Literature DB >> 22830413

RNA sequencing: platform selection, experimental design, and data interpretation.

Yongjun Chu1, David R Corey.   

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Year:  2012        PMID: 22830413      PMCID: PMC3426205          DOI: 10.1089/nat.2012.0367

Source DB:  PubMed          Journal:  Nucleic Acid Ther        ISSN: 2159-3337            Impact factor:   5.486


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  20 in total

1.  DNA sequencing with nanopores.

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2.  The transcriptional landscape of the yeast genome defined by RNA sequencing.

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Review 3.  Sequencing technologies - the next generation.

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4.  SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read.

Authors:  Juan Falgueras; Antonio J Lara; Noé Fernández-Pozo; Francisco R Cantón; Guillermo Pérez-Trabado; M Gonzalo Claros
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5.  TagDust--a program to eliminate artifacts from next generation sequencing data.

Authors:  Timo Lassmann; Yoshihide Hayashizaki; Carsten O Daub
Journal:  Bioinformatics       Date:  2009-09-07       Impact factor: 6.937

6.  Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Authors:  Mitchell Guttman; Manuel Garber; Joshua Z Levin; Julie Donaghey; James Robinson; Xian Adiconis; Lin Fan; Magdalena J Koziol; Andreas Gnirke; Chad Nusbaum; John L Rinn; Eric S Lander; Aviv Regev
Journal:  Nat Biotechnol       Date:  2010-05-02       Impact factor: 54.908

Review 7.  Assembling genomes using short-read sequencing technology.

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8.  Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.

Authors:  Markus Hafner; Markus Landthaler; Lukas Burger; Mohsen Khorshid; Jean Hausser; Philipp Berninger; Andrea Rothballer; Manuel Ascano; Anna-Carina Jungkamp; Mathias Munschauer; Alexander Ulrich; Greg S Wardle; Scott Dewell; Mihaela Zavolan; Thomas Tuschl
Journal:  Cell       Date:  2010-04-02       Impact factor: 41.582

9.  Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps.

Authors:  Sung Wook Chi; Julie B Zang; Aldo Mele; Robert B Darnell
Journal:  Nature       Date:  2009-06-17       Impact factor: 49.962

10.  TopHat: discovering splice junctions with RNA-Seq.

Authors:  Cole Trapnell; Lior Pachter; Steven L Salzberg
Journal:  Bioinformatics       Date:  2009-03-16       Impact factor: 6.937

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  46 in total

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2.  IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures.

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Review 3.  Single cells get together: High-resolution approaches to study the dynamics of early mouse development.

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4.  Identification of key factors regulating self-renewal and differentiation in EML hematopoietic precursor cells by RNA-sequencing analysis.

Authors:  Shan Zong; Shuyun Deng; Kenian Chen; Jia Qian Wu
Journal:  J Vis Exp       Date:  2014-11-11       Impact factor: 1.355

Review 5.  Microbial extracellular RNAs and their roles in human diseases.

Authors:  Heon-Jin Lee
Journal:  Exp Biol Med (Maywood)       Date:  2020-05-05

Review 6.  Biomarkers for kidney involvement in pediatric lupus.

Authors:  Beatrice Goilav; Chaim Putterman; Tamar B Rubinstein
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7.  An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile.

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8.  Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation.

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Journal:  Genes Genomics       Date:  2020-04-02       Impact factor: 1.839

9.  Understanding the pathogenesis of hip fracture in the elderly, osteoporotic theory is not reflected in the outcome of prevention programmes.

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Journal:  World J Orthop       Date:  2016-04-18

Review 10.  Current perspectives on genetically modified crops and detection methods.

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