Ghildiyal M, Zamore PD: Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009, 10: 94-108. 10.1038/nrg2504.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gomes AQ, Nolasco S, Soares H: Non-coding RNAs: multi-tasking molecules in the cell. Int J Mol Sci. 2013, 14: 16010-16039. 10.3390/ijms140816010.
Article
PubMed Central
PubMed
Google Scholar
Mattick JS: Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep. 2001, 2: 986-991. 10.1093/embo-reports/kve230.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jacquier A: The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet. 2009, 10: 833-844. 10.1038/nrg2683.
Article
CAS
PubMed
Google Scholar
Rinn JL, Chang HY: Genome regulation by long noncoding RNAs. Annu Rev Biochem. 2012, 81: 145-166. 10.1146/annurev-biochem-051410-092902.
Article
CAS
PubMed
Google Scholar
Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP: Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature. 2008, 455: 1193-1197. 10.1038/nature07415.
Article
CAS
PubMed
Google Scholar
Kiss T: Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell. 2002, 109: 145-148. 10.1016/S0092-8674(02)00718-3.
Article
CAS
PubMed
Google Scholar
Ambros V, Chen X: The regulation of genes and genomes by small RNAs. Development. 2007, 134: 1635-1641. 10.1242/dev.002006.
Article
CAS
PubMed
Google Scholar
Eggleston AK: RNA silencing. Nature. 2009, 457: 395-10.1038/457395a.
Article
CAS
PubMed
Google Scholar
Molnar A, Melnyk C, Baulcombe DC: Silencing signals in plants: a long journey for small RNAs. Genome Biol. 2011, 12: 215-10.1186/gb-2010-11-12-219.
Article
CAS
PubMed Central
PubMed
Google Scholar
Carthew RW, Sontheimer EJ: Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009, 136: 642-655. 10.1016/j.cell.2009.01.035.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lee HCCS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Liu Y: qiRNA is a new type of small interfering RNA induced by DNA damage. Nature. 2009, 459: 274-277. 10.1038/nature08041.
Article
CAS
PubMed Central
PubMed
Google Scholar
Brosnan CA, Voinnet O: The long and the short of noncoding RNAs. Curr Opin Cell Biol. 2009, 21: 416-425. 10.1016/j.ceb.2009.04.001.
Article
CAS
PubMed
Google Scholar
Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM, Yang YG, Qi Y: A role for small RNAs in DNA double-strand break repair. Cell. 2012, 149: 101-112. 10.1016/j.cell.2012.03.002.
Article
CAS
PubMed
Google Scholar
Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA: Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell. 2002, 110: 689-699. 10.1016/S0092-8674(02)00909-1.
Article
CAS
PubMed
Google Scholar
Le Thomas A, Fejes Tòth K, Aravin AA: To be or not to be a piRNA: genomic origin and processing of piRNAs. Genome Biol. 2014, 15 (1): 204-10.1186/gb4154.
Article
PubMed Central
PubMed
Google Scholar
Aravin AA, Bourc’his D: Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes Dev. 2008, 22: 970-975. 10.1101/gad.1669408.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Takamatsu K, Chuma S, Kojima-Kita K, Shiromoto Y, Asada N, Toyoda A, Fujiyama A, Totoki Y, Shibata T, Kimura T, Nakatsuji N, Noce T, Sasaki H, Nakano T: MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 2010, 24: 887-892. 10.1101/gad.1902110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Haag JR, Pikaard CS: Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol. 2011, 12: 483-492. 10.1038/nrm3152.
Article
CAS
PubMed
Google Scholar
Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G: A human snoRNA with microRNA-like functions. Mol Cell. 2008, 32: 519-528. 10.1016/j.molcel.2008.10.017.
Article
CAS
PubMed
Google Scholar
Melamed Z, Levy A, Ashwal-Fluss R, Lev-Maor G, Mekahel K, Atias N, Gilad S, Sharan R, Levy C, Kadener S, Ast G: Alternative splicing regulates biogenesis of miRNAs located across exon-intron junctions. Mol Cell. 2013, 50: 869-881. 10.1016/j.molcel.2013.05.007.
Article
CAS
PubMed
Google Scholar
Moustafa A, Beszteri B, Maier UG, Bowler C, Valentin K, Bhattacharya D: Genomic footprints of a cryptic plastid endosymbiosis in diatoms. Science. 2009, 324: 1724-1726. 10.1126/science.1172983.
Article
CAS
PubMed
Google Scholar
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, et al: The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature. 2008, 456: 239-244. 10.1038/nature07410.
Article
CAS
PubMed
Google Scholar
Armbrust EV, Berges JA, Bowler C, Green BR, Martinez D, Putnam NH, Zhou S, Allen AE, Apt KE, Bechner M, Brzezinski MA, Chaal BK, Chiovitti A, Davis AK, Demarest MS, Detter JC, Glavina T, Goodstein D, Hadi MZ, Hellsten U, Hildebrand M, Jenkins BD, Jurka J, Kapitonov VV, Kroger N, Lau WW, Lane TW, Larimer FW, Lippmeier JC, Lucas S, et al: The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 2004, 306: 79-86. 10.1126/science.1101156.
Article
CAS
PubMed
Google Scholar
Maumus F, Allen AE, Mhiri C, Hu H, Jabbari K, Vardi A, Grandbastien MA, Bowler C: Potential impact of stress activated retrotransposons on genome evolution in a marine diatom. BMC Genomics. 2009, 10: 624-10.1186/1471-2164-10-624.
Article
PubMed Central
PubMed
Google Scholar
Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O’Brien K, Sengamalay NA, Tallon LJ, Smith AD, Rayko E, Ahmed I, Le Crom S, Farrant GK, Sgro JY, Olson SA, Bondurant SS, Allen A, Rabinowicz PD, Sussman MR, Bowler C, Tirichine L: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nat Commun. 2013, 4: 2091-
Article
PubMed
Google Scholar
Norden-Krichmar TM, Allen AE, Gaasterland T, Hildebrand M: Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS One. 2011, 6: e22870-10.1371/journal.pone.0022870.
Article
CAS
PubMed Central
PubMed
Google Scholar
Huang A, He L, Wang G: Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis. BMC Genomics. 2011, 12: 337-10.1186/1471-2164-12-337.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mathelier A, Carbone A: MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. Bioinformatics. 2010, 26: 2226-2234. 10.1093/bioinformatics/btq329.
Article
CAS
PubMed
Google Scholar
De Riso V, Raniello R, Maumus F, Rogato A, Bowler C, Falciatore A: Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res. 2009, 37: e96-10.1093/nar/gkp448.
Article
PubMed Central
PubMed
Google Scholar
Depauw FA, Rogato A, Ribera D’Alcala M, Falciatore A: Exploring the molecular basis of responses to light in marine diatoms. J Exp Bot. 2012, 63: 1575-1591. 10.1093/jxb/ers005.
Article
CAS
PubMed
Google Scholar
Martin JHC, Coale KH, Johnson KS, Fitzwater SE, Gordon RM, Tanner SJ, Hunter CN, Elrod VA, Nowicki JL, Coley TL, Barber RT, Lindley S, Watson AJ, van Scoy K, Law CS, Liddicoat MI, Ling R, Stanton T, Stockel J, Collins C, Anderson A, Bidigare R, Ondrusek M, Latasa M, Millero FJ, Lee K, Yao W, Zhang JZ, Friederich G, Sakamoto C, et al: Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature. 1994, 371: 123-129. 10.1038/371123a0.
Article
CAS
Google Scholar
Boyd PW: Biogeochemistry: iron findings. Nature. 2007, 446: 989-991. 10.1038/446989a.
Article
CAS
PubMed
Google Scholar
Axtell MJ: Classification and comparison of small RNAs from plants. Annu Rev Plant Biol. 2013, 64: 137-159. 10.1146/annurev-arplant-050312-120043.
Article
CAS
PubMed
Google Scholar
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK: Criteria for annotation of plant MicroRNAs. Plant Cell. 2008, 20: 3186-3190. 10.1105/tpc.108.064311.
Article
CAS
PubMed Central
PubMed
Google Scholar
Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B: Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic Acids Res. 2012, 40: 4298-4305. 10.1093/nar/gks043.
Article
CAS
PubMed Central
PubMed
Google Scholar
Peng H, Shi J, Zhang Y, Zhang H, Liao S, Li W, Lei L, Han C, Ning L, Cao Y, Zhou Q, Chen Q, Duan E: A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm. Cell Res. 2012, 22: 1609-1612. 10.1038/cr.2012.141.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G: Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA. 2009, 15: 2147-2160. 10.1261/rna.1738409.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mathelier A, Carbone A: Large scale chromosomal mapping of human microRNA structural clusters. Nucleic Acids Res. 2013, 41: 4392-4408. 10.1093/nar/gkt112.
Article
CAS
PubMed Central
PubMed
Google Scholar
Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA: Structural basis for double-stranded RNA processing by Dicer. Science. 2006, 311: 195-198. 10.1126/science.1121638.
Article
CAS
PubMed
Google Scholar
Kozomara A, Griffiths Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39: D152-D157. 10.1093/nar/gkq1027.
Article
CAS
PubMed Central
PubMed
Google Scholar
Roesser JR: Both U2 snRNA and U12 snRNA are required for accurate splicing of exon 5 of the rat calcitonin/CGRP gene. RNA. 2004, 10: 1243-1250. 10.1261/rna.5210404.
Article
CAS
PubMed Central
PubMed
Google Scholar
Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP: Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods. 2007, 3: 12-10.1186/1746-4811-3-12.
Article
PubMed Central
PubMed
Google Scholar
Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R: Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs. Genes Dev. 2008, 22: 2773-2785. 10.1101/gad.1705308.
Article
CAS
PubMed Central
PubMed
Google Scholar
Couvillion MT, Sachidanandam R, Collins K: A growth-essential Tetrahymena Piwi protein carries tRNA fragment cargo. Genes Dev. 2010, 24: 2742-2747. 10.1101/gad.1996210.
Article
CAS
PubMed Central
PubMed
Google Scholar
Loss-Morais G, Waterhouse PM, Margis R: Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets. Biol Direct. 2013, 8: 6-10.1186/1745-6150-8-6.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nowacka M, Strozycki PM, Jackowiak P, Hojka-Osinska A, Szymanski M, Figlerowicz M: Identification of stable, high copy number, medium-sized RNA degradation intermediates that accumulate in plants under non-stress conditions. Plant Mol Biol. 2013, 83: 191-204. 10.1007/s11103-013-0079-3.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gebetsberger J, Polacek N: Slicing tRNAs to boost functional ncRNA diversity. RNA Biol. 2013, 10: 1798-1806.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5: 621-628. 10.1038/nmeth.1226.
Article
CAS
PubMed
Google Scholar
Slotkin RK, Martienssen R: Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007, 8: 272-285.
Article
CAS
PubMed
Google Scholar
Maheswari U, Mock T, Armbrust EV, Bowler C: Update of the Diatom EST Database: a new tool for digital transcriptomics. Nucleic Acids Res. 2009, 37 (Database issue): D1001-D1005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Law JA, Jacobsen SE: Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010, 11: 204-220. 10.1038/nrg2719.
Article
CAS
PubMed Central
PubMed
Google Scholar
Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC: miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature. 2007, 447: 1126-1129. 10.1038/nature05903.
Article
CAS
PubMed
Google Scholar
Liang C, Zhang X, Zou J, Xu D, Su F, Ye N: Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One. 2010, 5: e10698-10.1371/journal.pone.0010698.
Article
PubMed Central
PubMed
Google Scholar
Cock JM, Sterck L, Rouze P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collen J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, et al: The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature. 2010, 465: 617-621. 10.1038/nature09016.
Article
CAS
PubMed
Google Scholar
Billoud B, Nehr Z, Le Bail A, Charrier B: Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus. Nucleic Acids Res. 2014, 42: 417-429. 10.1093/nar/gkt856.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gross J, Wajid S, Price DC, Zelzion E, Li J, Chan CX, Bhattacharya D: Evidence for widespread exonic small RNAs in the glaucophyte alga Cyanophora paradoxa. PLoS One. 2013, 8: e67669-10.1371/journal.pone.0067669.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cerutti H, Ma X, Msanne J, Repas T: RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell. 2011, 10: 1164-1172. 10.1128/EC.05106-11.
Article
CAS
PubMed Central
PubMed
Google Scholar
Cheloufi S, Dos Santos CO, Chong MM, Hannon GJ: A dicer-independent miRNA biogenesis pathway that requires Ago catalysis. Nature. 2010, 465: 584-589. 10.1038/nature09092.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dueck A, Meister G: MicroRNA processing without Dicer. Genome Biol. 2010, 11: 123-10.1186/gb-2010-11-6-123.
Article
PubMed Central
PubMed
Google Scholar
Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN: MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004, 23: 4051-4060. 10.1038/sj.emboj.7600385.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wahl MC, Will CL, Luhrmann R: The spliceosome: design principles of a dynamic RNP machine. Cell. 2009, 136: 701-718. 10.1016/j.cell.2009.02.009.
Article
CAS
PubMed
Google Scholar
Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, Zhang Z, Cho S, Sherrill-Mix S, Wan L, Dreyfuss G: U1 snRNP determines mRNA length and regulates isoform expression. Cell. 2012, 150: 53-64. 10.1016/j.cell.2012.05.029.
Article
CAS
PubMed Central
PubMed
Google Scholar
Allen AE, Laroche J, Maheswari U, Lommer M, Schauer N, Lopez PJ, Finazzi G, Fernie AR, Bowler C: Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci U S A. 2008, 105: 10438-10443. 10.1073/pnas.0711370105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lommer M, Specht M, Roy AS, Kraemer L, Andreson R, Gutowska MA, Wolf J, Bergner SV, Schilhabel MB, Klostermeier UC Beiko RG, Rosenstiel P, Hippler M, Laroche J: Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol. 2012, 13: R66-10.1186/gb-2012-13-7-r66.
Article
PubMed Central
PubMed
Google Scholar
Sobala A, Hutvagner G: Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA. 2011, 2: 853-862. 10.1002/wrna.96.
Article
CAS
PubMed
Google Scholar
Franzen O, Arner E, Ferella M, Nilsson D, Respuela P, Carninci P, Hayashizaki Y, Aslund L, Andersson B, Daub CO: The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi. PLoS Negl Trop Dis. 2011, 5: e1283-10.1371/journal.pntd.0001283.
Article
CAS
PubMed Central
PubMed
Google Scholar
Thompson DM, Lu C, Green PJ, Parker R: tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA. 2008, 14: 2095-2103. 10.1261/rna.1232808.
Article
CAS
PubMed Central
PubMed
Google Scholar
Garcia-Silva MR, Frugier M, Tosar JP, Correa-Dominguez A, Ronalte-Alves L, Parodi-Talice A, Rovira C, Robello C, Goldenberg S, Cayota A: A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol Biochem Parasitol. 2010, 171: 64-73. 10.1016/j.molbiopara.2010.02.003.
Article
CAS
PubMed
Google Scholar
Rebollo R, Romanish MT, Mager DL: Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet. 2012, 46: 21-42. 10.1146/annurev-genet-110711-155621.
Article
CAS
PubMed
Google Scholar
Fedoroff NV: Presidential address. Transposable elements, epigenetics, and genome evolution. Science. 2012, 338: 758-767. 10.1126/science.338.6108.758.
Article
CAS
PubMed
Google Scholar
Mari-Ordonez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O: Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet. 2013, 45: 1029-1039. 10.1038/ng.2703.
Article
CAS
PubMed
Google Scholar
Kulis M, Queiros AC, Beekman R, Martin-Subero JI: Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. Biochim Biophys Acta. 1829, 2013: 1161-1174.
Google Scholar
Teixeira FK, Colot V: Repeat elements and the Arabidopsis DNA methylation landscape. Heredity (Edinb). 2010, 105: 14-23. 10.1038/hdy.2010.52.
Article
CAS
Google Scholar
Qian W, Miki D, Zhang H, Liu Y, Zhang X, Tang K, Kan Y, La H, Li X, Li S, Zhu X, Shi X, Zhang K, Pontes O, Chen X, Liu R, Gong Z, Zhu J-K: A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science. 2012, 336: 1445-1448. 10.1126/science.1219416.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lei J, Levin SA, Nie Q: Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation. Proc Natl Acad Sci U S A. 2014, 111: E880-E887. 10.1073/pnas.1324267111.
Article
CAS
PubMed Central
PubMed
Google Scholar
Huff JT, Zilberman D: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 2014, 156: 1286-1297. 10.1016/j.cell.2014.01.029.
Article
CAS
PubMed Central
PubMed
Google Scholar
Guillard RRL: Culture of phytoplankton for feeding marine invertebrates. Culture of Marine Invertebrate Animals USA: New York. Edited by: Smith WL, Chanley MH. 1975, 29-60.
Chapter
Google Scholar
Emde AK, Grunert M, Weese D, Reinert K, Sperling SR: MicroRazerS: rapid alignment of small RNA reads. Bioinformatics. 2010, 26: 123-124. 10.1093/bioinformatics/btp601.
Article
CAS
PubMed
Google Scholar
Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26: 841-842. 10.1093/bioinformatics/btq033.
Article
CAS
PubMed Central
PubMed
Google Scholar
Dale RK, Pedersen BS, Quinlan AR: Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics. 2011, 27: 3423-3424. 10.1093/bioinformatics/btr539.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A: Rfam: Wikipedia, clans and the “decimal” release. Nucleic Acids Res. 2011, 39: D141-D145. 10.1093/nar/gkq1129.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25: 955-964. 10.1093/nar/25.5.0955.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kielbasa SM, Wan R, Sato K, Horton P, Frith MC: Adaptive seeds tame genomic sequence comparison. Genome Res. 2011, 21: 487-493. 10.1101/gr.113985.110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hofacker IL: Vienna RNA secondary structure server. Nucleic Acids Res. 2003, 31: 3429-3431. 10.1093/nar/gkg599.
Article
CAS
PubMed Central
PubMed
Google Scholar
Darty K, Denise A, Ponty Y: VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009, 25: 1974-1975. 10.1093/bioinformatics/btp250.
Article
CAS
PubMed Central
PubMed
Google Scholar
Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V: A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics. 2008, 24: 2252-2253. 10.1093/bioinformatics/btn428.
Article
CAS
PubMed
Google Scholar
Hendrix D, Levine M, Shi W: miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol. 2010, 11: R39-10.1186/gb-2010-11-4-r39.
Article
PubMed Central
PubMed
Google Scholar
Schwach F, Moxon S, Moulton V, Dalmay T: Deciphering the diversity of small RNAs in plants: the long and short of it. Brief Funct Genomic Proteomic. 2009, 8: 472-481. 10.1093/bfgp/elp024.
Article
CAS
PubMed
Google Scholar
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ: Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005, 33: e179-10.1093/nar/gni178.
Article
PubMed Central
PubMed
Google Scholar
Tang F, Hajkova P, Barton SC, Lao K, Surani MA: MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res. 2006, 34: e9-10.1093/nar/gnj009.
Article
PubMed Central
PubMed
Google Scholar
Coesel S, Mangogna M, Ishikawa T, Heijde M, Rogato A, Finazzi G, Todo T, Bowler C, Falciatore A: Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO Rep. 2009, 10: 655-661. 10.1038/embor.2009.59.
Article
CAS
PubMed Central
PubMed
Google Scholar
Falciatore A, Casotti R, Leblanc C, Abrescia C, Bowler C: Transformation of Nonselectable Reporter Genes in Marine Diatoms. Mar Biotechnol (NY). 1999, 1: 239-251. 10.1007/PL00011773.
Article
CAS
Google Scholar