PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA–lncRNA interaction prediction

Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction

(2019) Ning Jiang et al.   Horticulture Research

Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences

(2019) Aodan Xu et al.   Frontiers in Genetics

RPITER: A Hierarchical Deep Learning Framework for ncRNA–Protein Interaction Prediction

(2019) Cheng Peng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of Long Non-Coding RNAs Based on Deep Learning

(2019) Xiu-Qin Liu et al.   Genes

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data

(2019) Tsukasa Fukunaga et al.   Frontiers in Genetics

A Hybrid Prediction Method for Plant lncRNA-Protein Interaction

(2019) Jael Sanyanda Wekesa et al.   Cells

Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants

(2019) Ismalia Bouba et al.   MATHEMATICAL BIOSCIENCES

Genome-wide Identification of LncRNAs and Analysis of CeRNA Networks during Tomato Resistance to Phytophthora infestans

(2019) Jun Cui et al.   PHYTOPATHOLOGY

A novel hybrid approach based on fuzzy multi-criteria decision-making tools for assessing sustainable alternatives of power generation in San Andrés Island

(2019) A.M. Rosso-Cerón et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

Predicting lncRNA-miRNA Interaction via Graph Convolution Auto-Encoder

(2019) Yu-An Huang et al.   Frontiers in Genetics

DeepMirTar: a deep-learning approach for predicting human miRNA targets

(2018) Ming Wen et al.   BIOINFORMATICS

Pattern recognition analysis on long noncoding RNAs: a tool for prediction in plants

(2018) Tatianne da Costa Negri et al.   BRIEFINGS IN BIOINFORMATICS

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools

(2018) Ivan V Antonov et al.   BRIEFINGS IN BIOINFORMATICS

Beyond one-hot encoding: Lower dimensional target embedding

(2018) Pau Rodríguez et al.   IMAGE AND VISION COMPUTING

Review of ensembles of multi-label classifiers: Models, experimental study and prospects

(2018) Jose M. Moyano et al.   Information Fusion

Wheat miR9678 Affects Seed Germination by Generating Phased siRNAs and Modulating Abscisic Acid/Gibberellin Signaling

(2018) Guanghui Guo et al.   PLANT CELL

Recurrent Neural Networks for Multivariate Time Series with Missing Values

(2018) Zhengping Che et al.   Scientific Reports

Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans

(2018) Ning Jiang et al.   Horticulture Research

miES: predicting the essentiality of miRNAs with machine learning and sequence features

(2018) Fei Song et al.   BIOINFORMATICS

New advances of lncRNAs in liver fibrosis, with specific focus on lncRNA-miRNA interactions

(2018) Er-Bao Bian et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Detection of long non–coding RNA homology, a comparative study on alignment and alignment–free metrics

(2018) Teresa M. R. Noviello et al.   BMC BIOINFORMATICS

Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models

(2018) Qi Zhao et al.   BMC GENOMICS

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions

(2018) Jun Cui et al.   PLANT JOURNAL

Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis

(2017) Jiapei Yan et al.   PLANT CELL

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance toPhytophthora infestansby co-expressing glutaredoxin

(2017) Jun Cui et al.   PLANT JOURNAL

Transcriptome signatures of tomato leaf induced by Phytophthora infestans and functional identification of transcription factor SpWRKY3

(2017) Jun Cui et al.   THEORETICAL AND APPLIED GENETICS

Non-coding RNAs and Their Roles in Stress Response in Plants

(2017) Jingjing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide

(2016) Akinobu Matsumoto et al.   NATURE

RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

(2015) Ming Zhou et al.   CURRENT OPINION IN PLANT BIOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

GREENC: a Wiki-based database of plant lncRNAs

(2015) Andreu Paytuví Gallart et al.   NUCLEIC ACIDS RESEARCH

CANTATAdb: A Collection of Plant Long Non-Coding RNAs

(2015) Michał W. Szcześniak et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

(2015) Jinyan Wang et al.   Scientific Reports

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

(2014) Y. Bai et al.   Briefings in Functional Genomics

Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress

(2014) Wei Zhang et al.   PLoS One

An integrated evolutionary analysis of miRNA–lncRNA in mammals

(2013) Li Guo et al.   MOLECULAR BIOLOGY REPORTS

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

RNA-directed DNA methylation in plants

(2013) Heng Zhang et al.   RNA Biology

Generalized Needleman–Wunsch algorithm for the recognition of T-cell epitopes

(2007) Loris Nanni et al.   EXPERT SYSTEMS WITH APPLICATIONS