Publications

Hsin-Yen Larry Wu and Polly Yingshan Hsu. Dispersed transcription start sites modulate uORF-mediated regulation in Arabidopsis. bioRxiv. LINK


Hsin-Yen Larry Wu, Qiaoyun Ai, Rita Teresa Teixeira, Phong Nguyen, Gaoyuan Song, Christian Montes, J. Mitch Elmore,  Justin W. Walley,  Polly Yingshan Hsu. (2024) Improved super-resolution ribosome profiling revealed prevalent translation of upstream ORFs and small ORFs in Arabidopsis. The Plant Cell. LINK


Hsin-Yen Larry Wu,  Joey Jen,  Polly Yingshan Hsu. (2024) What, where, and how: Regulation of translation and the translational landscape in plants. The Plant Cell. LINK


Hsin-Yen Larry Wu and Polly Yingshan Hsu. Arabidopsis uORF-containing mRNAs behave differently from NMD targets. bioRxiv. LINK 


Hsin-Yen Larry Wu and Polly Yingshan Hsu. (2022) A custom library construction method for super-resolution ribosome profiling in Arabidopsis. Plant Methods. LINK 


Kyle Palos, Anna C Nelson Dittrich, Li’ang Yu, Jordan R Brock, Caylyn E Railey, Hsin-Yen Larry Wu, Ewelina Sokolowska, Aleksandra Skirycz, Polly Yingshan Hsu, Brian D Gregory, Eric Lyons, Mark A Beilstein, Andrew D L Nelson. (2022) Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae. The Plant Cell. LINK 


Hsin-Yen Larry Wu and Polly Yingshan Hsu.  (2021) RiboPlotR: a visualization tool for periodic Ribo-seq reads. Plant Methods. LINK 


Hsin-Yen Larry Wu, Gaoyuan Song, Justin W Walley, Polly Yingshan Hsu .  (2019) Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling. Plant Physiology.  LINK


Gaoyuan Song, Polly Yingshan Hsu, Justin W Walley.  (2018) Assessment and refinement of sample preparation methods for deep and quantitative plant proteome profiling. Proteomics.  LINK


Polly Yingshan Hsu and Philip N. Benfey.  (2017) Small but mighty: functional peptides encoded by small ORFs in plants. Proteomics.  LINK

​

Jennifer A. Gray, Akiva Shalit-Kaneh , Dalena Nhu Chua, Polly Yingshan Hsu, Stacey L. Harmer.  (2017) The REVEILLE clock genes inhibit growth of juvenile and adult plants by control of cell size. Plant Physiology.  LINK


Polly Yingshan Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li , Carl J. Rothfels, Uwe Ohler and Philip N. Benfey.  (2016) Super-Resolution Ribosome Profiling Reveals Novel Translation Events in Arabidopsis. Proc. Natl. Acad. Sci. USA.  LINK​

​

Polly Yingshan Hsu and Stacey L. Harmer.  (2014) Global profiling of the circadian transcriptome using microarrays. Methods in Molecular Biology.  LINK

 

Polly Yingshan Hsu and Stacey L. Harmer.  (2014) Wheels within wheels: the plant circadian system. Trends in Plant Science.  LINK

     * Top 10 articles in 2014 in TIPS

​​

Polly Yingshan Hsu, Upendra K. Devisetty and Stacey L. Harmer.  (2013) Accurate timekeeping is controlled by a cycling activator in Arabidopsis. eLife.  LINK​

     * Editors’ choice  * Featured in eLife  * F1000 Recommended Article


Polly Yingshan Hsu and Stacey L. Harmer.  (2012) Circadian phase has profound effects on differential expression analysis. PLoS ONE. LINK

 

Reetika Rawat, Nozomu Takahashi*, Polly Yingshan Hsu*, Matthew A. Jones, Jacob Schwartz, Michelle R. Salemi, Brett S. Phinney, and Stacey L. Harmer.  (2011) REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genetics.  *contributed equally. LINK

 

Ying-Shan Hsu, Shiang-Jiun Chen, Chin-Mei Lee, and Ling-Long Kuo-Huang.  (2005) Anatomical characteristics of the secondary phloem in branches of Zelkova serrata Makino. Bot. Bull. Acad. Sin.  46:143-149. LINK