Predicting lncRNA–Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model

A network embedding-based multiple information integration method for the MiRNA-disease association prediction

(2019) Yuchong Gong et al.   BMC BIOINFORMATICS

SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug–drug interactions

(2019) Wen Zhang et al.   INFORMATION SCIENCES

NPInter v4.0: an integrated database of ncRNA interactions

(2019) Xueyi Teng et al.   NUCLEIC ACIDS RESEARCH

A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations

(2019) Wen Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MicroRNA

(2018) Thomas X. Lu et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The linear neighborhood propagation method for predicting long non-coding RNA–protein interactions

(2018) Wen Zhang et al.   NEUROCOMPUTING

HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy

(2018) Huan Hu et al.   RNA Biology

A brief review on software tools in generating Chou’s pseudo-factor representations for all types of biological sequences

(2018) Wei Zhao et al.   PROTEIN AND PEPTIDE LETTERS

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

(2018) Wen Zhang et al.   PLoS Computational Biology

KATZLGO: Large-scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks

(2017) Zuping Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

LPI-ETSLP: lncRNA–protein interaction prediction using eigenvalue transformation-based semi-supervised link prediction

(2017) Huan Hu et al.   Molecular BioSystems

iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition

(2017) Wang-Ren Qiu et al.   Oncotarget

Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks

(2017) Yun Xiao et al.   Scientific Reports

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

Relevance search for predicting lncRNA–protein interactions based on heterogeneous network

(2016) Jianghong Yang et al.   NEUROCOMPUTING

RAID v2.0: an updated resource of RNA-associated interactions across organisms

(2016) Ying Yi et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions

(2016) Mengqu Ge et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences

(2015) Wei Chen et al.   Molecular BioSystems

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

(2015) V. Suresh et al.   NUCLEIC ACIDS RESEARCH

Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model

(2015) Ao Li et al.   Biomed Research International

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions

(2014) Wei Chen et al.   BIOINFORMATICS

HeteSim: A General Framework for Relevance Measure in Heterogeneous Networks

(2014) Chuan Shi et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Pseudogene PTENP1 Functions as a Competing Endogenous RNA to Suppress Clear-Cell Renal Cell Carcinoma Progression

(2014) G. Yu et al.   MOLECULAR CANCER THERAPEUTICS

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Computational prediction of associations between long non-coding RNAs and proteins

(2013) Qiongshi Lu et al.   BMC GENOMICS

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

(2013) Per Johnsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Emerging epigenetic mechanisms of long non-coding RNAs

(2013) K. Schaukowitch et al.   NEUROSCIENCE

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

MicroRNA-21 (miR-21) represses tumor suppressor PTEN and promotes growth and invasion in non-small cell lung cancer (NSCLC)

(2010) Ji-guang Zhang et al.   CLINICA CHIMICA ACTA

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Long intronic noncoding RNA transcription: Expression noise or expression choice?

(2008) Rodrigo Louro et al.   GENOMICS

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Endogenous small interfering RNAs in animals

(2008) Katsutomo Okamura et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS