Ye Ding

发表

Potent effect of target structure on microRNA function

Dang D. Long, V. Ambros, Rosalind C. Lee, 2007, Nature Structural &Molecular Biology.

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble.

C. Lawrence, C. Chan, Ye Ding, 2005, RNA.

mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts

Dang D. Long, V. Ambros, Ye Ding, 2008, Nature Methods.

A statistical sampling algorithm for RNA secondary structure prediction.

C. Lawrence, Ye Ding, 2003, Nucleic acids research.

Clustering of RNA secondary structures with application to messenger RNAs.

C. Lawrence, C. Chan, Ye Ding, 2006, Journal of molecular biology.

prediction Statistical and Bayesian approaches to RNA secondary structure

Ye Ding, 2006 .

Statistical and Bayesian approaches to RNA secondary structure prediction.

Ye Ding, 2006, RNA.

Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

Ye Ding, A. van den Berg, B. Kroesen, 2012, PloS one.

CLIP-based prediction of mammalian microRNA binding sites

William A. Rennie, Dang D. Long, Ye Ding, 2013, Nucleic acids research.

STarMir Tools for Prediction of microRNA Binding Sites.

William A. Rennie, Ye Ding, C. Carmack, 2016, Methods in molecular biology.

Identification of bacterial sRNA regulatory targets using ribosome profiling

Jing Wang, William A. Rennie, Chaochun Liu, 2015, Nucleic acids research.

microRNA seedless sites attenuate strong-seed-site-mediated target repression

Ye Ding, Hongyu Zhao, Hui Lu, 2019, bioRxiv.

Single-cell microRNA/mRNA co-sequencing reveals non-genetic heterogeneity and novel regulatory mechanisms

Ye Ding, R. Fan, Yang Liu, 2018, bioRxiv.

RATIONAL STATISTICAL DESIGN OF ANTISENSE OLIGONUCLEOTIDES FOR HIGH THROUGHPUT FUNCTIONAL GENOMICS AND DRUG TARGET VALIDATION

Ye Ding, 2002 .

STarMirDB: A database of microRNA binding sites

William A. Rennie, Dang D. Long, Ye Ding, 2016, RNA biology.

The Bin3 RNA methyltransferase targets 7SK RNA to control transcription and translation

William A. Rennie, Ye Ding, M. Cosgrove, 2012, Wiley interdisciplinary reviews. RNA.

Relevance of kinetochore size and microtubule-binding capacity for stable chromosome attachment during mitosis in PtK1 cells

Ye Ding, A. Heagle, B. McEwen, 1998, Chromosome Research.

Rational design leads to more potent RNA interference against hepatitis B virus: factors effecting silencing efficiency.

Dang D. Long, Anton P. McCaffrey, Ryan M Spengler, 2009, Molecular therapy : the journal of the American Society of Gene Therapy.

Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation.

Jun Liu, William A. Rennie, Shaveta Kanoria, 2017, Genome research.

mirWIP: microRNA Target Prediction Based on miRNP Enriched Transcripts

Min Han, C. Steven Carmack, Dang D. Long, 2011 .

N 6-methyladenosine enhances post-transcriptional gene regulation by microRNAs

William A. Rennie, Ye Ding, C. Carmack, 2022, Bioinformatics advances.

Effects of genetic variations on microRNA: target interactions

William A. Rennie, Ye Ding, C. Carmack, 2014, Nucleic acids research.

Ab initio identification of functionally interacting pairs of cis-regulatory elements.

Noam Shomron, Michael B. Stadler, Michael B Stadler, 2008, Genome research.

The imprinted H19 lncRNA antagonizes let-7 microRNAs.

Chaochun Liu, Wang Min, Jing Ma, 2013, Molecular cell.

Characterization of the mammalian miRNA turnover landscape

Jun Liu, Jun Lu, Ye Ding, 2015, Nucleic acids research.

MicroRNA binding sites in C. elegans 3′ UTRs

William A. Rennie, Chaochun Liu, Adam Wolenc, 2014, RNA biology.

An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis.

Ye Ding, In-Hyun Park, Jianjun Chen, 2013, Cell reports.

RNA Secondary Structure Prediction and Gene Regulation by Small RNAs

Ye Ding, Ye Ding, 2010 .

STarMir: a web server for prediction of microRNA binding sites

Jun Lu, Ye Ding, William A. Rennie, 2014, Nucleic Acids Res..

A structural interpretation of the effect of GC-content on efficiency of RNA interference

Ye Ding, C. Steven Carmack, Dang D. Long, 2009, BMC Bioinformatics.

Identification of novel genes that regulate androgen receptor signaling and growth of androgen-deprived prostate cancer cells

Ye Ding, I. Roninson, M. Shtutman, 2015, Oncotarget.

Sfold web server for statistical folding and rational design of nucleic acids

Ye Ding, Charles E. Lawrence, Chi Yu Chan, 2004, Nucleic Acids Res..

A structural analysis of in vitro catalytic activities of hammerhead ribozymes

Ye Ding, Yu Shao, Chi Yu Chan, 2007, BMC Bioinformatics.

Effect of target secondary structure on RNAi efficiency.

Chi Yu Chan, Anil Maliyekkel, Charles E Lawrence, 2007, RNA.

RNA Interference Technology: Rational design of siRNAs with the Sfold software

Ye Ding, Ye Ding, Charles E. Lawrence, 2005 .

1 Rational Design of siRNAs with the S fold Software

Ye Ding, Charles E. Lawrence, 2003 .

Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing

T. Harkins, Ye Ding, C. Carmack, 2010, Proceedings of the National Academy of Sciences.

Tumor-specific silencing of COPZ2 gene encoding coatomer protein complex subunit ζ2 renders tumor cells dependent on its paralogous gene COPZ1

T. Harkins, Ye Ding, C. Carmack, 2011, Proceedings of the National Academy of Sciences.

NpgRJ_NSMB_1226 287..294

Dang D. Long, V. Ambros, Rosalind C. Lee, 2019 .

Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

Burak Dura, Yang Liu, Miaomiao Zhang, 2019, Nature Communications.

A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction

Ye Ding, Charles E. Lawrence, C. Lawrence, 1999, Comput. Chem..

Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles

Chi Yu Chan, C. Chan, Ye Ding, 2007, Journal of mathematical biology.

Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation

Ye Ding, R. Fan, Yang Liu, 2019, Nature Communications.

Structure clustering features on the Sfold Web server

Ye Ding, Charles E. Lawrence, Chi Yu Chan, 2005, Bioinform..

Pacific Symposium on Biocomputing 13:64-74(2008) ANALYSIS OF MICRORNA-TARGET INTERACTIONS BY A TARGET STRUCTURE BASED HYBRIDIZATION MODEL

Ye Ding, Dang D. Long, Chi Yu Chan, 2022 .

A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions

Y. Kluger, S. Weissman, Ye Ding, 2016, Nature Communications.

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation

Chi Yu Chan, C. Chan, Ye Ding, 2006, Nucleic acids research.

Ab initio identification of functionally interacting pairs of cis-regulatory elements.

Michael B. Stadler, C. Burge, Ye Ding, 2008, Genome research.