Literature DB >> 23616640

miRNA-Seq normalization comparisons need improvement.

Xiaobei Zhou1, Alicia Oshlack, Mark D Robinson.   

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Year:  2013        PMID： 23616640      PMCID： PMC3683906          DOI： 10.1261/rna.037895.112

Source DB:  PubMed          Journal:  RNA        ISSN： 1355-8382            Impact factor:   4.942


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  7 in total

1.  Evaluation of normalization methods in mammalian microRNA-Seq data.

Authors:  Lana Xia Garmire; Shankar Subramaniam
Journal:  RNA       Date:  2012-04-24       Impact factor: 4.942

2.  A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.

Authors:  Marie-Agnès Dillies; Andrea Rau; Julie Aubert; Christelle Hennequet-Antier; Marine Jeanmougin; Nicolas Servant; Céline Keime; Guillemette Marot; David Castel; Jordi Estelle; Gregory Guernec; Bernd Jagla; Luc Jouneau; Denis Laloë; Caroline Le Gall; Brigitte Schaëffer; Stéphane Le Crom; Mickaël Guedj; Florence Jaffrézic
Journal:  Brief Bioinform       Date:  2012-09-17       Impact factor: 11.622

3.  A scaling normalization method for differential expression analysis of RNA-seq data.

Authors:  Mark D Robinson; Alicia Oshlack
Journal:  Genome Biol       Date:  2010-03-02       Impact factor: 13.583

4.  Sequencing technology does not eliminate biological variability.

Authors:  Kasper D Hansen; Zhijin Wu; Rafael A Irizarry; Jeffrey T Leek
Journal:  Nat Biotechnol       Date:  2011-07-11       Impact factor: 54.908

5.  Transcript length bias in RNA-seq data confounds systems biology.

Authors:  Alicia Oshlack; Matthew J Wakefield
Journal:  Biol Direct       Date:  2009-04-16       Impact factor: 4.540

6.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

7.  Using generalized procrustes analysis (GPA) for normalization of cDNA microarray data.

Authors:  Huiling Xiong; Dapeng Zhang; Christopher J Martyniuk; Vance L Trudeau; Xuhua Xia
Journal:  BMC Bioinformatics       Date:  2008-01-16       Impact factor: 3.169
  7 in total
  16 in total

Review 1.  The validity of circulating microRNAs in oncology: five years of challenges and contradictions.

Authors:  J Jarry; D Schadendorf; C Greenwood; A Spatz; L C van Kempen
Journal:  Mol Oncol       Date:  2014-03-06       Impact factor: 6.603

Review 2.  Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.

Authors:  A Maxwell Burroughs; Yoshinari Ando
Journal:  Methods       Date:  2018-08-20       Impact factor: 3.608

3.  Performance evaluation of transcriptomics data normalization for survival risk prediction.

Authors:  Ai Ni; Li-Xuan Qin
Journal:  Brief Bioinform       Date:  2021-11-05       Impact factor: 13.994

4.  Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs.

Authors:  Helena Kelly; Tim Downing; Nina L Tuite; Terry J Smith; Michael J Kerin; Róisín M Dwyer; Eoin Clancy; Thomas Barry; Kate Reddington
Journal:  PLoS One       Date:  2015-09-10       Impact factor: 3.240

5.  Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization.

Authors:  Mauro D Locati; Inez Terpstra; Wim C de Leeuw; Mateusz Kuzak; Han Rauwerda; Wim A Ensink; Selina van Leeuwen; Ulrike Nehrdich; Herman P Spaink; Martijs J Jonker; Timo M Breit; Rob J Dekker
Journal:  Nucleic Acids Res       Date:  2015-04-13       Impact factor: 16.971

6.  Optimization of miRNA-seq data preprocessing.

Authors:  Shirley Tam; Ming-Sound Tsao; John D McPherson
Journal:  Brief Bioinform       Date:  2015-04-17       Impact factor: 11.622

7.  SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

Authors:  Hugo Varet; Loraine Brillet-Guéguen; Jean-Yves Coppée; Marie-Agnès Dillies
Journal:  PLoS One       Date:  2016-06-09       Impact factor: 3.240

Review 8.  Circulating microRNAs as Potential Biomarkers of Infectious Disease.

Authors:  Carolina N Correia; Nicolas C Nalpas; Kirsten E McLoughlin; John A Browne; Stephen V Gordon; David E MacHugh; Ronan G Shaughnessy
Journal:  Front Immunol       Date:  2017-02-16       Impact factor: 7.561

9.  Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms.

Authors:  Rounak Nassirpour; Sachin Mathur; Mark M Gosink; Yizheng Li; Ahmed M Shoieb; Joanna Wood; Shawn P O'Neil; Bruce L Homer; Laurence O Whiteley
Journal:  BMC Genomics       Date:  2014-06-18       Impact factor: 3.969

10.  iSRAP - a one-touch research tool for rapid profiling of small RNA-seq data.

Authors:  Camelia Quek; Chol-Hee Jung; Shayne A Bellingham; Andrew Lonie; Andrew F Hill
Journal:  J Extracell Vesicles       Date:  2015-11-09
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