miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

Keywords

Biology, Computational biology, Identification (biology), microRNA, Chordate

References

• Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes.Лукоянчев Степан Сергеевич — 2005
• Antisense Transcription in the Mammalian TranscriptomeShintaro Katayama, Yuji Tomaru, Takeya Kasukawa — 2005
• let-7: Developmental timing conserved through evolutionJason M. Tennessen, Carl S. Thummel — 2008
• A Slicer-Mediated Mechanism for Repeat-Associated siRNA 5' End Formation in DrosophilaLalith Gunawardane, Kuniaki Saito, Kazumichi M. Nishida — 2007
• A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.Evgeny A. Glazov, Pauline Cottee, W Barris — 2008
• Tunicates and not cephalochordates are the closest living relatives of vertebratesFrédéric Delsuc, Henner Brinkmann, Daniel Chourrout — 2006
• Control of protein synthesis and mRNA degradation by microRNAs.Jidong Liu — 2008
• Small non-coding RNAs in animal developmentGiovanni Stefani, Frank J. Slack — 2008
• A distinct class of small RNAs arises from pre-miRNA–proximal regions in a simple chordateWeiyang Shi, David A. Hendrix, Mike Levine — 2009
• microRNA biogenesis and function in plantsXuemei Chen — 2005
• Evolutionary origin and genomic organization of micro-RNA genes in immunoglobulin lambda variable region gene family.Sabyasachi Das — 2009
• Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.J. Graham Ruby, Alexander Stark, Wendy K. Johnston — 2007
• What do natural antisense transcripts regulate?Andreas Werner, Mark Carlile, Daniel Swan — 2009
• A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identificationMalik Yousef, Louise C. Showe, Michael K. Showe — 2009
• The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila.Katsutomo Okamura, Joshua W. Hagen, Hong Duan — 2007
• Endogenous small interfering RNAs in animalsKatsutomo Okamura, Eric C. Lai — 2008
• Intronic microRNA precursors that bypass Drosha processingJ. Graham Ruby, Calvin H. Jan, David P. Bartel — 2007
• The deep evolution of metazoan microRNAsBenjamin M. Wheeler, Alysha M. Heimberg, Vanessa N. Moy — 2009
• Evidence for a microRNA expansion in the bilaterian ancestorSimon Prochnik, Daniel S. Rokhsar, Aziz Aboobaker — 2006
• Endo-siRNAs: yet another layer of complexity in RNA silencingTimothy W. Nilsen — 2008

Cited by

• Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis1[W][OA]施雪华 — 2011
• An investigation into the existence of cyprinid herpesvirus-3 encoded microRNAsOwen Donohoe — 2013
• DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.Jianhua Yang, Liang‐Hu Qu — 2012
• miRDeep*: an integrated application tool for miRNA identification from RNA sequencing dataJiyuan An, John Lai, Melanie Lehman — 2012
• MicroRNAs en el diagnóstico y prognosis del cáncer pulmonarFederico Ávila Moreno, Francisco Urrea, Blanca L. Ortiz Quintero — 2011
• Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2Sebastian D. Mackowiak — 2011
• Bioinformatics analysis of HPV associated host microRNA functions and identification of viral microRNAKui Qian — 2013
• Genetic and genomic analysis of small RNA pathways in nematodesZhen Shi — 2013
• Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolutionAnita Tripathi, Kavita Goswami, Neeti Sanan‐Mishra — 2015
• Common applications of next-generation sequencing technologies in genomic researchChien‐Yueh Lee, Yu‐Chiao Chiu, Liang-Bo Wang — 2013
• Bioinformatic Analysis of microRNA Genes in Free-Living and Parasitic Nematodes (Bioinformatische Analyse von microRNA Genen in frei lebenden und parasitären Nematoden)R. Ahmed — 2015
• Detection of construction biases in biological databases: the case of miRBaseGuilherme B. Saturnino, Godinho, Caio Padoan de Sá, Denise Fagundes-Lima — 2014
• Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profilesWeiwu Jin, Eveline M. Ibeagha‐Awemu, Guanxiang Liang — 2014
• mirPD: A pattern-based approach for identifying microRNAs from deep sequencing dataXiaohan Sun, Junying Zhang, Aimin Li — 2013
• Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs.Vesselin Baev, Ivan Milev, Mladen Naydenov — 2011
• Fibroblast growth factor signalling controls nervous system patterning and pigment cell formation in Ciona intestinalisClaudia Racioppi, Ashwani Kumar Kamal, Florian Razy‐Krajka — 2014
• Small RNA library preparation for next-generation sequencing by single ligation, extension and circularization technologyYoung‐Soo Kwon — 2011
• Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysisMarek Żywicki, Kamilla Bąkowska‐Żywicka, Norbert Polacek — 2012
• sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experimentsGuillermo Barturen, Antonio Rueda, Maarten Hamberg — 2014
• Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural FeaturesGoro Terai, Hiroaki Okida, Kiyoshi Asai — 2012

Related papers

• The evolution of anural larvae in molgulid ascidians.J Huber, Karen Burke da Silva, William Bates — 2000
• It's a long way from amphioxus: descendants of the earliest chordateJordi García‐Fernàndez, Èlia Benito‐Gutiérrez — 2009
• Seeing chordate evolution through the Ciona genome sequenceCristian Cañestro, Susan Bassham, John H. Postlethwait — 2003
• Anteroposterior patterning in hemichordates and the origins of the chordate nervous system.Christopher J. Lowe, Mike Wu, Adrian Salic — 2003