EnhancerPred2.0: predicting enhancers and their strength based on position-specific trinucleotide propensity and electron–ion interaction potential feature selection

RNA-MethylPred: A high-accuracy predictor to identify N6-methyladenosine in RNA

(2016) Cang-Zhi Jia et al.   ANALYTICAL BIOCHEMISTRY

iACP: a sequence-based tool for identifying anticancer peptides

(2016) Wei Chen et al.   Oncotarget

iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition

(2016) Xuan Xiao et al.   Oncotarget

Identification of apolipoprotein using feature selection technique

(2016) Hua Tang et al.   Scientific Reports

EnhancerPred: a predictor for discovering enhancers based on the combination and selection of multiple features

(2016) Cangzhi Jia et al.   Scientific Reports

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

(2015) Bin Liu et al.   BIOINFORMATICS

iORI-PseKNC: A predictor for identifying origin of replication with pseudo k-tuple nucleotide composition

(2015) Wen-Chao Li et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

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

(2015) Wei Chen et al.   Molecular BioSystems

Improving tRNAscan-SE Annotation Results via Ensemble Classifiers

(2015) Quan Zou et al.   Molecular Informatics

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

DELTA: A Distal Enhancer Locating Tool Based on AdaBoost Algorithm and Shape Features of Chromatin Modifications

(2015) Yiming Lu et al.   PLoS One

Predicting cancerlectins by the optimal g-gap dipeptides

(2015) Hao Lin et al.   Scientific Reports

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

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

(2014) Shou-Hui Guo et al.   BIOINFORMATICS

High-throughput functional testing of ENCODE segmentation predictions

(2014) Jamie C. Kwasnieski et al.   GENOME RESEARCH

iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition

(2014) Yan Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

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

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

O-GlcNAcPRED: a sensitive predictor to capture protein O-GlcNAcylation sites

(2013) Cang-Zhi Jia et al.   Molecular BioSystems

Modeling RFID signal distribution based on neural network combined with continuous ant colony optimization

(2013) Zengqiang Chen et al.   NEUROCOMPUTING

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteineS-nitrosylation sites in proteins

(2013) Yan Xu et al.   PeerJ

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

(2012) Michael Fernández et al.   NUCLEIC ACIDS RESEARCH

LIBSVM

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

G-protein-coupled receptor prediction using pseudo-amino-acid composition and multiscale energy representation of different physiochemical properties

(2011) Zia ur-Rehman et al.   ANALYTICAL BIOCHEMISTRY

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

PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs

(2011) Ping Xuan et al.   BIOINFORMATICS

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

PU.1 and C/EBP  synergistically program distinct response to NF- B activation through establishing monocyte specific enhancers

(2011) F. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Efficient Localization of Hot Spots in Proteins Using a Novel S-Transform Based Filtering Approach

(2010) S. S. Sahu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition

(2010) Hao Lin et al.   JOURNAL OF THEORETICAL BIOLOGY

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS