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List of works by Shaojie Zhang

A memory efficient method for structure-based RNA multiple alignment.

scientific article published on 29 April 2011

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

scientific article published in July 2006

Accurate and Efficient Mapping of the Cross-Linked microRNA-mRNA Duplex Reads

scientific article published on 29 May 2019

CRISPR-Cas9 nuclear dynamics and target recognition in living cells.

scientific article published on 22 August 2016

CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging

scientific article published on 30 October 2018

Cell cycle- and genomic distance-dependent dynamics of a discrete chromosomal region

scientific article published on 07 March 2019

Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment

scientific article

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.

scientific article published on 21 June 2017

Computational analysis of RNA structures with chemical probing data

scientific article

Consensus folding of unaligned RNA sequences revisited

scientific article published in March 2006

De novo discovery of structural motifs in RNA 3D structures through clustering

scientific article published on 9 March 2018

Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data

scientific article (publication date: 21 August 2012)

Discovering non-coding RNA elements in Drosophila 3' untranslated regions ⬇️

scientific article

Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

scientific article published on 27 October 2020

Efficient alignment of RNA secondary structures using sparse dynamic programming

scientific article

Efficient haplotype matching between a query and a panel for genealogical search

scientific article published on 01 July 2019

Epigenetic regulation of microRNA genes and the role of miR-34b in cell invasion and motility in human melanoma

scientific article

Epigenetic regulation of microRNA-375 and its role in melanoma development in humans.

scientific article published on 26 June 2011

FastR: fast database search tool for non-coding RNA.

scientific article published in January 2004

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements

scientific article

Finding stable local optimal RNA secondary structures ⬇️

scientific article published on September 8, 2011

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

scientific article published on 16 October 2013

Incorporating phylogenetic-based covarying mutations into RNAalifold for RNA consensus structure prediction

scientific article (publication date: 27 April 2013)

Multi-allelic positional Burrows-Wheeler transform.

scientific article published on 6 June 2019

Multicolor CRISPR labeling of chromosomal loci in human cells.

scientific article

Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow.

scientific article

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions

scientific article published on 06 December 2018

Predicting folding pathways between RNA conformational structures guided by RNA stacks ⬇️

scientific article published on March 21, 2012

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.

scientific article

RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies

scientific article published on 01 June 2021

RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.

scientific article published on 8 August 2010

RNAMotifScanX: a graph alignment approach for RNA structural motif identification.

scientific article

RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts

scientific article published on 25 July 2019

STAR3D: a stack-based RNA 3D structural alignment tool

scientific article published on 15 July 2015

Searching genomes for noncoding RNA using FastR.

scientific article

Simultaneous folding of alternative RNA structures with mutual constraints: an application to next-generation sequencing-based RNA structure probing

scientific article

Structural alignment of pseudoknotted RNA.

scientific article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

scientific article

The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules

scientific article

Transcriptomic Profiling of Ribosomal Protein Pseudogenes in Diverse Human Tissues

Translation repression via modulation of the cytoplasmic poly(A)-binding protein in the inflammatory response

scientific article

WebSTAR3D: a web server for RNA 3D structural alignment

scientific article published on 6 August 2016

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