C. Calixto

发表

TranSuite: a software suite for accurate translation and characterization of transcripts

John W. S. Brown, Runxuan Zhang, Wenbin Guo, 2020, bioRxiv.

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

John W. S. Brown, Runxuan Zhang, C. Hornyik, 2019, Front. Plant Sci..

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

H. Hirt, Yamile Marquez, John W. S. Brown, 2017, Nucleic acids research.

AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

H. Hirt, Yamile Marquez, John W. S. Brown, 2016, bioRxiv.

AtRTD 2 : A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

H. Hirt, Yamile Marquez, John W. S. Brown, 2016 .

AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript‐specific expression in Arabidopsis thaliana

E. Eyras, Yamile Marquez, John W. S. Brown, 2015, The New phytologist.

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome[CC-BY]

John W. S. Brown, Runxuan Zhang, Heather Knight, 2018, Plant Cell.

Analyses of sexual reproductive success in transgenic and/or mutant plants.

G. Goldman, M. H. Goldman, C. Calixto, 2009, Journal of integrative plant biology.

Integrative RNA Biology

Matthew R. Gazzara, Lela Lackey, J. Brown, 2016 .

Evolutionary Relationships Among Barley and Arabidopsis Core Circadian Clock and Clock-Associated Genes

John W. S. Brown, R. Waugh, C. Calixto, 2015, Journal of Molecular Evolution.

Deposited in DRO : 08 November 2018 Version of attached

Runxuan Zhang, H. G. Nimmo, Wenbin Guo, 2018 .

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome[CC-BY]

John W. S. Brown, Runxuan Zhang, Heather Knight, 2018, Plant Cell.

How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)

John W. S. Brown, C. Simpson, Runxuan Zhang, 2018, Plant, cell & environment.

TSIS: an R package to infer alternative splicing isoform switches for time-series data

Wenbin Guo, John W. S. Brown, Runxuan Zhang, 2017, Bioinform..

Gene expression TSIS : an R package to infer alternative splicing isoform switches for time-series data

John W. S. Brown, Runxuan Zhang, Wenbin Guo, 2017 .

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

M. Bayer, I. Milne, John W. S. Brown, 2016, Nature Genetics.

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

E. Huq, A. Wachter, L. Milne, 2021, Genome Biology.

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Peter J. Shaw, Cristiane P. G. Calixto, Sang Hyon Kim, 2010, Nucleic acids research.

High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants.

Runxuan Zhang, John W. S. Brown, Runxuan Zhang, 2017, The New phytologist.

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

I. Milne, John W. S. Brown, Runxuan Zhang, 2020, RNA biology.

A powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

Iain Milne, Gordon Stephen, Wenbin Guo, 2019, bioRxiv.

High-Resolution RT-PCR Analysis of Alternative Barley Transcripts.

L. Milne, C. Mayer, John W. S. Brown, 2018, Methods in molecular biology.

Alternative Splicing of Barley Clock Genes in Response to Low Temperature

John W. S. Brown, C. Simpson, R. Waugh, 2016, PloS one.

Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

C. T. Hotta, John W. S. Brown, M. S. Carneiro, 2019, bioRxiv.

Alternative splicing of circadian clock genes correlates with 1 temperature in field-grown sugarcane 2 Running title : Rhythms of alternative splicing in sugarcane correlate with temperature 3

C. T. Hotta, John W. S. Brown, M. S. Carneiro, 2019 .

Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing.

John W. S. Brown, Runxuan Zhang, H. G. Nimmo, 2021, Methods in molecular biology.

Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

Ping Lin, Wenbin Guo, John W. S. Brown, 2017, BMC Systems Biology.

Analyses of sexual reproductive success in transgenic and/or mutant plants.

G. Goldman, C. Calixto, M. Goldman, 2009, Journal of integrative plant biology.