080807563881500_bby054-B142) 2017; 2017 Yang (2020080807563881500_bby054-B90) 2011; 27 Csardi (2020080807563881500_bby054-B171) 2006; 1695 Li (2020080807563881500_bby054-B81) 2009; 25 Chung (2020080807563881500_bby054-B150) 2017; 45 Sinha (2020080807563881500_bby054-B153) 2017; 36 Lima (2020080807563881500_bby054-B13) 2011; 47 Xue (2020080807563881500_bby054-B167) 2016; 11 Liu (2020080807563881500_bby054-B32) 2004; 101 Cho (2020080807563881500_bby054-B110) 2012; 41 He (2020080807563881500_bby054-B138) 2012; 7 Pan (2020080807563881500_bby054-B139) 2017; 18 Oh (2020080807563881500_bby054-B118) 2017; 12 Xie (2020080807563881500_bby054-B121) 2013; 29 Chen (2020080807563881500_bby054-B21) 2008; 18 Okamura (2020080807563881500_bby054-B4) 2007; 130 Lim (2020080807563881500_bby054-B53) 2003; 17 Mapleson (2020080807563881500_bby054-B93) 2013; 320 Szczesniak (2020080807563881500_bby054-B123) 2014; 42 Li (2020080807563881500_bby054-B73) 2014; 42 Pantano (2020080807563881500_bby054-B127) 2016; 32 Pasquinelli (2020080807563881500_bby054-B24) 2000; 408 Chou (2020080807563881500_bby054-B68) 2016; 44 Winter (2020080807563881500_bby054-B178) 2013; 41 Liu (2020080807563881500_bby054-B100) 2012; 13 Sayed (2020080807563881500_bby054-B18) 2011; 91 Weber (2020080807563881500_bby054-B19) 2010; 56 Xie (2020080807563881500_bby054-B8) 2005; 138 Liu (2020080807563881500_bby054-B49) 2017; 45 Agarwal (2020080807563881500_bby054-B63) 2015; 4 Hutvagner (2020080807563881500_bby054-B29) 2002; 297 Kulski (2020080807563881500_bby054-B34) 2016 Keerthikumar (2020080807563881500_bby054-B76) 2016; 428 Jha (2020080807563881500_bby054-B92) 2013; 8 Mhuantong (2020080807563881500_bby054-B87) 2009; 10 Yoon (2020080807563881500_bby054-B42) 2009; 10 Meyer (2020080807563881500_bby054-B135) 2008; 25 Jiang (2020080807563881500_bby054-B84) 2007; 35 Liu (2020080807563881500_bby054-B120) 2013; 29 Nawrocki (2020080807563881500_bby054-B46) 2015; 43 Han (2020080807563881500_bby054-B9) 2004; 101 Fehlmann (2020080807563881500_bby054-B152) 2016; 13 Huang (2020080807563881500_bby054-B107) 2007; 4 Sablok (2020080807563881500_bby054-B99) 2013; 587 Kadri (2020080807563881500_bby054-B88) 2009; 10 Yang (2020080807563881500_bby054-B128) 2017; 45 Alon (2020080807563881500_bby054-B130) 2013; 1038 Kertesz (2020080807563881500_bby054-B66) 2007; 39 Boutet (2020080807563881500_bby054-B173) 2012; 10 Jiang (2020080807563881500_bby054-B119) 2009; 37 Bao (2020080807563881500_bby054-B57) 2016; 17 Ruby (2020080807563881500_bby054-B35) 2006; 127 Vitsios (2020080807563881500_bby054-B161) 2015; 31 Georgakilas (2020080807563881500_bby054-B101) 2014; 5 Zhao (2020080807563881500_bby054-B164) 2017; 18 Fromm (2020080807563881500_bby054-B159) 2015; 49 Vlachos (2020080807563881500_bby054-B126) 2015; 43 Kim (2020080807563881500_bby054-B7) 2011; 30 Yu (2020080807563881500_bby054-B12) 2005; 307 Paicu (2020080807563881500_bby054-B86) 2017; 33 Chan (2020080807563881500_bby054-B50) 2016; 1375 LeCun (2020080807563881500_bby054-B44) 1998; 86 Lee (2020080807563881500_bby054-B140) 2016 Pan (2020080807563881500_bby054-B157) 2017; 2017 Lee (2020080807563881500_bby054-B23) 1993; 75 (2020080807563881500_bby054-B125) 2017; 45 Preusse (2020080807563881500_bby054-B129) 2016; 11 Memczak (2020080807563881500_bby054-B71) 2013; 495 Ho (2020080807563881500_bby054-B38) 1995 Drucker (2020080807563881500_bby054-B40) 1997 Chen (2020080807563881500_bby054-B134) 2017 Achkar (2020080807563881500_bby054-B6) 2016; 21 Li (2020080807563881500_bby054-B15) 2015; 13 Gkirtzou (2020080807563881500_bby054-B89) 2010; 5 Joshi (2020080807563881500_bby054-B48) 2012; 99 Li (2020080807563881500_bby054-B165) 2009; 25 Tav (2020080807563881500_bby054-B54) 2016; 44 An (2020080807563881500_bby054-B91) 2013; 41 Grishok (2020080807563881500_bby054-B25) 2001; 106 Ahmed (2020080807563881500_bby054-B58) 2013; 14 Backes (2020080807563881500_bby054-B179) 2018; 46 Rogers (2020080807563881500_bby054-B10) 2013; 25 Chen (2020080807563881500_bby054-B45) 2018; 2018 Zhou (2020080807563881500_bby054-B122) 2017; 45 Lukasik (2020080807563881500_bby054-B148) 2016; 32 Bartel (2020080807563881500_bby054-B1) 2004; 116 Bellaousov (2020080807563881500_bby054-B52) 2013; 41 Mitchell (2020080807563881500_bby054-B20) 2008; 105 Liu (2020080807563881500_bby054-B137) 2010; 11 Dai (2020080807563881500_bby054-B115) 2011; 39 Akhtar (2020080807563881500_bby054-B141) 2016; 44 Wen (2020080807563881500_bby054-B60) 2011; 17 Tyagi (2020080807563881500_bby054-B85) 2008; 372 Amsel (2020080807563881500_bby054-B163) 2017; 18 Kozomara (2020080807563881500_bby054-B22) 2014; 42 Leinonen (2020080807563881500_bby054-B78) 2011; 39 Friedlander (2020080807563881500_bby054-B55) 2012; 40 Zhang (2020080807563881500_bby054-B70) 2013; 13 Kallio (2020080807563881500_bby054-B147) 2011; 12 Bortolomeazzi (2020080807563881500_bby054-B131) 2017 Van Peer (2020080807563881500_bby054-B156) 2014; 2014 Hsu (2020080807563881500_bby054-B146) 2008; 36 Blazie (2020080807563881500_bby054-B174) 2017; 206 Rao (2020080807563881500_bby054-B14) 2011; 30 Cortes (2020080807563881500_bby054-B39) 1995; 20 Aldridge (2020080807563881500_bby054-B33) 2012; 822 Vitsios (2020080807563881500_bby054-B97) 2017; 45 Loher (2020080807563881500_bby054-B106) 2012; 28 Li (2020080807563881500_bby054-B69) 2014; 42 Bartel (2020080807563881500_bby054-B3) 2009; 136 Lee (2020080807563881500_bby054-B28) 2003; 425 Heikkinen (2020080807563881500_bby054-B111) 2011; 27 Haunsberger (2020080807563881500_bby054-B149) 2017; 33 Karagkouni (2020080807563881500_bby054-B105) 2018; 46 Peterson (2020080807563881500_bby054-B143) 2014; 5 Zhang (2020080807563881500_bby054-B151) 2016; 32 Xue (2020080807563881500_bby054-B83) 2005; 6 Stegmayer (2020080807563881500_bby054-B96) 2017; 14 Calin (2020080807563881500_bby054-B27) 2002; 99 Langmead (2020080807563881500_bby054-B80) 2009; 10 Yang (2020080807563881500_bby054-B162) 2017; 8 Helwak (2020080807563881500_bby054-B37) 2013; 153 Hutvagner (2020080807563881500_bby054-B26) 2001; 293 Afonso-Grunz (2020080807563881500_bby054-B144) 2015; 72 Sun (2020080807563881500_bby054-B172) 2009; 15 Zhou (2020080807563881500_bby054-B11) 2015; 10 Alon (2020080807563881500_bby054-B160) 2015; 31 Bottini (2020080807563881500_bby054-B132) 2017 2020080807563881500_bby054-B136 Krol (2020080807563881500_bby054-B2) 2010; 11 Fahlgren (2020080807563881500_bby054-B104) 2010; 592 Gruber (2020080807563881500_bby054-B82) 2010 Altuvia (2020080807563881500_bby054-B5) 2005; 33 Barrett (2020080807563881500_bby054-B77) 2013; 41 Xiao (2020080807563881500_bby054-B67) 2009; 37 Bottini (2020080807563881500_bby054-B59) 2017; 45 Tokar (2020080807563881500_bby054-B113) 2018; 46 Chien (2020080807563881500_bby054-B102) 2011; 39 Nam (2020080807563881500_bby054-B170) 2006; 34 Morin (2020080807563881500_bby054-B31) 2008; 18 Wong (2020080807563881500_bby054-B155) 2018; 34 Nalluri (2020080807563881500_bby054-B154) 2017; 7 Hansen (2020080807563881500_bby054-B94) 2014; 42 Chi (2020080807563881500_bby054-B36) 2009; 460 Mathelier (2020080807563881500_bby054-B168) 2010; 26 Baldassarre (2020080807563881500_bby054-B176) 2017; 8 |
| References_xml | – volume: 45 start-page: e42. issue: 6 year: 2017 ident: 2020080807563881500_bby054-B61 article-title: miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1185 – volume: 587 start-page: 2629 issue: 16 year: 2013 ident: 2020080807563881500_bby054-B99 article-title: isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets publication-title: FEBS Lett doi: 10.1016/j.febslet.2013.06.047 – volume: 12 start-page: 107. year: 2011 ident: 2020080807563881500_bby054-B169 article-title: MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-107 – volume: 75 start-page: 843 issue: 5 year: 1993 ident: 2020080807563881500_bby054-B23 article-title: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 publication-title: Cell doi: 10.1016/0092-8674(93)90529-Y – volume: 45 start-page: e71 year: 2017 ident: 2020080807563881500_bby054-B59 article-title: From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data publication-title: Nucleic Acids Res – volume: 33 start-page: 592 year: 2017 ident: 2020080807563881500_bby054-B149 article-title: miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw660 – volume: 14 start-page: S2 issue: Suppl 1) year: 2013 ident: 2020080807563881500_bby054-B116 article-title: A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing publication-title: BMC Genomics doi: 10.1186/1471-2164-14-S1-S2 – volume: 49 start-page: 213 year: 2015 ident: 2020080807563881500_bby054-B159 article-title: A uniform system for the annotation of vertebrate microRNA genes and the evolution of the human microRNAome publication-title: Annu Rev Genet doi: 10.1146/annurev-genet-120213-092023 – volume: 6 start-page: 26. year: 2011 ident: 2020080807563881500_bby054-B51 article-title: ViennaRNA package 2.0 publication-title: Algorithms Mol Biol doi: 10.1186/1748-7188-6-26 – volume: 4 start-page: 1045 issue: 12 year: 2007 ident: 2020080807563881500_bby054-B107 article-title: Using expression profiling data to identify human microRNA targets publication-title: Nat Methods doi: 10.1038/nmeth1130 – volume: 41 start-page: 727 issue: 2 year: 2013 ident: 2020080807563881500_bby054-B91 article-title: miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data publication-title: Nucleic Acids Res doi: 10.1093/nar/gks1187 – volume: 320 start-page: 47 issue: 1 year: 2013 ident: 2020080807563881500_bby054-B93 article-title: MirPlex: a tool for identifying miRNAs in high-throughput sRNA datasets without a genome publication-title: J Exp Zool B Mol Dev Evol doi: 10.1002/jez.b.22483 – volume: 1375 start-page: 75 year: 2016 ident: 2020080807563881500_bby054-B50 article-title: MetaMirClust: discovery and exploration of evolutionarily conserved miRNA clusters publication-title: Methods Mol Biol doi: 10.1007/7651_2015_237 – volume: 12 start-page: 697. issue: 8 year: 2015 ident: 2020080807563881500_bby054-B112 article-title: miRWalk2.0: a comprehensive atlas of microRNA-target interactions publication-title: Nat Methods doi: 10.1038/nmeth.3485 – volume: 43 start-page: W460 issue: W1 year: 2015 ident: 2020080807563881500_bby054-B126 article-title: DIANA-miRPath v3.0: deciphering microRNA function with experimental support publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv403 – volume: 2014 start-page: bau080 year: 2014 ident: 2020080807563881500_bby054-B156 article-title: miRBase Tracker: keeping track of microRNA annotation changes publication-title: Database doi: 10.1093/database/bau080 – volume: 8 start-page: e66857. issue: 6 year: 2013 ident: 2020080807563881500_bby054-B92 article-title: miReader: discovering Novel miRNAs in species without sequenced genome publication-title: PLoS One doi: 10.1371/journal.pone.0066857 – volume: 13 start-page: 33 issue: 1 year: 2013 ident: 2020080807563881500_bby054-B70 article-title: PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress publication-title: BMC Plant Biol doi: 10.1186/1471-2229-13-33 – volume: 14 start-page: S9. issue: Suppl 14 year: 2013 ident: 2020080807563881500_bby054-B58 article-title: PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-S14-S9 – volume: 42 start-page: D68 issue: D1 year: 2014 ident: 2020080807563881500_bby054-B22 article-title: miRBase: annotating high confidence microRNAs using deep sequencing data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1181 – volume: 25 start-page: 2383 issue: 7 year: 2013 ident: 2020080807563881500_bby054-B10 article-title: Biogenesis, turnover, and mode of action of plant microRNAs publication-title: Plant Cell doi: 10.1105/tpc.113.113159 – volume: 36 start-page: D165 year: 2008 ident: 2020080807563881500_bby054-B146 article-title: miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm1012 – volume: 17 start-page: 473 issue: 9 year: 2011 ident: 2020080807563881500_bby054-B177 article-title: MicroRNA-offset RNAs (moRNAs): by-product spectators or functional players? publication-title: Trends Mol Med doi: 10.1016/j.molmed.2011.05.005 – volume: 35 start-page: W339 year: 2007 ident: 2020080807563881500_bby054-B84 article-title: MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm368 – start-page: 69 year: 2010 ident: 2020080807563881500_bby054-B82 article-title: RNAz 2.0: improved noncoding RNA detection publication-title: Pac Symp Biocomput – volume: 136 start-page: 215 issue: 2 year: 2009 ident: 2020080807563881500_bby054-B3 article-title: MicroRNAs: target recognition and regulatory functions publication-title: Cell doi: 10.1016/j.cell.2009.01.002 – volume: 101 start-page: 1093 issue: 4 year: 2004 ident: 2020080807563881500_bby054-B9 article-title: The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0307969100 – volume: 45 start-page: 1113 issue: 10 year: 2013 ident: 2020080807563881500_bby054-B79 article-title: The cancer genome atlas pan-cancer analysis project publication-title: Nat Genet doi: 10.1038/ng.2764 – volume: 43 start-page: 59 issue: 1 year: 1982 ident: 2020080807563881500_bby054-B43 article-title: Self-organized formation of topologically correct feature maps publication-title: Biol Cybernet doi: 10.1007/BF00337288 – volume: 293 start-page: 834 issue: 5531 year: 2001 ident: 2020080807563881500_bby054-B26 article-title: A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA publication-title: Science doi: 10.1126/science.1062961 – volume: 5 start-page: e11843 issue: 8 year: 2010 ident: 2020080807563881500_bby054-B89 article-title: MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors publication-title: PLoS One doi: 10.1371/journal.pone.0011843 – volume: 38 start-page: D119 issue: Suppl 1 year: 2010 ident: 2020080807563881500_bby054-B103 article-title: TransmiR: a transcription factor-microRNA regulation database publication-title: Nucleic Acids Res doi: 10.1093/nar/gkp803 – volume: 32 start-page: 2069 issue: 13 year: 2016 ident: 2020080807563881500_bby054-B151 article-title: IsomiR Bank: a research resource for tracking IsomiRs publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw070 – volume: 822 start-page: 19 year: 2012 ident: 2020080807563881500_bby054-B33 article-title: Introduction to miRNA profiling technologies and cross-platform comparison publication-title: Methods Mol Biol doi: 10.1007/978-1-61779-427-8_2 – volume: 46 start-page: D239 issue: D1 year: 2018 ident: 2020080807563881500_bby054-B105 article-title: DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx1141 – volume: 41 start-page: 5503 issue: 10 year: 2013 ident: 2020080807563881500_bby054-B178 article-title: Loop-miRs: active microRNAs generated from single-stranded loop regions publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt251 – volume: 86 start-page: 2278 issue: 11 year: 1998 ident: 2020080807563881500_bby054-B44 article-title: Gradient-based learning applied to document recognition publication-title: Proc IEEE doi: 10.1109/5.726791 – volume: 10 start-page: 328. year: 2009 ident: 2020080807563881500_bby054-B98 article-title: miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression publication-title: Bmc Bioinformatics doi: 10.1186/1471-2105-10-328 – volume: 27 start-page: 1247 issue: 9 year: 2011 ident: 2020080807563881500_bby054-B111 article-title: Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr144 – start-page: 434 volume-title: Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics year: 2016 ident: 2020080807563881500_bby054-B140 doi: 10.1145/2975167.2975212 – volume: 45 start-page: D925 issue: D1 year: 2017 ident: 2020080807563881500_bby054-B150 article-title: YM500v3: a database for small RNA sequencing in human cancer research publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1084 – volume: 7 start-page: e51673 issue: 12 year: 2012 ident: 2020080807563881500_bby054-B138 article-title: MiRmat: mature microRNA sequence prediction publication-title: PLoS One doi: 10.1371/journal.pone.0051673 – volume: 33 start-page: 2446 issue: 16 year: 2017 ident: 2020080807563881500_bby054-B86 article-title: miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx210 – volume: 45 start-page: D128 issue: D1 year: 2017 ident: 2020080807563881500_bby054-B125 article-title: RNAcentral: a comprehensive database of non-coding RNA sequences publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1008 – volume: 5 start-page: 23. year: 2014 ident: 2020080807563881500_bby054-B143 article-title: Common features of microRNA target prediction tools publication-title: Front Genet doi: 10.3389/fgene.2014.00023 – volume: 116 start-page: 281 issue: 2 year: 2004 ident: 2020080807563881500_bby054-B1 article-title: MicroRNAs: genomics, biogenesis, mechanism, and function publication-title: Cell doi: 10.1016/S0092-8674(04)00045-5 – volume: 45 start-page: e177 issue: 21 year: 2017 ident: 2020080807563881500_bby054-B97 article-title: Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx836 – volume: 32 start-page: 1316 issue: 9 year: 2016 ident: 2020080807563881500_bby054-B109 article-title: Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw002 – volume: 2017 start-page: 9139504. year: 2017 ident: 2020080807563881500_bby054-B142 article-title: A review on recent computational methods for predicting noncoding RNAs publication-title: Biomed Res Int – volume: 34 start-page: W451 year: 2006 ident: 2020080807563881500_bby054-B65 article-title: RNAhybrid: microRNA target prediction easy, fast and flexible publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl243 – volume: 42 start-page: e124 issue: 16 year: 2014 ident: 2020080807563881500_bby054-B94 article-title: miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/gku598 – volume: 11 start-page: R90 issue: 8 year: 2010 ident: 2020080807563881500_bby054-B62 article-title: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites publication-title: Genome Biol doi: 10.1186/gb-2010-11-8-r90 – volume: 13 start-page: 661 issue: 1 year: 2012 ident: 2020080807563881500_bby054-B100 article-title: MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs publication-title: BMC Genomics doi: 10.1186/1471-2164-13-661 – volume: 12 start-page: 998 issue: 9 year: 2015 ident: 2020080807563881500_bby054-B158 article-title: SimiRa: a tool to identify coregulation between microRNAs and RNA-binding proteins publication-title: RNA Biol doi: 10.1080/15476286.2015.1068496 – volume: 7 start-page: e42390 issue: 8 year: 2012 ident: 2020080807563881500_bby054-B124 article-title: miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets publication-title: PLoS One doi: 10.1371/journal.pone.0042390 – volume: 11 start-page: e0151771. issue: 3 year: 2016 ident: 2020080807563881500_bby054-B129 article-title: miTALOS v2: analyzing tissue specific microRNA function publication-title: PLoS One doi: 10.1371/journal.pone.0151771 – volume: 31 start-page: 2568 issue: 15 year: 2015 ident: 2020080807563881500_bby054-B160 article-title: DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv187 – volume-title: Next Generation Sequencing-Advances, Applications and Challenges year: 2016 ident: 2020080807563881500_bby054-B34 doi: 10.5772/60489 – volume: 1 start-page: E60 issue: 3 year: 2003 ident: 2020080807563881500_bby054-B166 article-title: Identification of Drosophila MicroRNA targets publication-title: PLoS Biol doi: 10.1371/journal.pbio.0000060 – ident: 2020080807563881500_bby054-B136 – volume: 10 start-page: R25 issue: 3 year: 2009 ident: 2020080807563881500_bby054-B80 article-title: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome publication-title: Genome Biol doi: 10.1186/gb-2009-10-3-r25 – volume: 39 start-page: 9345 issue: 21 year: 2011 ident: 2020080807563881500_bby054-B102 article-title: Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr604 – volume: 44 start-page: 24 issue: 1 year: 2016 ident: 2020080807563881500_bby054-B141 article-title: Bioinformatic tools for microRNA dissection publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv1221 – volume: 13 start-page: 234 issue: 4 year: 2015 ident: 2020080807563881500_bby054-B15 article-title: MicroRNAs regulating signaling pathways: potential biomarkers in systemic sclerosis publication-title: Genomics Proteomics Bioinformatics doi: 10.1016/j.gpb.2015.07.001 – volume: 13 start-page: 1161 issue: 6 year: 2016 ident: 2020080807563881500_bby054-B117 article-title: MiRTDL: a deep learning approach for miRNA target prediction publication-title: IEEE/ACM Trans Comput Biol Bioinform doi: 10.1109/TCBB.2015.2510002 – year: 2017 ident: 2020080807563881500_bby054-B131 article-title: A survey of software tools for microRNA discovery and characterization using RNA-seq publication-title: Brief Bioinform – volume: 45 start-page: D812 issue: D1 year: 2017 ident: 2020080807563881500_bby054-B128 article-title: dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw1079 – volume: 91 start-page: 827 issue: 3 year: 2011 ident: 2020080807563881500_bby054-B18 article-title: MicroRNAs in development and disease publication-title: Physiol Rev doi: 10.1152/physrev.00006.2010 – volume: 74 start-page: 2239 issue: 12 year: 2017 ident: 2020080807563881500_bby054-B145 article-title: miRNAs target databases: developmental methods and target identification techniques with functional annotations publication-title: Cell Mol Life Sci doi: 10.1007/s00018-017-2469-1 – volume: 297 start-page: 2056 issue: 5589 year: 2002 ident: 2020080807563881500_bby054-B29 article-title: A microRNA in a multiple-turnover RNAi enzyme complex publication-title: Science doi: 10.1126/science.1073827 – volume: 115 start-page: 199 issue: 2 year: 2003 ident: 2020080807563881500_bby054-B30 article-title: Asymmetry in the assembly of the RNAi enzyme complex publication-title: Cell doi: 10.1016/S0092-8674(03)00759-1 – volume: 7 start-page: 39684. year: 2017 ident: 2020080807563881500_bby054-B154 article-title: miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures publication-title: Sci Rep doi: 10.1038/srep39684 – volume: 10 start-page: 327 issue: 3 year: 2012 ident: 2020080807563881500_bby054-B173 article-title: Alternative polyadenylation mediates microRNA regulation of muscle stem cell function publication-title: Cell Stem Cell doi: 10.1016/j.stem.2012.01.017 – volume: 8 start-page: 234 issue: 9 year: 2017 ident: 2020080807563881500_bby054-B176 article-title: Circulating microRNAs and bioinformatics tools to discover novel diagnostic biomarkers of pediatric diseases publication-title: Genes doi: 10.3390/genes8090234 – volume: 12 start-page: e0174999 issue: 3 year: 2017 ident: 2020080807563881500_bby054-B118 article-title: Literature-based condition-specific miRNA-mRNA target prediction publication-title: PLoS One doi: 10.1371/journal.pone.0174999 – volume: 2017 start-page: 6037168. year: 2017 ident: 2020080807563881500_bby054-B157 article-title: Visual display of 5p-arm and 3p-arm miRNA expression with a mobile application publication-title: Biomed Res Int doi: 10.1155/2017/6037168 – volume: 11 start-page: e0168392. issue: 12 year: 2016 ident: 2020080807563881500_bby054-B167 article-title: Integrated strategy improves the prediction accuracy of miRNA in large dataset publication-title: Plos One doi: 10.1371/journal.pone.0168392 – volume: 592 start-page: 51 year: 2010 ident: 2020080807563881500_bby054-B104 article-title: miRNA target prediction in plants publication-title: Methods Mol Biol doi: 10.1007/978-1-60327-005-2_4 – volume: 13 start-page: 1084 issue: 11 year: 2016 ident: 2020080807563881500_bby054-B152 article-title: Distribution of microRNA biomarker candidates in solid tissues and body fluids publication-title: RNA Biol doi: 10.1080/15476286.2016.1234658 – volume: 153 start-page: 654 issue: 3 year: 2013 ident: 2020080807563881500_bby054-B37 article-title: Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding publication-title: Cell doi: 10.1016/j.cell.2013.03.043 – volume: 206 start-page: 757 issue: 2 year: 2017 ident: 2020080807563881500_bby054-B174 article-title: Alternative polyadenylation directs tissue-specific miRNA targeting in Caenorhabditis elegans somatic tissues publication-title: Genetics doi: 10.1534/genetics.116.196774 – volume: 1038 start-page: 159 year: 2013 ident: 2020080807563881500_bby054-B130 article-title: Identifying RNA editing sites in miRNAs by deep sequencing publication-title: Methods Mol Biol doi: 10.1007/978-1-62703-514-9_9 – volume: 34 start-page: W455 year: 2006 ident: 2020080807563881500_bby054-B170 article-title: ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/gkl321 – year: 1995 ident: 2020080807563881500_bby054-B38 – volume: 16 start-page: 460 issue: 5 year: 2006 ident: 2020080807563881500_bby054-B64 article-title: A genome-wide map of conserved microRNA targets in C. elegans publication-title: Curr Biol doi: 10.1016/j.cub.2006.01.050 – volume: 39 start-page: 1278 issue: 10 year: 2007 ident: 2020080807563881500_bby054-B66 article-title: The role of site accessibility in microRNA target recognition publication-title: Nat Genet doi: 10.1038/ng2135 – volume: 25 start-page: 1 issue: 5 year: 2008 ident: 2020080807563881500_bby054-B135 article-title: Text mining infrastructure in R publication-title: J Stat Softw – volume: 33 start-page: 2697 issue: 8 year: 2005 ident: 2020080807563881500_bby054-B5 article-title: Clustering and conservation patterns of human microRNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/gki567 – volume: 408 start-page: 86 issue: 6808 year: 2000 ident: 2020080807563881500_bby054-B24 article-title: Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA publication-title: Nature doi: 10.1038/35040556 – volume: 2018 start-page: bay004 year: 2018 ident: 2020080807563881500_bby054-B45 article-title: miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal publication-title: Database doi: 10.1093/database/bay004 – volume: 8 start-page: 322. year: 2017 ident: 2020080807563881500_bby054-B162 article-title: isomiR2Function: an integrated workflow for identifying MicroRNA variants in plants publication-title: Front Plant Sci – volume: 14 start-page: 1316 issue: 6 year: 2017 ident: 2020080807563881500_bby054-B96 article-title: High class-imbalance in pre-miRNA prediction: a novel approach based on deepSOM publication-title: IEEE/ACM Trans Comput Biol Bioinform doi: 10.1109/TCBB.2016.2576459 – volume: 30 start-page: 814 issue: 5 year: 2011 ident: 2020080807563881500_bby054-B7 article-title: The role of Mediator in small and long noncoding RNA production in Arabidopsis thaliana publication-title: EMBO J doi: 10.1038/emboj.2011.3 – volume: 7 start-page: 113 issue: 12 year: 2016 ident: 2020080807563881500_bby054-B133 article-title: A review of computational methods for finding non-coding RNA genes publication-title: Genes doi: 10.3390/genes7120113 – volume: 32 start-page: 2722 issue: 17 year: 2016 ident: 2020080807563881500_bby054-B148 article-title: Tools4miRs—one place to gather all the tools for miRNA analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/btw189 – volume: 130 start-page: 89 issue: 1 year: 2007 ident: 2020080807563881500_bby054-B4 article-title: The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila publication-title: Cell doi: 10.1016/j.cell.2007.06.028 – volume: 372 start-page: 831 issue: 4 year: 2008 ident: 2020080807563881500_bby054-B85 article-title: CID-miRNA: a web server for prediction of novel miRNA precursors in human genome publication-title: Biochem Biophys Res Commun doi: 10.1016/j.bbrc.2008.05.134 – volume: 138 start-page: 2145 issue: 4 year: 2005 ident: 2020080807563881500_bby054-B8 article-title: Expression of Arabidopsis MIRNA genes publication-title: Plant Physiol doi: 10.1104/pp.105.062943 – volume: 46 start-page: D160 year: 2018 ident: 2020080807563881500_bby054-B179 article-title: miRCarta: a central repository for collecting miRNA candidates publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx851 – volume: 42 start-page: D92 issue: D1 year: 2014 ident: 2020080807563881500_bby054-B73 article-title: starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1248 – volume: 10 start-page: 366. year: 2009 ident: 2020080807563881500_bby054-B87 article-title: MicroPC (microPC): a comprehensive resource for predicting and comparing plant microRNAs publication-title: BMC Genomics doi: 10.1186/1471-2164-10-366 – volume: 26 start-page: 2226 issue: 18 year: 2010 ident: 2020080807563881500_bby054-B168 article-title: MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq329 – volume: 27 start-page: 2614 issue: 18 year: 2011 ident: 2020080807563881500_bby054-B90 article-title: miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr430 – volume: 39 start-page: D19 year: 2011 ident: 2020080807563881500_bby054-B78 article-title: The sequence read archive publication-title: Nucleic Acids Res doi: 10.1093/nar/gkq1019 – volume: 56 start-page: 1733 issue: 11 year: 2010 ident: 2020080807563881500_bby054-B19 article-title: The microRNA spectrum in 12 body fluids publication-title: Clin Chem doi: 10.1373/clinchem.2010.147405 – volume: 42 start-page: D74 year: 2014 ident: 2020080807563881500_bby054-B123 article-title: miRNEST 2.0: a database of plant and animal microRNAs publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1156 – volume: 31 start-page: 3365 issue: 20 year: 2015 ident: 2020080807563881500_bby054-B161 article-title: Chimira: analysis of small RNA sequencing data and microRNA modifications publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv380 – volume: 18 start-page: 359. issue: 1 year: 2017 ident: 2020080807563881500_bby054-B163 article-title: Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum publication-title: Bmc Bioinformatics doi: 10.1186/s12859-017-1772-z – volume: 106 start-page: 23 issue: 1 year: 2001 ident: 2020080807563881500_bby054-B25 article-title: Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing publication-title: Cell doi: 10.1016/S0092-8674(01)00431-7 – volume: 42 start-page: D1070 issue: D1 year: 2014 ident: 2020080807563881500_bby054-B69 article-title: HMDD v2.0: a database for experimentally supported human microRNA and disease associations publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1023 – volume: 45 start-page: e121 issue: 13 year: 2017 ident: 2020080807563881500_bby054-B49 article-title: Identification of active miRNA promoters from nuclear run-on RNA sequencing publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx318 – volume: 21 start-page: 1034 issue: 12 year: 2016 ident: 2020080807563881500_bby054-B6 article-title: miRNA biogenesis: a dynamic pathway publication-title: Trends Plant Sci doi: 10.1016/j.tplants.2016.09.003 – volume: 36 start-page: 1600141. issue: 7 year: 2017 ident: 2020080807563881500_bby054-B153 article-title: ParSel: parallel selection of micro-RNAs for survival classification in cancers publication-title: Mol Inform doi: 10.1002/minf.201600141 – volume: 37 start-page: D105 year: 2009 ident: 2020080807563881500_bby054-B67 article-title: miRecords: an integrated resource for microRNA-target interactions publication-title: Nucleic Acids Res doi: 10.1093/nar/gkn851 – volume: 41 start-page: D252 issue: D1 year: 2012 ident: 2020080807563881500_bby054-B110 article-title: MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting publication-title: Nucleic Acids Res doi: 10.1093/nar/gks1168 – year: 2017 ident: 2020080807563881500_bby054-B134 article-title: MicroRNAs and complex diseases: from experimental results to computational models publication-title: Brief Bioinform – volume: 99 start-page: 370 issue: 6 year: 2012 ident: 2020080807563881500_bby054-B48 article-title: Identification of mirtrons in rice using MirtronPred: a tool for predicting plant mirtrons publication-title: Genomics doi: 10.1016/j.ygeno.2012.04.002 – volume: 44 start-page: D239 issue: D1 year: 2016 ident: 2020080807563881500_bby054-B68 article-title: miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database publication-title: Nucleic Acids Res doi: 10.1093/nar/gkv1258 – volume: 428 start-page: 688 issue: 4 year: 2016 ident: 2020080807563881500_bby054-B76 article-title: ExoCarta: a web-based compendium of exosomal cargo publication-title: J Mol Biol doi: 10.1016/j.jmb.2015.09.019 – volume: 10 start-page: 402 issue: 6 year: 2009 ident: 2020080807563881500_bby054-B42 article-title: Hidden Markov models and their applications in biological sequence analysis publication-title: Curr Genomics doi: 10.2174/138920209789177575 – volume: 41 start-page: W471 year: 2013 ident: 2020080807563881500_bby054-B52 article-title: RNAstructure: web servers for RNA secondary structure prediction and analysis publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt290 – volume: 2014 start-page: bau099 year: 2014 ident: 2020080807563881500_bby054-B47 article-title: miRIAD-integrating microRNA inter- and intragenic data publication-title: Database doi: 10.1093/database/bau099 – volume: 37 start-page: D98 year: 2009 ident: 2020080807563881500_bby054-B119 article-title: miR2Disease: a manually curated database for microRNA deregulation in human disease publication-title: Nucleic Acids Res doi: 10.1093/nar/gkn714 – volume: 29 start-page: 638 issue: 5 year: 2013 ident: 2020080807563881500_bby054-B121 article-title: miRCancer: a microRNA-cancer association database constructed by text mining on literature publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt014 – volume: 127 start-page: 1193 issue: 6 year: 2006 ident: 2020080807563881500_bby054-B35 article-title: Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans publication-title: Cell doi: 10.1016/j.cell.2006.10.040 – start-page: 155 year: 1997 ident: 2020080807563881500_bby054-B40 article-title: Support vector regression machines publication-title: Advances in Neural Information Processing Systems – volume: 25 start-page: 1754 issue: 14 year: 2009 ident: 2020080807563881500_bby054-B165 article-title: Fast and accurate short read alignment with Burrows-Wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 15 start-page: 1640 issue: 9 year: 2009 ident: 2020080807563881500_bby054-B172 article-title: SNPs in human miRNA genes affect biogenesis and function publication-title: RNA doi: 10.1261/rna.1560209 – volume: 17 start-page: 193 issue: 2 year: 2016 ident: 2020080807563881500_bby054-B175 article-title: Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks publication-title: Brief Bioinform doi: 10.1093/bib/bbv033 – volume: 28 start-page: 3322 issue: 24 year: 2012 ident: 2020080807563881500_bby054-B106 article-title: Interactive exploration of RNA22 microRNA target predictions publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts615 – volume: 460 start-page: 479 issue: 7254 year: 2009 ident: 2020080807563881500_bby054-B36 article-title: Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps publication-title: Nature doi: 10.1038/nature08170 – volume: 43 start-page: D130 year: 2015 ident: 2020080807563881500_bby054-B46 article-title: Rfam 12.0: updates to the RNA families database publication-title: Nucleic Acids Res doi: 10.1093/nar/gku1063 – volume: 17 start-page: 991 issue: 8 year: 2003 ident: 2020080807563881500_bby054-B53 article-title: The microRNAs of Caenorhabditis elegans publication-title: Genes Dev doi: 10.1101/gad.1074403 – volume: 34 start-page: 713 issue: 4 year: 2018 ident: 2020080807563881500_bby054-B155 article-title: OncomiR: an online resource for exploring pan-cancer microRNA dysregulation publication-title: Bioinformatics doi: 10.1093/bioinformatics/btx627 – volume: 307 start-page: 932 issue: 5711 year: 2005 ident: 2020080807563881500_bby054-B12 article-title: Methylation as a crucial step in plant microRNA biogenesis publication-title: Science doi: 10.1126/science.1107130 – volume: 44 start-page: W181 issue: W1 year: 2016 ident: 2020080807563881500_bby054-B54 article-title: miRNAFold: a web server for fast miRNA precursor prediction in genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw459 – volume: 47 start-page: 163 issue: 2 year: 2011 ident: 2020080807563881500_bby054-B13 article-title: MicroRNA regulation of core apoptosis pathways in cancer publication-title: Eur J Cancer doi: 10.1016/j.ejca.2010.11.005 – volume: 17 start-page: 820 issue: 5 year: 2011 ident: 2020080807563881500_bby054-B60 article-title: MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action publication-title: RNA doi: 10.1261/rna.2387911 – volume: 505 start-page: 344 issue: 7483 year: 2014 ident: 2020080807563881500_bby054-B16 article-title: The multilayered complexity of ceRNA crosstalk and competition publication-title: Nature doi: 10.1038/nature12986 – volume: 39 start-page: W155 year: 2011 ident: 2020080807563881500_bby054-B115 article-title: psRNATarget: a plant small RNA target analysis server publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr319 – volume: 45 start-page: D1009 issue: D1 year: 2017 ident: 2020080807563881500_bby054-B74 article-title: PceRBase: a database of plant competing endogenous RNA publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw916 – volume: 4 year: 2015 ident: 2020080807563881500_bby054-B63 article-title: Predicting effective microRNA target sites in mammalian mRNAs publication-title: Elife doi: 10.7554/eLife.05005 – volume: 17 start-page: 487. issue: 1 year: 2016 ident: 2020080807563881500_bby054-B57 article-title: LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length publication-title: BMC Bioinformatics doi: 10.1186/s12859-016-1353-6 – volume: 5 start-page: 5700 issue: 1 year: 2014 ident: 2020080807563881500_bby054-B101 article-title: microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs publication-title: Nat Commun doi: 10.1038/ncomms6700 – volume: 12 start-page: 507. year: 2011 ident: 2020080807563881500_bby054-B147 article-title: Chipster: user-friendly analysis software for microarray and other high-throughput data publication-title: BMC Genomics doi: 10.1186/1471-2164-12-507 – volume: 425 start-page: 415 issue: 6956 year: 2003 ident: 2020080807563881500_bby054-B28 article-title: The nuclear RNase III Drosha initiates microRNA processing publication-title: Nature doi: 10.1038/nature01957 – volume: 495 start-page: 333 issue: 7441 year: 2013 ident: 2020080807563881500_bby054-B71 article-title: Circular RNAs are a large class of animal RNAs with regulatory potency publication-title: Nature doi: 10.1038/nature11928 – volume: 147 start-page: 358 issue: 2 year: 2011 ident: 2020080807563881500_bby054-B72 article-title: A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA publication-title: Cell doi: 10.1016/j.cell.2011.09.028 – volume: 99 start-page: 15524 issue: 24 year: 2002 ident: 2020080807563881500_bby054-B27 article-title: Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.242606799 – volume: 4 start-page: e20. issue: 1 year: 2008 ident: 2020080807563881500_bby054-B41 article-title: Getting started in text mining publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.0040020 – volume: 15 start-page: 275. year: 2014 ident: 2020080807563881500_bby054-B95 article-title: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-15-275 – volume: 42 start-page: D86 issue: D1 year: 2014 ident: 2020080807563881500_bby054-B108 article-title: PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways publication-title: Nucleic Acids Res doi: 10.1093/nar/gkt1028 – volume: 1695 start-page: 1 year: 2006 ident: 2020080807563881500_bby054-B171 article-title: The igraph software package for complex network research publication-title: InterJ Complex Syst – volume: 146 start-page: 353 issue: 3 year: 2011 ident: 2020080807563881500_bby054-B17 article-title: A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? publication-title: Cell doi: 10.1016/j.cell.2011.07.014 – volume: 20 start-page: 273 issue: 3 year: 1995 ident: 2020080807563881500_bby054-B39 article-title: Support-vector networks publication-title: Mach Learn doi: 10.1007/BF00994018 – volume: 18 start-page: 136 year: 2017 ident: 2020080807563881500_bby054-B139 article-title: RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach publication-title: BMC Bioinformatics doi: 10.1186/s12859-017-1561-8 – volume: 10 start-page: 1819 issue: 11 year: 2015 ident: 2020080807563881500_bby054-B11 article-title: Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance publication-title: Cell Rep doi: 10.1016/j.celrep.2015.02.047 – volume: 101 start-page: 9740 issue: 26 year: 2004 ident: 2020080807563881500_bby054-B32 article-title: An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0403293101 – volume: 32 start-page: 673 issue: 5 year: 2016 ident: 2020080807563881500_bby054-B127 article-title: Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv632 – volume: 18 start-page: 610 issue: 4 year: 2008 ident: 2020080807563881500_bby054-B31 article-title: Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells publication-title: Genome Res doi: 10.1101/gr.7179508 – volume: 25 start-page: 1966 issue: 15 year: 2009 ident: 2020080807563881500_bby054-B81 article-title: SOAP2: an improved ultrafast tool for short read alignment publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp336 – volume: 11 start-page: 597 issue: 9 year: 2010 ident: 2020080807563881500_bby054-B2 article-title: The widespread regulation of microRNA biogenesis, function and decay publication-title: Nat Rev Genet doi: 10.1038/nrg2843 – volume: 39 start-page: W132 year: 2011 ident: 2020080807563881500_bby054-B56 article-title: miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr247 – volume: 41 start-page: D991 year: 2013 ident: 2020080807563881500_bby054-B77 article-title: NCBI GEO: archive for functional genomics data sets–update publication-title: Nucleic Acids Res doi: 10.1093/nar/gks1193 – volume: 30 start-page: 1082 issue: 9 year: 2011 ident: 2020080807563881500_bby054-B14 article-title: MicroRNA-221/222 confers breast cancer fulvestrant resistance by regulating multiple signaling pathways publication-title: Oncogene doi: 10.1038/onc.2010.487 – volume: 46 start-page: D354 issue: D1 year: 2018 ident: 2020080807563881500_bby054-B75 article-title: miRandola 2017: a curated knowledge base of non-invasive biomarkers publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx854 – volume: 11 start-page: 476. year: 2010 ident: 2020080807563881500_bby054-B137 article-title: Improving performance of mammalian microRNA target prediction publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-11-476 – volume: 40 start-page: 37 issue: 1 year: 2012 ident: 2020080807563881500_bby054-B55 article-title: miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades publication-title: Nucleic Acids Res doi: 10.1093/nar/gkr688 – volume: 10 start-page: S35. issue: Suppl 1 year: 2009 ident: 2020080807563881500_bby054-B88 article-title: HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-10-S1-S35 – volume: 72 start-page: 3127 issue: 16 year: 2015 ident: 2020080807563881500_bby054-B144 article-title: Principles of miRNA-mRNA interactions: beyond sequence complementarity publication-title: Cell Mol Life Sci doi: 10.1007/s00018-015-1922-2 – volume: 6 start-page: 310 year: 2005 ident: 2020080807563881500_bby054-B83 article-title: Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-6-310 – volume: 18 start-page: 180 issue: 1 year: 2017 ident: 2020080807563881500_bby054-B164 article-title: QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing publication-title: Bmc Bioinformatics doi: 10.1186/s12859-017-1601-4 – volume: 46 start-page: D360 issue: D1 year: 2018 ident: 2020080807563881500_bby054-B113 article-title: mirDIP 4.1-integrative database of human microRNA target predictions publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx1144 – volume: 45 start-page: D43 issue: D1 year: 2017 ident: 2020080807563881500_bby054-B122 article-title: ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkw965 – year: 2017 ident: 2020080807563881500_bby054-B132 article-title: Recent computational developments on CLIP-seq data analysis and microRNA targeting implications publication-title: Brief Bioinform – volume: 18 start-page: 997 issue: 10 year: 2008 ident: 2020080807563881500_bby054-B21 article-title: Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases publication-title: Cell Res doi: 10.1038/cr.2008.282 – volume: 46 start-page: D296 year: 2018 ident: 2020080807563881500_bby054-B114 article-title: miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx1067 – volume: 105 start-page: 10513 issue: 30 year: 2008 ident: 2020080807563881500_bby054-B20 article-title: Circulating microRNAs as stable blood-based markers for cancer detection publication-title: Proc Natl Acad Sci USA doi: 10.1073/pnas.0804549105 – volume: 29 start-page: 409 issue: 3 year: 2013 ident: 2020080807563881500_bby054-B120 article-title: SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts698 |
| SSID | ssj0020781 |
| Score | 2.67416 |
| SecondaryResourceType | review_article |
| Snippet | Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional,... MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional,... |
| SourceID | pubmedcentral proquest pubmed crossref oup |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 1836 |
| SubjectTerms | Algorithms Bioinformatics Computational Biology - methods Data mining Epigenetics Gene expression Machine Learning MicroRNAs MicroRNAs - chemistry MicroRNAs - genetics miRNA Network analysis Nucleic Acid Conformation Predictions Review Ribonucleic acid RNA Target recognition Trends |
| Title | Trends in the development of miRNA bioinformatics tools |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/29982332 https://www.proquest.com/docview/2955280767 https://www.proquest.com/docview/2067128777 https://pubmed.ncbi.nlm.nih.gov/PMC7414524 |
| Volume | 20 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV3dS8MwEA8yEHwRv63OEdEXH8raNGnSxyGOIThBNthb6bUpFmYrrnvYf-9l7eoqQ59z_chdLvc77vILIfdB4muFUMCGiEc2B5HgPihiO-WxQoCs0lSY08gvY3805c8zMaubaBY7SviB14cM-gArfCHutBh9DUP-5HXWpFWGrqY6QyRtQ-6-ISFtPdoKO62jbFuI8ndj5FakGR6Rwxoi0kFl02Oyp_MTsl9dGrk6JbJqY6VZThG80eSn64cWKf3I3sYDCllRM6IaFmZaFsV8cUamw6fJ48iurz-wY-Gw0tYqFqAgiDzAJMCw1LgSUtDa5dplgLOW6G0SndBJuIpBuJGrUo75lowcGQfeOenkRa4vCWWRdqQfu4jNgEMaoQkQFgVMK5GyxAss8rDRThjX3ODmiop5WNWovRA1GVaatMhdI_tZMWLslOqhkv8U6G70H9ZuswhZIISh5_GlRW6bYVzwpooR5bpYogzGVwyqUqLMRWWu5jM4J8U8j1lEtgzZCBgy7fZInr2vSbURWXHB-NV__31NDhAzrdvMmOySTvm11DeIS0rorZflN8EC4F4 |
| linkProvider | Oxford University Press |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Trends+in+the+development+of+miRNA+bioinformatics+tools&rft.jtitle=Briefings+in+bioinformatics&rft.au=Chen%2C+Liang&rft.au=Heikkinen%2C+Liisa&rft.au=Wang%2C+Changliang&rft.au=Yang%2C+Yang&rft.date=2019-09-27&rft.issn=1477-4054&rft.eissn=1477-4054&rft.volume=20&rft.issue=5&rft.spage=1836&rft_id=info:doi/10.1093%2Fbib%2Fbby054&rft.externalDBID=NO_FULL_TEXT |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1467-5463&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1467-5463&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1467-5463&client=summon |