PseUI: Pseudouridine sites identification based on RNA sequence information

Protein-protein interface hot spots prediction based on a hybrid feature selection strategy

(2018) Yanhua Qiao et al.   BMC BIOINFORMATICS

PDC-SGB: Prediction of effective drug combinations using a stochastic gradient boosting algorithm

(2017) Qian Xu et al.   JOURNAL OF THEORETICAL BIOLOGY

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

(2017) Pengmian Feng et al.   Molecular Therapy-Nucleic Acids

pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical–chemical properties

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

DBSI server: DNA binding site identifier

(2016) Shravan Sukumar et al.   BIOINFORMATICS

iRSpot-EL: identify recombination spots with an ensemble learning approach

(2016) Bin Liu et al.   BIOINFORMATICS

iPTM-mLys: identifying multiple lysine PTM sites and their different types

(2016) Wang-Ren Qiu et al.   BIOINFORMATICS

iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework

(2016) Bin Liu et al.   BIOINFORMATICS

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

(2016) Qingjun Yuan et al.   BIOINFORMATICS

Identifying RNA 5-methylcytosine sites via pseudo nucleotide compositions

(2016) Pengmian Feng et al.   Molecular BioSystems

Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences

(2016) Mickael Leclercq et al.   NUCLEIC ACIDS RESEARCH

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition

(2015) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

PPUS: a web server to predict PUS-specific pseudouridine sites: Table 1.

(2015) Yan-Hui Li et al.   BIOINFORMATICS

iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudok-tuple nucleotide composition

(2015) Bin Liu et al.   BIOINFORMATICS

Comparing K-mer based methods for improved classification of 16S sequences

(2015) Hilde Vinje et al.   BMC BIOINFORMATICS

Phogly–PseAAC: Prediction of lysine phosphoglycerylation in proteins incorporating with position-specific propensity

(2015) Yan Xu et al.   JOURNAL OF THEORETICAL BIOLOGY

Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter

(2015) Ezzeddin Kamil Mohamed Hashim et al.   JOURNAL OF THEORETICAL BIOLOGY

iPPI-Esml: An ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC

(2015) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

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

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

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

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

(2015) Wen-Ju Sun et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies

(2014) A. Mary Thangakani et al.   BIOINFORMATICS

Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0

(2014) Xiaolei Zhu et al.   BIOINFORMATICS

Towards a piRNA prediction using multiple kernel fusion and support vector machine

(2014) J. Brayet et al.   BIOINFORMATICS

BigDataScript: a scripting language for data pipelines

(2014) P. Cingolani et al.   BIOINFORMATICS

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

(2014) Wei Chen et al.   BIOINFORMATICS

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

Some remarks on predicting multi-label attributes in molecular biosystems

(2013) Kuo-Chen Chou   Molecular BioSystems

DBSI: DNA-binding site identifier

(2013) Xiaolei Zhu et al.   NUCLEIC ACIDS RESEARCH

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

RNA pseudouridylation: new insights into an old modification

(2013) Junhui Ge et al.   TRENDS IN BIOCHEMICAL SCIENCES

Prediction of mitochondrial proteins of malaria parasite using bi-profile Bayes feature extraction

(2011) Cangzhi Jia et al.   BIOCHIMIE

High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles

(2011) Yejun Wang et al.   BIOINFORMATICS

KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features

(2011) Xiaolei Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

(2010) Jiangning Song et al.   BIOINFORMATICS

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

An accurate feature-based method for identifying DNA-binding residues on protein surfaces

(2010) Yi Xiong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Computational Identification of Protein Methylation Sites through Bi-Profile Bayes Feature Extraction

(2009) Jianlin Shao et al.   PLoS One