Genes
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP,
Nusbaum C, Bartel DP.
Genes Dev. 2010 May 15;24(10):992-1009.
Deciphering the porcine intestinal microRNA transcriptome.
Sharbati S, Friedländer MR, Sharbati J, Hoeke L, Chen W, Keller A, Stähler PF, Rajewsky N, Einspanier R.
BMC Genomics. 2010 Apr 30;11:275.
The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting
CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J,
Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backström N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J,
Völker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D,
Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R,
Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton
L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK.
Nature. 2010 Apr 1;464(7289):757-62.
MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing.
Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C, Thomsen B.
Anim Genet. 2010 Apr 1;41(2):159-68.
Identification and characterization of microRNAs from porcine skeletal muscle.
Xie SS, Huang TH, Shen Y, Li XY, Zhang XX, Zhu MJ, Qin HY, Zhao SH.
Anim Genet. 2010 Apr 1;41(2):179-90.
MicroRNAs of Bombyx mori identified by Solexa sequencing.
Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q.
BMC Genomics. 2010 Mar 3;11:148.
miRBase: microRNA sequences and annotation.
Griffiths-Jones S.
Curr Protoc Bioinformatics. 2010 Mar;Chapter 12:Unit 12.9.1-10.
Finding sRNA generative locales from high-throughput sequencing data with NiBLS.
MacLean D, Moulton V, Studholme DJ.
BMC Bioinformatics. 2010 Feb 18;11:93.
Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus.
Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR.
BMC Genomics. 2010 Feb 18;11:119.
An "in-depth" description of the small non-coding RNA population of Schistosoma japonicum schistosomulum.
Wang Z, Xue X, Sun J, Luo R, Xu X, Jiang Y, Zhang Q, Pan W.
PLoS Negl Trop Dis. 2010 Feb 9;4(2):e596.
Computational identification of Ciona intestinalis microRNAs.
Keshavan R, Virata M, Keshavan A, Zeller RW.
Zoolog Sci. 2010 Feb;27(2):162-70.
Cloning and bioinformatic identification of small RNAs in the filarial nematode, Brugia malayi.
Poole CB, Davis PJ, Jin J, McReynolds LA.
Mol Biochem Parasitol. 2010 Feb;169(2):87-94.
Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum.
Hao L, Cai P, Jiang N, Wang H, Chen Q.
BMC Genomics. 2010 Jan 21;11:55.
Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM).
Agarwal S, Vaz C, Bhattacharya A, Srinivasan A.
BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S29.
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm.
Hsieh CH, Chang DT, Hsueh CH, Wu CY, Oyang YJ.
BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S52.
DuplexFinder: predicting the miRNA-miRNA* duplex from the animal precursors.
Zou Q, Guo M, Liu Y, Xuan P.
Int J Bioinform Res Appl. 2010;6(1):69-81.
Genome-wide profiling of populus small RNAs.
Klevebring D, Street NR, Fahlgren N, Kasschau KD, Carrington JC, Lundeberg J, Jansson S.
BMC Genomics. 2009 Dec 20;10:620.
Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach.
Huang J, Hao P, Chen H, Hu W, Yan Q, Liu F, Han ZG.
PLoS One. 2009 Dec 8;4(12):e8206.
Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito
miRNAs.
Li S, Mead EA, Liang S, Tu Z.
BMC Genomics. 2009 Dec 4;10:581.
A discovery of novel microRNAs in the silkworm (Bombyx mori) genome.
Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J.
Genomics. 2009 Dec;94(6):438-44.
A genome-wide analysis of small regulatory RNAs in the human pathogen group A Streptococcus.
Perez N, Treviño J, Liu Z, Ho SC, Babitzke P, Sumby P.
PLoS One. 2009 Nov 2;4(11):e7668.
Repertoire and evolution of miRNA genes in four divergent nematode species.
de Wit E, Linsen SE, Cuppen E, Berezikov E.
Genome Res. 2009 Nov;19(11):2064-74.
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.
Copeland CC, Marz M, Rose D, Hertel J, Brindley PJ, Santana CB, Kehr S, Attolini CS, Stadler PF.
BMC Genomics. 2009 Oct 8;10:464.
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.
Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA.
Genome Res. 2009 Oct;19(10):1766-75.
Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia.
Zhang YQ, Chen DL, Tian HF, Zhang BH, Wen JF.
Comput Biol Chem. 2009 Oct;33(5):391-6.
Characterization of bovine miRNAs by sequencing and bioinformatics analysis.
Jin W, Grant JR, Stothard P, Moore SS, Guan LL.
BMC Mol Biol. 2009 Sep 16;10:90.
In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and
comparative genomic approach.
Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T, Zheng Y.
Genomics. 2009 Aug;94(2):125-31.
Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea.
Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR.
RNA. 2009 Aug;15(8):1483-91.
High-resolution profiling and discovery of planarian small RNAs.
Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, Alvarado AS, Kim JK,
Rajewsky N.
Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11546-51.
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments.
Hackenberg M, Sturm M, Langenberger D, Falcón-Pérez JM, Aransay AM.
Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W68-76.
Identification and characteristics of cattle microRNAs by homology searching and small RNA cloning.
Long JE, Chen HX.
Biochem Genet. 2009 Jun;47(5-6):329-43.
Large-scale sequence analyses of Atlantic cod.
Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem A, Breines R, Nordeide JT, Moum T,
Nederbragt AJ, Stenseth NC, Jakobsen KS.
N Biotechnol. 2009 Jun;25(5):263-71.
Statistical models for local occurrences of RNA structures.
Hansen NR.
J Comput Biol. 2009 Jun;16(6):845-58.
Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach.
Oulas A, Boutla A, Gkirtzou K, Reczko M, Kalantidis K, Poirazi P.
Nucleic Acids Res. 2009 Jun;37(10):3276-87.
High throughput sequencing of microRNAs in chicken somites.
Rathjen T, Pais H, Sweetman D, Moulton V, Munsterberg A, Dalmay T.
FEBS Lett. 2009 May 6;583(9):1422-6.
Identification of microRNA in the protist Trichomonas vaginalis.
Lin WC, Li SC, Lin WC, Shin JW, Hu SN, Yu XM, Huang TY, Chen SC, Chen HC, Chen SJ, Huang PJ, Gan RR, Chiu CH, Tang P.
Genomics. 2009 May;93(5):487-93.
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity.
van der Burgt A, Fiers MW, Nap JP, van Ham RC.
BMC Genomics. 2009 Apr 30;10:204.
Parallel DNA pyrosequencing unveils new zebrafish microRNAs.
Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MA.
BMC Genomics. 2009 Apr 27;10:195.
The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Bovine Genome Sequencing and Analysis Consortium.
Science. 2009 Apr 24;324(5926):522-8.
microPred: effective classification of pre-miRNAs for human miRNA gene prediction.
Batuwita R, Palade V.
Bioinformatics. 2009 Apr 15;25(8):989-95.
Identification and characterization of new miRNAs cloned from normal mouse mammary gland.
Sdassi N, Silveri L, Laubier J, Tilly G, Costa J, Layani S, Vilotte JL, Le Provost F.
BMC Genomics. 2009 Apr 7;10:149.
Non-coding RNA annotation of the genome of Trichoplax adhaerens.
Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF.
Nucleic Acids Res. 2009 Apr;37(5):1602-15.
Cloning, characterization and expression analysis of porcine microRNAs.
Reddy AM, Zheng Y, Jagadeeswaran G, Macmil SL, Graham WB, Roe BA, Desilva U, Zhang W, Sunkar R.
BMC Genomics. 2009 Feb 5;10:65.
Structural profiles of human miRNA families from pairwise clustering.
Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J.
Bioinformatics. 2009 Feb 1;25(3):291-4.
Annotation of 390 bovine miRNA genes by sequence similarity with other species.
Strozzi F, Mazza R, Malinverni R, Williams JL.
Anim Genet. 2009 Feb;40(1):125.
Computational identification of novel microRNA homologs in the chimpanzee genome.
Baev V, Daskalova E, Minkov I.
Comput Biol Chem. 2009 Feb;33(1):62-70.
A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate.
Shi W, Hendrix D, Levine M, Haley B.
Nat Struct Mol Biol. 2009 Feb;16(2):183-9.
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models.
Kadri S, Hinman V, Benos PV.
BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S35.
Genic regions of a large salamander genome contain long introns and novel genes.
Smith JJ, Putta S, Zhu W, Pao GM, Verma IM, Hunter T, Bryant SV, Gardiner DM, Harkins TT, Voss SR.
BMC Genomics. 2009 Jan 13;10:19.
Computational prediction of amphioxus microRNA genes and their targets.
Luo Y, Zhang S.
Gene. 2009 Jan 1;428(1-2):41-6.
miROrtho: computational survey of microRNA genes.
Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM.
Nucleic Acids Res. 2009 Jan;37(Database issue):D111-7.
Non-coding RNAs revealed during identification of genes involved in chicken immune responses.
Ahanda ML, Ruby T, Wittzell H, Bed'Hom B, Chaussé AM, Morin V, Oudin A, Chevalier C, Young JR, Zoorob R.
Immunogenetics. 2009 Jan;61(1):55-70.
Regulatory RNomics and gene expression.
Ghosh Z, Mallick B, Gautheret D, Malhotra P, Sachidanandam R.
J Biomed Biotechnol. 2009;2009:691286.
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.
Chen X, Li Q, Wang J, Guo X, Jiang X, Ren Z, Weng C, Sun G, Wang X, Liu Y, Ma L, Chen JY, Wang J, Zen K, Zhang J, Zhang CY.
Genome Biol. 2009;10(7):R78.
Using a kernel density estimation based classifier to predict species-specific microRNA precursors.
Chang DT, Wang CC, Chen JW.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S2.
Filtering of false positive microRNA candidates by a clustering-based approach.
Leung WS, Lin MC, Cheung DW, Yiu SM.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S3.
Identification of conserved microRNAs in Bombyx mori (silkworm) and regulation of fibroin L chain production by microRNAs in
heterologous system.
Cao J, Tong C, Wu X, Lv J, Yang Z, Jin Y.
Insect Biochem Mol Biol. 2008 Dec;38(12):1066-71.
Duplicated RNA genes in teleost fish genomes.
Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF.
J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.
MicroRNA genes.
Zhou L, He H, Mi JX, Li C, Lee B, Mi QS.
Ann N Y Acad Sci. 2008 Dec;1150:72-5.
Annotation of mammalian primary microRNAs.
Saini HK, Enright AJ, Griffiths-Jones S.
BMC Genomics. 2008 Nov 27;9:564.
Prediction of human miRNAs using tissue-selective motifs in 3' UTRs.
Chang YM, Juan HF, Lee TY, Chang YY, Yeh YM, Li WH, Shih AC.
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17061-6.
CoGemiR: a comparative genomics microRNA database.
Maselli V, Di Bernardo D, Banfi S.
BMC Genomics. 2008 Oct 6;9:457.
Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development.
Huang TH, Zhu MJ, Li XY, Zhao SH.
PLoS ONE. 2008 Sep 16;3(9):e3225.
The silkworm (Bombyx mori) microRNAs and their expressions in multiple developmental stages.
Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J.
PLoS ONE. 2008 Aug 20;3(8):e2997.
CID-miRNA: a web server for prediction of novel miRNA precursors in human genome.
Tyagi S, Vaz C, Gupta V, Bhatia R, Maheshwari S, Srinivasan A, Bhattacharya A.
Biochem Biophys Res Commun. 2008 Aug 8;372(4):831-4.
Identification and characterization of new microRNAs from pig.
Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS.
Mamm Genome. 2008 Aug;19(7-8):570-80.
In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum).
Singh J, Nagaraju J.
Insect Mol Biol. 2008 Aug;17(4):427-36.
Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in
biology.
Ibáñez-Ventoso C, Vora M, Driscoll M.
PLoS ONE. 2008 Jul 30;3(7):e2818.
Identification of novel chicken microRNAs and analysis of their genomic organization.
Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH.
Gene. 2008 Jul 15;418(1-2):34-40.
MicroRNA prediction with a novel ranking algorithm based on random walks.
Xu Y, Zhou X, Zhang W.
Bioinformatics. 2008 Jul 1;24(13):i50-8.
Molecular evolution of a primate-specific microRNA family.
Zhang R, Wang YQ, Su B.
Mol Biol Evol. 2008 Jul;25(7):1493-502.
Mireval: a web tool for simple microRNA prediction in genome sequences.
Ritchie W, Théodule FX, Gautheret D.
Bioinformatics. 2008 Jun 1;24(11):1394-6.
Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum.
Luo Q, Zhou Q, Yu X, Lin H, Hu S, Yu J.
J Genet Genomics. 2008 Jun;35(6):349-55.
[Computational approaches to microRNA discovery]
Hou YY, Ying XM, Li WJ.
Yi Chuan. 2008 Jun;30(6):687-96.
Identification of microRNA precursors with support vector machine and string kernel.
Xu JH, Li F, Sun QF.
Genomics Proteomics Bioinformatics. 2008 Jun;6(2):121-8.
Conservation of small RNA pathways in platypus.
Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ.
Genome Res. 2008 Jun;18(6):995-1004.
Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.
Fu X, Adamski M, Thompson EM.
Mol Biol Evol. 2008 Jun;25(6):1067-80.
Genomic organization of zebrafish microRNAs.
Thatcher EJ, Bond J, Paydar I, Patton JG.
BMC Genomics. 2008 May 29;9:253.
Identification and characteristics of microRNAs from Bombyx mori.
He PA, Nie Z, Chen J, Chen J, Lv Z, Sheng Q, Zhou S, Gao X, Kong L, Wu X, Jin Y, Zhang Y.
BMC Genomics. 2008 May 28;9:248.
Cloning, characterization, and expression of microRNAs from the Asian malaria mosquito, Anopheles stephensi.
Mead EA, Tu Z.
BMC Genomics. 2008 May 23;9:244.
Genome analysis of the platypus reveals unique signatures of evolution.
Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger
A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler
EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF,
Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas
Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ,
Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M,
Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P,
Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M,
Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK.
Nature. 2008 May 8;453(7192):175-83.
Functional genomic, computational and proteomic analysis of C. elegans microRNAs.
Lehrbach NJ, Miska EA.
Brief Funct Genomic Proteomic. 2008 May;7(3):228-35.
Deep sequencing of chicken microRNAs.
Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ, Markis M, Isaacs G, Huang E, Morgan RW.
BMC Genomics. 2008 Apr 22;9:185.
Mapping of small RNAs in the human ENCODE regions.
Borel C, Gagnebin M, Gehrig C, Kriventseva EV, Zdobnov EM, Antonarakis SE.
Am J Hum Genet. 2008 Apr;82(4):971-81.
Discovering microRNAs from deep sequencing data using miRDeep.
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N.
Nat Biotechnol. 2008 Apr;26(4):407-15.
The birth and death of microRNA genes in Drosophila.
Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI.
Nat Genet. 2008 Mar;40(3):351-5.
New miRNAs cloned from neuroblastoma.
Afanasyeva EA, Hotz-Wagenblatt A, Glatting KH, Westermann F.
BMC Genomics. 2008 Jan 29;9:52.
miRNAminer: a tool for homologous microRNA gene search.
Artzi S, Kiezun A, Shomron N.
BMC Bioinformatics. 2008 Jan 23;9:39.
Identification of novel homologous microRNA genes in the rhesus macaque genome.
Yue J, Sheng Y, Orwig KE.
BMC Genomics. 2008 Jan 10;9:8.
In vitro and in silico annotation of conserved and nonconserved microRNAs in the genome of the marsupial Monodelphis domestica.
Devor EJ, Samollow PB.
J Hered. 2008 Jan-Feb;99(1):66-72.
Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing.
Hafner M, Landgraf P, Ludwig J, Rice A, Ojo T, Lin C, Holoch D, Lim C, Tuschl T.
Methods. 2008 Jan;44(1):3-12.
miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8.
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD.
Nucleic Acids Res. 2008 Jan;36(Database issue):D165-9.
Specificity and sensitivity of PROMIR, ERPIN and MIR-ABELA in predicting pre-microRNAs in the chicken genome.
Sebastian B, Aggrey SE.
In Silico Biol. 2008;8(5-6):377-81.
MiR-433 and miR-127 arise from independent overlapping primary transcripts encoded by the miR-433-127 locus.
Song G, Wang L.
PLoS ONE. 2008;3(10):e3574.
Identification and characterization of novel microRNAs from Schistosoma japonicum.
Xue X, Sun J, Zhang Q, Wang Z, Huang Y, Pan W.
PLoS ONE. 2008;3(12):e4034.
A probabilistic method for small RNA flowgram matching.
Vacic V, Jin H, Zhu JK, Lonardi S.
Pac Symp Biocomput. 2008;:75-86.
Identifying human microRNAs.
Bentwich I.
Curr Top Microbiol Immunol. 2008;320:257-69.
Ab initio identification of human microRNAs based on structure motifs.
Brameier M, Wiuf C.
BMC Bioinformatics. 2007 Dec 18;8:478.
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.
Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.
Genome Res. 2007 Dec;17(12):1850-64.
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.
Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M.
Genome Res. 2007 Dec;17(12):1865-79.
miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity.
Terai G, Komori T, Asai K, Kin T.
RNA. 2007 Dec;13(12):2081-90.
Cloning and expression profiling of testis-expressed microRNAs.
Ro S, Park C, Sanders KM, McCarrey JR, Yan W.
Dev Biol. 2007 Nov 15;311(2):592-602.
Finding a common motif of RNA sequences using genetic programming: the GeRNAMo system.
Michal S, Ivry T, Cohen O, Sipper M, Barash D.
IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):596-610.
Computational prediction and experimental validation of Ciona intestinalis microRNA genes.
Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T.
BMC Genomics. 2007 Nov 29;8:445.
Identification of novel Drosophila melanogaster microRNAs.
Sandmann T, Cohen SM.
PLoS ONE. 2007 Nov 28;2(11):e1265.
miRNomics-The bioinformatics of microRNA genes.
Ghosh Z, Chakrabarti J, Mallick B.
Biochem Biophys Res Commun. 2007 Nov 9;363(1):6-11
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke
J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder
ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN,
Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM,
Kellis M.
Nature. 2007 Nov 8;450(7167):219-32.
Genomic analysis of human microRNA transcripts.
Saini HK, Griffiths-Jones S, Enright AJ.
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17719-24.
And now introducing mammalian mirtrons.
Chan SP, Slack FJ.
Dev Cell. 2007 Nov;13(5):605-7.
Initial sequence and comparative analysis of the cat genome.
Pontius JU, Mullikin JC, Smith DR; Agencourt Sequencing Team, Lindblad-Toh K, Gnerre S, Clamp M, Chang J, Stephens R, Neelam B,
Volfovsky N, Schäffer AA, Agarwala R, Narfström K, Murphy WJ, Giger U, Roca AL, Antunes A, Menotti-Raymond M, Yuhki N,
Pecon-Slattery J, Johnson WE, Bourque G, Tesler G; NISC Comparative Sequencing Program, O'Brien SJ.
Genome Res. 2007 Nov;17(11):1675-89.
Mammalian mirtron genes.
Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC.
Mol Cell. 2007 Oct 26;28(2):328-36.
Mammalian microRNA prediction through a support vector machine model of sequence and structure.
Sheng Y, Engström PG, Lenhard B.
PLoS ONE. 2007 Sep 26;2(9):e946.
MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans.
Huang TH, Fan B, Rothschild MF, Hu ZL, Li K, Zhao SH.
BMC Bioinformatics. 2007 Sep 17;8:341.
Raising the estimate of functional human sequences.
Pheasant M, Mattick JS.
Genome Res. 2007 Sep;17(9):1245-53.
RScan: fast searching structural similarities for structured RNAs in large databases.
Xue C, Liu GP.
BMC Genomics. 2007 Jul 31;8:257.
Sorting of Drosophila small silencing RNAs.
Tomari Y, Du T, Zamore PD.
Cell. 2007 Jul 27;130(2):299-308.
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features.
Jiang P, Wu H, Wang W, Ma W, Sun X, Lu Z.
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W339-44.
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.
Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC.
Nature. 2007 Jun 28;447(7148):1126-9.
Identification and expression-profiling of Xenopus tropicalis miRNAs including plant miRNA-like RNAs at metamorphosis.
Hikosaka A, Takaya K, Jinno M, Kawahara A.
FEBS Lett. 2007 Jun 26;581(16):3013-8.
Characterization of microRNA expression profiles in normal human tissues.
Liang Y, Ridzon D, Wong L, Chen C.
BMC Genomics. 2007 Jun 12;8:166.
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures.
Ng KL, Mishra SK.
Bioinformatics. 2007 Jun 1;23(11):1321-30.
A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii.
Zhao T, Li G, Mi S, Li S, Hannon GJ, Wang XJ, Qi Y.
Genes Dev. 2007 May 15;21(10):1190-203.
A bootstrap based analysis pipeline for efficient classification of phylogenetically related animal miRNAs.
Huang Y, Gu X.
BMC Genomics. 2007 Mar 6;8:66.
Reliable prediction of Drosha processing sites improves microRNA gene prediction.
Helvik SA, Snove O Jr, Saetrom P.
Bioinformatics. 2007 Jan 15;23(2):142-9.
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.
Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8.
miRGen: a database for the study of animal microRNA genomic organization and function.
Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG.
Nucleic Acids Res. 2007 Jan;35(Database issue):D149-55.
Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).
Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q.
Genome Biol. 2007;8(6):R96.
Computational and transcriptional evidence for microRNAs in the honey bee genome.
Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM, Samanta MP, Miller J, Elsik CG.
Genome Biol. 2007;8(6):R97.
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome.
Mahony S, Corcoran DL, Feingold E, Benos PV.
Genome Biol. 2007;8(5):R84.
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP.
Cell. 2006 Dec 15;127(6):1193-207.
Analysis of short RNAs in the malaria parasite and its red blood cell host.
Rathjen T, Nicol C, McConkey G, Dalmay T.
FEBS Lett. 2006 Oct 2;580(22):5185-8.
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis.
Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van
Zonneveld AJ, Mano H, Plasterk R, Cuppen E.
Genome Res. 2006 Oct;16(10):1289-98.
Computational prediction of microRNA genes in silkworm genome.
Tong CZ, Jin YF, Zhang YZ.
J Zhejiang Univ Sci B. 2006 Oct;7(10):806-16.
Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking sequences.
Gu J, He T, Pei Y, Li F, Wang X, Zhang J, Zhang X, Li Y.
Mamm Genome. 2006 Oct;17(10):1033-41.
New porcine microRNA genes found by homology search.
Kim HJ, Cui XS, Kim EJ, Kim WJ, Kim NH.
Genome. 2006 Oct;49(10):1283-6.
MicroRNAs from the Planarian Schmidtea mediterranea: a model system for stem cell biology.
Palakodeti D, Smielewska M, Graveley BR.
RNA. 2006 Sep;12(9):1640-9.
Entamoeba histolytica: computational identification of putative microRNA candidates.
De S, Pal D, Ghosh SK.
Exp Parasitol. 2006 Aug;113(4):239-43.
Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.
Missal K, Zhu X, Rose D, Deng W, Skogerbo G, Chen R, Stadler PF.
J Exp Zoolog B Mol Dev Evol. 2006 Jul 15;306(4):379-92.
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.
Hertel J, Stadler PF.
Bioinformatics. 2006 Jul 15;22(14):e197-202.
Bioinformatic discovery of microRNA precursors from human ESTs and introns.
Li SC, Pan CY, Lin WC.
BMC Genomics. 2006 Jul 3;7:164.
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs.
Dezulian T, Schaefer M, Wiese R, Weigel D, Huson DH.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W400-4.
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.
Nam JW, Kim J, Kim SK, Zhang BT.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W455-8.
Identification of microRNAs from different tissues of chicken embryo and adult chicken.
Xu H, Wang X, Du Z, Li N.
FEBS Lett. 2006 Jun 26;580(15):3610-6.
Combining multi-species genomic data for microRNA identification using a Naive Bayes classifier.
Yousef M, Nebozhyn M, Shatkay H, Kanterakis S, Showe LC, Showe MK.
Bioinformatics. 2006 Jun 1;22(11):1325-34.
Approaches to microRNA discovery.
Berezikov E, Cuppen E, Plasterk RH.
Nat Genet. 2006 Jun;38 Suppl:S2-7.
MicroRNA enrichment among short 'ultraconserved' sequences in insects.
Tran T, Havlak P, Miller J.
Nucleic Acids Res. 2006 May 12;34(9):e65.
Cloning and expression of new microRNAs from zebrafish.
Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J, Verheul M, Cuppen E, Plasterk RH.
Nucleic Acids Res. 2006 May 12;34(9):2558-69.
Identification and classification of conserved RNA secondary structures in the human genome.
Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D.
PLoS Comput Biol. 2006 Apr;2(4):e33.
The colorectal microRNAome.
Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK,
Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE.
Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3687-92.
Genomics of microRNA.
Kim VN, Nam JW.
Trends Genet. 2006 Mar;22(3):165-73.
Identification of plant microRNA homologs.
Dezulian T, Remmert M, Palatnik JF, Weigel D, Huson DH.
Bioinformatics. 2006 Feb 1;22(3):359-60.
Twelve novel C. elegans RNA candidates isolated by two-dimensional polyacrylamide gel electrophoresis.
Hokii Y, Kubo A, Ogasawara T, Nogi Y, Taneda A, Arai R, Muto A, Ushida C.
Gene. 2006 Jan 3;365:83-7.
Identification and analysis of microRNAs.
Bagga S, Pasquinelli AE.
Genet Eng (N Y). 2006;27:1-20.
An approach for the identification of microRNA with an application to Anopheles gambiae.
Chatterjee R, Chaudhuri K.
Acta Biochim Pol. 2006;53(2):303-9.
miRBase: the microRNA sequence database.
Griffiths-Jones S.
Methods Mol Biol. 2006;342:129-38.
Mouse microRNA profiles determined with a new and sensitive cloning method.
Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP, Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M,
Choi YL, Plasterk RH, Cuppen E, Mano H.
Nucleic Acids Res. 2006;34(17):e115.
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.
Xue C, Li F, He T, Liu GP, Li Y, Zhang X.
BMC Bioinformatics. 2005 Dec 29;6:310.
Identification of clustered microRNAs using an ab initio prediction method.
Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M.
BMC Bioinformatics. 2005 Nov 7;6:267.
Identification and characterization of small RNAs involved in RNA silencing.
Aravin A, Tuschl T.
FEBS Lett. 2005 Oct 31;579(26):5830-40.
MicroRNA identification based on sequence and structure alignment.
Wang X, Zhang J, Li F, Gu J, He T, Zhang X, Li Y.
Bioinformatics. 2005 Sep 15;21(18):3610-4.
Elucidation of the small RNA component of the transcriptome.
Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ.
Science. 2005 Sep 2;309(5740):1567-9.
Identification of hundreds of conserved and nonconserved human microRNAs.
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z.
Nat Genet. 2005 Jul;37(7):766-70.
Human microRNA prediction through a probabilistic co-learning model of sequence and structure.
Nam JW, Shin KR, Han J, Lee Y, Kim VN, Zhang BT.
Nucleic Acids Res. 2005 Jun 24;33(11):3570-81.
Mammalian microRNAs derived from genomic repeats.
Smalheiser NR, Torvik VI.
Trends Genet. 2005 Jun;21(6):322-6.
Clustering and conservation patterns of human microRNAs.
Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H.
Nucleic Acids Res. 2005 May 12;33(8):2697-706.
Profile-based detection of microRNA precursors in animal genomes.
Legendre M, Lambert A, Gautheret D.
Bioinformatics. 2005 Apr 1;21(7):841-5.
Phylogenetic shadowing and computational identification of human microRNA genes.
Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E.
Cell. 2005 Jan 14;120(1):21-4.
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
Hubbard SJ, Grafham DV, Beattie KJ, Overton IM, McLaren SR, Croning MD, Boardman PE, Bonfield JK, Burnside J, Davies RM, Farrell
ER, Francis MD, Griffiths-Jones S, Humphray SJ, Hyland C, Scott CE, Tang H, Taylor RG, Tickle C, Brown WR, Birney E, Rogers J, Wilson
SA.
Genome Res. 2005 Jan;15(1):174-83.
New human and mouse microRNA genes found by homology search.
Weber MJ.
FEBS J. 2005 Jan;272(1):59-73.
Identification of mammalian microRNA host genes and transcription units.
Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A.
Genome Res. 2004 Oct;14(10A):1902-10.
The microRNA Registry.
Griffiths-Jones S.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11.
Identification of microRNAs and other tiny noncoding RNAs by cDNA cloning.
Ambros V, Lee RC.
Methods Mol Biol. 2004;265:131-58.
RSEARCH: finding homologs of single structured RNA sequences.
Klein RJ, Eddy SR.
BMC Bioinformatics. 2003 Sep 22;4:44.
Computational and experimental identification of C. elegans microRNAs.
Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J.
Mol Cell. 2003 May;11(5):1253-63.
The microRNAs of Caenorhabditis elegans.
Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP.
Genes Dev. 2003 Apr 15;17(8):991-1008.
Vertebrate microRNA genes.
Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP.
Science. 2003 Mar 7;299(5612):1540.
A uniform system for microRNA annotation.
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun
G, Tuschl T.
RNA. 2003 Mar;9(3):277-9.
New microRNAs from mouse and human.
Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T.
RNA. 2003 Feb;9(2):175-9.
Computational identification of Drosophila microRNA genes.
Lai EC, Tomancak P, Williams RW, Rubin GM.
Genome Biol. 2003;4(7):R42.
Towards a complete description of the microRNA complement of animal genomes.
Brennecke J, Cohen SM.
Genome Biol. 2003;4(9):228.
Identification of tissue-specific microRNAs from mouse.
Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T.
Curr Biol. 2002 Apr 30;12(9):735-9.
MicroRNAs: hidden in the genome.
Moss EG.
Curr Biol. 2002 Feb 19;12(4):R138-40.
Identification of novel genes coding for small expressed RNAs.
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T.
Science. 2001 Oct 26;294(5543):853-8.
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans.
Lau NC, Lim LP, Weinstein EG, Bartel DP.
Science. 2001 Oct 26;294(5543):858-62.
An extensive class of small RNAs in Caenorhabditis elegans.
Lee RC, Ambros V.
Science. 2001 Oct 26;294(5543):862-4.