Posts by Collection

Portfolio item number 1

Short description of portfolio item number 1

Portfolio item number 2

Short description of portfolio item number 2

DPMIND: degradome-based plant miRNA-target interaction and network database

Published in Bioinformatics, 2017

Recommended citation: Fei Y, Wang R, Li H, Liu S, Zhang H, Huang J^#. DPMIND: degradome-based plant miRNA-target interaction and network database. Bioinformatics, 34(9): 1618–1620, 2018.
Download Paper

Construction and analysis of degradome-dependent microRNA regulatory networks in soybean

Published in BMC Genomics, 2018

Recommended citation: Wang R, Yang Z, Fei Y, Feng J, Zhu H, Huang F, Zhang H, Huang J^#. Construction and analysis of degradome-dependent microRNA regulatory networks in soybean. BMC Genomics, 20(1): 534, 2019.
Download Paper

WPMIAS: Whole-degradome-based Plant MicroRNA-target Interaction Analysis Server

Published in Bioinformatics, 2019

Recommended citation: Fei Y, Mao Y, Shen C, Wang R, Zhang H, Huang J^#. WPMIAS: Whole-degradome-based Plant MicroRNA-target Interaction Analysis Server. Bioinformatics, 36(6): 1937–1939, 2020.
Download Paper

poly(UG)-tailed RNAs in genome protection and epigenetic inheritance

Published in Nature, 2020

Recommended citation: Shukla A*, Yan J*, Pagano D J, Dodson A E, Fei Y, Gorham J, Seidman J G, Wickens M, Kennedy S^#. poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature, 582(7811): 283–288, 2020.
Download Paper

A Conserved NRDE-2/MTR-4 Complex Mediates Nuclear RNAi in Caenorhabditis elegans

Published in Genetics, 2020

Recommended citation: Wan G, Yan J, Fei Y, Pagano D J, Kennedy S^#. A Conserved NRDE-2/MTR-4 Complex Mediates Nuclear RNAi in Caenorhabditis elegans. Genetics, 216(4): 1071-1085, 2020.
Download Paper

ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans

Published in EMBO Journal, 2021

Recommended citation: Wan G ^#, Bajaj L, Fields B, Dodson A E, Pagano D J, Fei Y, Kennedy S ^#. ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans. EMBO Journal, 40(3): e105612, 2021.
Download Paper

PhasiRNAnalyzer: an integrated analyser for plant phased siRNA

Published in RNA Biology, 2021

Recommended citation: Fei Y, Feng J, Wang R, Zhang B, Zhang H, Huang J^#. PhasiRNAnalyzer: an integrated analyser for plant phased siRNA. RNA Biology, 18(11): 1622–1629, 2021.
Download Paper

RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data

Published in Journal of Experimental Botany, 2022

Recommended citation: Zhang B, Fei Y, Feng J, Zhu X, Wang R, Xiao H, Zhang H, Huang J^#. RiceNCexp: a rice non-coding RNA co-expression atlas based on massive RNA-seq and small-RNA seq data. Journal of Experimental Botany, 73(18): 6068–6077, 2022.
Download Paper

Advances and opportunities in RNA structure experimental determination and computational modeling

Published in Nature Methods, 2022

Recommended citation: Zhang J*, Fei Y*, Sun L ^#, Zhang Q C^#. Advances and opportunities in RNA structure experimental determination and computational modeling. Bioinformatics, 19(10): 1193–1207, 2022.
Download Paper

RNA structural dynamics modulate EGFR-TKI resistance through controlling YRDC translation in NSCLC cells

Published in Genomics, Proteomics & Bioinformatics, 2022

Recommended citation: Shi B*, An K*, Wang Y, Fei Y, Guo C, Zhang Q C, Yang Y, Tian X, Kan Q^#. RNA Structural Dynamics Modulate EGFR-TKI Resistance Through Controlling YRDC Translation in NSCLC Cells. Genomics, Proteomics & Bioinformatics, 21(4): 850–865, 2023.
Download Paper

PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences

Published in Bioinformatics, 2023

Recommended citation: Feng Z, Feng J, Zhang B, Fei Y, Zhang, H, Huang J^#. PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences. Bioinformatics, 39(11): btad676, 2023.
Download Paper

RASP v2.0: an updated atlas for RNA structure probing data

Published in Nucleic Acids Research, 2025

Recommended citation: Mu K*, Fei Y*,^#, Xu Y, Zhang Q C^#. RASP v2.0: an updated atlas for RNA structure probing data. Nucleic Acids Research, 53(D1): D211–D219, 2025.
Download Paper

Predicting small molecule–RNA interactions without RNA tertiary structures

Published in Nature Biotechnology, 2026

Recommended citation: Fei Y*, Wang P*, Zhang J*, Shan X, Cai Z, Ma J, Wang Y^#, Zhang Q C^#. Predicting small molecule–RNA interactions without RNA tertiary structures. Nature Biotechnology, 2026, Online.
Download Paper

Honors & Awards

Published: January 01, 2026

1. Best Presenter, the 3rd Postdoctoral Forum on “Life Sciences, Medicine, and Pharmacy”, Tsinghua University, 2023
2. Best Poster, the 3rd Postdoctoral Forum on “Life Sciences, Medicine, and Pharmacy”, Tsinghua University, 2023
3. Gold Award for Poster, Cold Spring Harbor Asia Conference, “RNA Therapeutics: Current Status and Future”, 2023
4. Outstanding Postdoctoral Fellowship, Postdoctoral Foundation of Tsinghua-Peking Center for Life Sciences, 2023
5. Distinguished Postdoctoral Fellowship, Postdoctoral Foundation of Tsinghua-Peking Center for Life Sciences, 2021
6. Outstanding Graduate Thesis, Nanjing Agricultural University, 2020
7. Outstanding Graduate, Nanjing Agricultural University, 2019
8. Innovation Project for Doctoral Thesis (Class I), Nanjing Agricultural University, 2019
9. Presidential Scholarship, Nanjing Agricultural University, 2018
10. Zhongshan Scholar Research Star Award, Nanjing Agricultural University, 2018
11. Outstanding Volunteer, Nanjing Agricultural University, 2016
12. Outstanding Graduate Student Leader, Nanjing Agricultural University, 2016
13. First-Class Academic Scholarship for Students, Nanjing Agricultural University, 2016, 2017, and 2018
14. First-Class Academic Scholarship for Students, Nanjing Agricultural University, 2014 and 2015
15. Outstanding in Mid-Term Assessment for Students, Nanjing Agricultural University, 2015 and 2017

Conference Talks

Published: January 01, 2026

1. The 13th National Ribonucleic Acid (RNA) Symposium, Chengdu, Sichuan, 2025-12
2. The 1st National Conference on Artificial Intelligence in Biology, Hangzhou, Zhejiang, 2025-6

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.