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RNA alignment

miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy

Alexander S. Baras, Christopher J. Mitchell, Jason R. Myers, Simone Gupta, Lien-Chun Weng, John M. Ashton, Toby C. Cornish, Akhilesh Pandey, Marc K. Halushka

published 16 Nov 2015

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RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Corinna Theis, Craig L. Zirbel, Christian Höner zu Siederdissen, Christian Anthon, Ivo L. Hofacker, Henrik Nielsen, Jan Gorodkin

published 28 Oct 2015

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The Gonococcal Transcriptome during Infection of the Lower Genital Tract in Women

Ryan McClure, Kathleen Nudel, Paola Massari, Brian Tjaden, Xiaohong Su, Peter A. Rice, Caroline A. Genco

published 05 Aug 2015

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HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages

Valentina Vongrad, Jochen Imig, Pejman Mohammadi, Shivendra Kishore, Lukasz Jaskiewicz, Jonathan Hall, Huldrych F. Günthard, Niko Beerenwinkel, Karin J. Metzner

published 30 Jul 2015

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Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

David L. A. Wood, Katia Nones, Anita Steptoe, Angelika Christ, Ivon Harliwong, Felicity Newell, Timothy J. C. Bruxner, David Miller, Nicole Cloonan, Sean M. Grimmond

published 12 May 2015

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Novel Exons and Splice Variants in the Human Antibody Heavy Chain Identified by Single Cell and Single Molecule Sequencing

Christopher Vollmers, Lolita Penland, Jad N. Kanbar, Stephen R. Quake

published 22 Jan 2015

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IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries

Patricio Jeraldo, Krishna Kalari, Xianfeng Chen, Jaysheel Bhavsar, Ashutosh Mangalam, Bryan White, Heidi Nelson, Jean-Pierre Kocher, Nicholas Chia

published 15 Dec 2014

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Predicting A-to-I RNA Editing by Feature Selection and Random Forest

Yang Shu, Ning Zhang, Xiangyin Kong, Tao Huang, Yu-Dong Cai

published 22 Oct 2014

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JAGuaR: Junction Alignments to Genome for RNA-Seq Reads

Yaron S. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard D. Corbett, Yisu Li, Johnson Pang, Yussanne P. Ma, Steven J. M. Jones, İnanç Birol

published 25 Jul 2014

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Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA

Kevin C. Miranda, Daniel T. Bond, Joshua Z. Levin, Xian Adiconis, Andrey Sivachenko, Carsten Russ, Dennis Brown, Chad Nusbaum, Leileata M. Russo

published 09 May 2014

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Molecular Archaeology of Flaviviridae Untranslated Regions: Duplicated RNA Structures in the Replication Enhancer of Flaviviruses and Pestiviruses Emerged via Convergent Evolution

Dmitri J. Gritsun, Ian M. Jones, Ernest A. Gould, Tamara S. Gritsun

published 19 Mar 2014

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Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico

Jun-Jie Hong, Tzong-Yuan Wu, Tsair-Yuan Chang, Chung-Yung Chen

published 05 Nov 2013

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Evaluation of Alignment Algorithms for Discovery and Identification of Pathogens Using RNA-Seq

Ivan Borozan, Stuart N. Watt, Vincent Ferretti

published 30 Oct 2013

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