NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning

Modelling Distributions of Asian and African Rice Based on MaxEnt

(2023) Yunan Lin et al.   Sustainability

A computational framework of routine test data for the cost-effective chronic disease prediction

(2023) Mingzhu Liu et al.   BRIEFINGS IN BIOINFORMATICS

A cost-effective machine learning-based method for preeclampsia risk assessment and driver genes discovery

(2023) Hao Wang et al.   Cell and Bioscience

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants

(2022) Rachel Shahan et al.   DEVELOPMENTAL CELL

Species-specific function of conserved regulators in orchestrating rice root architecture

(2022) Tushar Garg et al.   DEVELOPMENT

Plant Public RNA‐seq Database: a comprehensive online database for expression analysis of ~45 000 plant public RNA‐Seq libraries

(2022) Yiming Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

DEMOC: a deep embedded multi-omics learning approach for clustering single-cell CITE-seq data

(2022) Guanhua Zou et al.   BRIEFINGS IN BIOINFORMATICS

devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data

(2022) Francisco X. Galdos et al.   Nature Communications

A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis

(2022) Alan E. Murphy et al.   Nature Communications

The miR172/ IDS1 signaling module confers salt tolerance through maintaining ROS homeostasis in cereal crops

(2021) Xiliu Cheng et al.   NEW PHYTOLOGIST

eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition

(2021) Hao Wang et al.   BIOINFORMATICS

HelPredictor models single-cell transcriptome to predict human embryo lineage allocation

(2021) Pengfei Liang et al.   BRIEFINGS IN BIOINFORMATICS

Single-cell RNA analysis reveals the potential risk of organ-specific cell types vulnerable to SARS-CoV-2 infections

(2021) Zilong Zhang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Publisher Correction: Amplification-free single-cell whole-genome sequencing gets a makeover

(2020) Vesna Todorovic   NATURE METHODS

Machine Learning of Single-cell Transcriptome Highly Identify mRNA Signature by Comparing F-score Selection with Differential Expression Analysis

(2020) Pengfei Liang et al.   Molecular Therapy-Nucleic Acids

Application of deep learning methods in biological networks

(2020) Shuting Jin et al.   BRIEFINGS IN BIOINFORMATICS

Robust Transcription Factor Binding Site Prediction Using Deep Neural Networks

(2020) Kanu Geete et al.   Current Bioinformatics

An Ensembled SVM Based Approach For Predicting Adverse Drug Reactions

(2020) Pratik Joshi et al.   Current Bioinformatics

Plant specialized metabolism

(2020) Ling Yuan et al.   PLANT SCIENCE

Contribution of phenylpropanoid metabolism to plant development and plant‐environment interactions

(2020) Nai‐Qian Dong et al.   Journal of Integrative Plant Biology

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

(2020) Rahul Shaw et al.   Molecular Plant

Transcriptional landscape of rice roots at the single-cell resolution

(2020) Qing Liu et al.   Molecular Plant

Loss of COMT activity reduces lateral root formation and alters the response to water limitation in sorghum brown midrib ( bmr ) 12 mutant

(2020) Manny Saluja et al.   NEW PHYTOLOGIST

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

Molecular Mechanisms of Root Development in Rice

(2019) Funing Meng et al.   Rice

Improved Pre-miRNAs Identification Through Mutual Information of Pre-miRNA Sequences and Structures

(2019) Xiangzheng Fu et al.   Frontiers in Genetics

Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing

(2019) Tom Denyer et al.   DEVELOPMENTAL CELL

A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root

(2019) Tian-Qi Zhang et al.   Molecular Plant

High-Throughput Single-Cell Transcriptome Profiling of Plant Cell Types

(2019) Christine N. Shulse et al.   Cell Reports

New 3D graphical representation for RNA structure analysis and its application in the pre-miRNA identification of plants

(2018) Xiangzheng Fu et al.   RSC Advances

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

(2018) Qian Zhang et al.   Molecular Plant

Nitrogen fertilizer application affects lodging resistance by altering secondary cell wall synthesis in japonica rice (Oryza sativa)

(2017) Wujun Zhang et al.   JOURNAL OF PLANT RESEARCH

Transcriptomic Profiling Maps Anatomically Patterned Subpopulations among Single Embryonic Cardiac Cells

(2016) Guang Li et al.   DEVELOPMENTAL CELL

Random Forests and Kernel Methods

(2016) Erwan Scornet   IEEE TRANSACTIONS ON INFORMATION THEORY

Breeding high-yield superior quality hybrid super rice by rational design

(2016) Qian Qian et al.   National Science Review

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

(2015) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

(2012) Davide Albanese et al.   BIOINFORMATICS

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

(2011) Hinako Takehisa et al.   PLANT JOURNAL

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Functional genomics of root growth and development in Arabidopsis

(2008) Anjali Iyer-Pascuzzi et al.   CURRENT OPINION IN PLANT BIOLOGY

Hormone interactions at the root apical meristem

(2008) Eva Benková et al.   PLANT MOLECULAR BIOLOGY

Molecular Genetics of Rice Root Development

(2008) J. Rebouillat et al.   Rice