Bioinplant Paper

Online Databases/Tools by Bioinplant Lab:

PscLncRNA: A database for plant single-cell lncRNA analysis. Xu et al., 2024, New Phytologist

The database of N3: plants,genomes,technologies. Xie et al., 2024, Nature Plant

PlantscRNAdb: A database for plant single-cell RNA analysis. Chen et al., 2021, Molecular Plant

PlantcircBase: A database for plant circular RNAs. Chu et al., 2017, Molecular Plant

BnPedigome: A genomic database for the pedigrees and breeding of Brassica napus. Zou et al., 2019, Plant Biotechnology Journal

RiceRelativesGD: A genomic database of rice relatives for rice breeding. Mao et al., 2019, Database

Local Software by Bioinplant Lab:

ePmiRNA_finder: Multi-layer feature selection methods and classifiers for plant-derived miRNA identification from animal miRNA sequencing data. . Chen et al., 2021, PLoS One

DipHiC: A pipeline for polyploid genome scaffolding using diploid ancestry information and HiC data . Wu et al., 2021, Nature Communications

Scan_phasiRNA: A program to find loci with 21nt phased siRNAs (such as ta-siRNA gene TAS) using the Howell algorithm (Download). Shen et al., 2009, Plant Systematics and Evolution

eTM_finder: A tool to predict eTMs (endogenous target mimics) of miRNAs in plants (Download). Ye et al., 2014, Frontiers in Plant Science

circseq-cup: A program to assemble full-length sequences of circular RNAs (Download). Ye et al., 2016, RNA Biology

PcircRNA-finder: A program to identify circular RNAs in plants (Download). Chen et al., 2016, Bioinformatics

circRNA_pocket: A tool to show genomic features of circRNAs (Download). Zhang et al., 2016, 已获得计算机软件著作权【Patent registration number：2017SR231288】

TOD-Bayes: A naïve Bayes algorithm for tissue origin diagnosis of synchronous multifocal tumors in the hepatobiliary and pancreatic system (Download). 2017, International Journal of Cancer

Other Public Bioinformatic Tools: