Zhang R - Search Results

1

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

Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS. Zhang R, et al. Nucleic Acids Res. 2017 May 19;45(9):5061-5073. doi: 10.1093/nar/gkx267. Nucleic Acids Res. 2017. PMID: 28402429 Free PMC article.

2

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

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW. Zhang R, et al. New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25. New Phytol. 2015. PMID: 26111100 Free PMC article.

3

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

Brown JW, Calixto CP, Zhang R. Brown JW, et al. Among authors: zhang r. New Phytol. 2017 Jan;213(2):525-530. doi: 10.1111/nph.14208. Epub 2016 Sep 23. New Phytol. 2017. PMID: 27659901 Free article. Review.

4

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

Guo W, Calixto CPG, Tzioutziou N, Lin P, Waugh R, Brown JWS, Zhang R. Guo W, et al. Among authors: zhang r. BMC Syst Biol. 2017 Jun 19;11(1):62. doi: 10.1186/s12918-017-0440-2. BMC Syst Biol. 2017. PMID: 28629365 Free PMC article.

5

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

Guo W, Calixto CPG, Brown JWS, Zhang R. Guo W, et al. Among authors: zhang r. Bioinformatics. 2017 Oct 15;33(20):3308-3310. doi: 10.1093/bioinformatics/btx411. Bioinformatics. 2017. PMID: 29028262 Free PMC article.

Although computational methods are available to study differential alternative splicing, few tools for detection of isoform switches exist and these are based on pairwise comparisons. Here, we provide the TSIS R package, which is the first tool for detecting significant tr …

Although computational methods are available to study differential alternative splicing, few tools for detection of isoform switches exist a …

6

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

James AB, Calixto CPG, Tzioutziou NA, Guo W, Zhang R, Simpson CG, Jiang W, Nimmo GA, Brown JWS, Nimmo HG. James AB, et al. Among authors: zhang r. Plant Cell Environ. 2018 Jul;41(7):1539-1550. doi: 10.1111/pce.13193. Epub 2018 May 2. Plant Cell Environ. 2018. PMID: 29532482 Free PMC article.

7

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome.

Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Calixto CPG, et al. Among authors: zhang r. Plant Cell. 2018 Jul;30(7):1424-1444. doi: 10.1105/tpc.18.00177. Epub 2018 May 15. Plant Cell. 2018. PMID: 29764987 Free PMC article.

8

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

Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS. Calixto CPG, et al. Among authors: zhang r. Front Plant Sci. 2019 Feb 28;10:235. doi: 10.3389/fpls.2019.00235. eCollection 2019. Front Plant Sci. 2019. PMID: 30891054 Free PMC article.

9

Application of a Sensitive and Reproducible Label-Free Proteomic Approach to Explore the Proteome of Individual Meiotic-Phase Barley Anthers.

Lewandowska D, Zhang R, Colas I, Uzrek N, Waugh R. Lewandowska D, et al. Among authors: zhang r. Front Plant Sci. 2019 Apr 2;10:393. doi: 10.3389/fpls.2019.00393. eCollection 2019. Front Plant Sci. 2019. PMID: 31001307 Free PMC article.

10

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.

Rapazote-Flores P, Bayer M, Milne L, Mayer CD, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. Rapazote-Flores P, et al. Among authors: zhang r. BMC Genomics. 2019 Dec 11;20(1):968. doi: 10.1186/s12864-019-6243-7. BMC Genomics. 2019. PMID: 31829136 Free PMC article.

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