Automated identification of reference genes based on RNA-seq data

[1]  M. Loureiro,et al.  Identification of reference genes for quantitative RT-PCR analysis of microRNAs and mRNAs in castor bean (Ricinus communis L.) under drought stress. , 2016, Plant physiology and biochemistry : PPB.

[2]  M. Gonzalo Claros,et al.  AutoFlow, a Versatile Workflow Engine Illustrated by Assembling an Optimised de novo Transcriptome for a Non-Model Species, such as Faba Bean (Vicia faba) , 2016 .

[3]  Xinjian Peng,et al.  Identification of reliable reference genes for quantitative gene expression studies in oral squamous cell carcinomas compared to adjacent normal tissues in the F344 rat model. , 2016, Oncology reports.

[4]  Jack L. Martin Validation of Reference Genes for Oral Cancer Detection Panels in a Prospective Blinded Cohort , 2016, PloS one.

[5]  Guiqing Liu,et al.  Evaluation of Reference Genes for Reverse Transcription Quantitative PCR Studies of Physiological Responses in the Ghost Moth, Thitarodes armoricanus (Lepidoptera, Hepialidae) , 2016, PloS one.

[6]  Paolo Ribeca,et al.  Genome sequence of the olive tree, Olea europaea , 2016, GigaScience.

[7]  Jiewei Zhang,et al.  Validation of Reference Genes for Gene Expression by Quantitative Real-Time RT-PCR in Stem Segments Spanning Primary to Secondary Growth in Populus tomentosa , 2016, PloS one.

[8]  Weicai Li,et al.  Validation of Reference Genes for RT-qPCR Studies of Gene Expression in Preharvest and Postharvest Longan Fruits under Different Experimental Conditions , 2016, Front. Plant Sci..

[9]  M. Gonzalo Claros,et al.  Automatic Workflow for the Identification of Constitutively-Expressed Genes Based on Mapped NGS Reads , 2016, IWBBIO.

[10]  S. Avnet,et al.  Identification and Validation of Housekeeping Genes for Gene Expression Analysis of Cancer Stem Cells , 2016, PloS one.

[11]  M. Schmid,et al.  Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M , 2015, PLoS genetics.

[12]  M. Gonzalo Claros,et al.  ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome , 2015, Front. Plant Sci..

[13]  Suzanne W. Hoogstrate,et al.  BURSTING POLLEN is required to organize the pollen germination plaque and pollen tube tip in Arabidopsis thaliana. , 2015, The New phytologist.

[14]  Joshua C. Johnson,et al.  Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR , 2014, BMC Research Notes.

[15]  P. Courtoy,et al.  Validation of housekeeping gene and impact on normalized gene expression in clear cell Renal Cell Carcinoma: critical reassessment of YBX3/ZONAB/CSDA expression , 2014, BMC Molecular Biology.

[16]  E. Levanon,et al.  Human housekeeping genes, revisited. , 2013, Trends in genetics : TIG.

[17]  J. Jakše,et al.  Validation of candidate reference genes in RT-qPCR studies of developing olive fruit and expression analysis of four genes involved in fatty acids metabolism , 2013, Molecular Breeding.

[18]  I. Brum,et al.  Reference gene for primary culture of prostate cancer cells , 2013, Molecular Biology Reports.

[19]  P. Hernández,et al.  Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (Olea europaea L.) , 2013, BMC Plant Biology.

[20]  Yoo Jin Jung,et al.  The transcriptional landscape and mutational profile of lung adenocarcinoma , 2012, Genome research.

[21]  Robert Gentleman,et al.  Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer , 2012, Nature Genetics.

[22]  Maurício Rocha-Martins,et al.  Avoiding Pitfalls of Internal Controls: Validation of Reference Genes for Analysis by qRT-PCR and Western Blot throughout Rat Retinal Development , 2012, PloS one.

[23]  Günter P. Wagner,et al.  Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples , 2012, Theory in Biosciences.

[24]  B. Ruperti,et al.  Evaluation of RNA extraction methods and identification of putative reference genes for real-time quantitative polymerase chain reaction expression studies on olive (Olea europaea L.) fruits. , 2012, Journal of agricultural and food chemistry.

[25]  M. Kalita,et al.  Rubisco-bis-phosphate oxygenase ( RuBP )- A potential housekeeping gene for qPCR assays in tea , 2012 .

[26]  J. Degenhardt,et al.  Isolation and characterization of terpene synthases potentially involved in flavor development of ripening olive (Olea europaea) fruits. , 2012, Journal of plant physiology.

[27]  Cathy Vaillancourt,et al.  Quantitative PCR Pitfalls: The Case of the Human Placenta , 2012, Molecular Biotechnology.

[28]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[29]  Jun Wang,et al.  AB227. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings , 2012, Cell Research.

[30]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..

[31]  Rasko Leinonen,et al.  The sequence read archive: explosive growth of sequencing data , 2011, Nucleic Acids Res..

[32]  T. Vashisth,et al.  An efficient RNA isolation procedure and identification of reference genes for normalization of gene expression in blueberry , 2011, Plant Cell Reports.

[33]  Wang-jin Lu,et al.  Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions , 2011, Planta.

[34]  Sumei Chen,et al.  Reference Gene Selection for Quantitative Real-Time PCR in Chrysanthemum Subjected to Biotic and Abiotic Stress , 2011, Molecular biotechnology.

[35]  Cheng-Wei Chang,et al.  Identification of Reference Genes across Physiological States for qRT-PCR through Microarray Meta-Analysis , 2011, PloS one.

[36]  Edmund M. Clarke,et al.  Analysis and verification of the HMGB1 signaling pathway , 2010, BMC Bioinformatics.

[37]  Pjotr Prins,et al.  BioRuby: bioinformatics software for the Ruby programming language , 2010, Bioinform..

[38]  B. Román,et al.  Evaluation of candidate reference genes for expression studies in Pisumsativum under different experimental conditions , 2010, Planta.

[39]  M. Alves-Ferreira,et al.  Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data , 2010, BMC Plant Biology.

[40]  M. De Loose,et al.  Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR , 2010, BMC Molecular Biology.

[41]  M. Gonzalo Claros,et al.  SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read , 2010, BMC Bioinformatics.

[42]  G. Galla,et al.  Computational annotation of genes differentially expressed along olive fruit development , 2009, BMC Plant Biology.

[43]  Zhen Zhang,et al.  Selection of reliable reference genes for gene expression studies in peach using real-time PCR , 2009, BMC Molecular Biology.

[44]  Vlad Popovici,et al.  Selecting control genes for RT-QPCR using public microarray data , 2009, BMC Bioinformatics.

[45]  I. Maia,et al.  Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions , 2009, BMC Molecular Biology.

[46]  David S. Skibbe,et al.  Male reproductive development: gene expression profiling of maize anther and pollen ontogeny , 2008, Genome Biology.

[47]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[48]  I. van Mechelen,et al.  Using Ribosomal Protein Genes as Reference: A Tale of Caution , 2008, PloS one.

[49]  E. Wurmbach,et al.  De-regulation of common housekeeping genes in hepatocellular carcinoma , 2007, BMC genomics.

[50]  S. Lund,et al.  An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development , 2006, BMC Plant Biology.

[51]  P. Carinci,et al.  Comparative study of gene expression by cDNA microarray in human colorectal cancer tissues and normal mucosa. , 2006, International journal of oncology.

[52]  Mukesh Jain,et al.  Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. , 2006, Biochemical and biophysical research communications.

[53]  L. Hoffmann,et al.  Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. , 2005, Journal of experimental botany.

[54]  Andreas Nitsche,et al.  Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization? , 2005, Journal of Molecular Medicine.

[55]  M. Stitt,et al.  Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w] , 2005, Plant Physiology.

[56]  B. Tilton,et al.  Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues. , 2005, Molecular and cellular probes.

[57]  S. Strauss,et al.  Validating internal controls for quantitative plant gene expression studies , 2004, BMC Plant Biology.

[58]  Claus Lindbjerg Andersen,et al.  Normalization of Real-Time Quantitative Reverse Transcription-PCR Data: A Model-Based Variance Estimation Approach to Identify Genes Suited for Normalization, Applied to Bladder and Colon Cancer Data Sets , 2004, Cancer Research.

[59]  M. Pfaffl,et al.  Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations , 2004, Biotechnology Letters.

[60]  J. S. Coker,et al.  Selection of candidate housekeeping controls in tomato plants using EST data. , 2003, BioTechniques.

[61]  G. Pertea,et al.  Comparative Analyses of Potato Expressed Sequence Tag Libraries1 , 2003, Plant Physiology.

[62]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[63]  T. Hudson,et al.  Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. , 2002, Genome research.

[64]  P. J. Higgins,et al.  Control selection for RNA quantitation. , 2000, BioTechniques.

[65]  T. Grisar,et al.  Housekeeping genes as internal standards: use and limits. , 1999, Journal of biotechnology.

[66]  J. de Dios Alché,et al.  The major olive pollen allergen (Ole e I) shows both gametophytic and sporophytic expression during anther development, and its synthesis and storage takes place in the RER. , 1999, Journal of cell science.

[67]  S. Walker,et al.  Quantitative RT-PCR : Pitfalls and Potential , 1999 .

[68]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .

[69]  M. Stitt,et al.  Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization , 2005 .