iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule

i6mA-Pred: Identifying DNA N6-methyladenine sites in the rice genome

(2019) Wei Chen et al.   BIOINFORMATICS

iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding

(2019) Nguyen Quoc Khanh Le et al.   ANALYTICAL BIOCHEMISTRY

Classifying the molecular functions of Rab GTPases in membrane trafficking using deep convolutional neural networks

(2018) Nguyen-Quoc-Khanh Le et al.   ANALYTICAL BIOCHEMISTRY

A novel methodology on distributed representations of proteins using their interacting ligands

(2018) Hakime Öztürk et al.   BIOINFORMATICS

iDNA6mA-PseKNC: Identifying DNA N 6 -methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC

(2018) Pengmian Feng et al.   GENOMICS

pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC

(2018) Xiang Cheng et al.   GENOMICS

iMethyl-STTNC: Identification of N 6 -methyladenosine sites by extending the Idea of SAAC into Chou's PseAAC to formulate RNA sequences

(2018) Shahid Akbar et al.   JOURNAL OF THEORETICAL BIOLOGY

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

(2018) Jiangning Song et al.   JOURNAL OF THEORETICAL BIOLOGY

Implications of Newly Identified Brain eQTL Genes and Their Interactors in Schizophrenia

(2018) Lei Cai et al.   Molecular Therapy-Nucleic Acids

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition

(2018) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iPro70-FMWin: identifying Sigma70 promoters using multiple windowing and minimal features

(2018) Md. Siddiqur Rahman et al.   MOLECULAR GENETICS AND GENOMICS

iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into PseAAC

(2018) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou’s PseAAC to pseudo-tri-nucleotide composition

(2018) Muhammad Tahir et al.   MOLECULAR GENETICS AND GENOMICS

PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids

(2018) Abel Chandra et al.   Scientific Reports

pSSbond-PseAAC: Prediction of disulfide bonding sites by integration of PseAAC and statistical moments

(2018) Yaser Daanial Khan et al.   JOURNAL OF THEORETICAL BIOLOGY

iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier

(2017) Wang-Ren Qiu et al.   GENOMICS

Using word embeddings in Twitter election classification

(2017) Xiao Yang et al.   Information Retrieval Journal

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins

(2017) Nguyen-Quoc-Khanh Le et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC

(2017) Xiang Cheng et al.   Molecular BioSystems

Using word embeddings in Twitter election classification

(2017) Xiao Yang et al.   Information Retrieval Journal

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

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs

(2016) Nguyen-Quoc-Khanh Le et al.   BMC BIOINFORMATICS

Detection and tracking of overlapping cell nuclei for large scale mitosis analyses

(2016) Yingbo Li et al.   BMC BIOINFORMATICS

pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach

(2016) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

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

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

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

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

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

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

PSNO: Predicting Cysteine S-Nitrosylation Sites by Incorporating Various Sequence-Derived Features into the General Form of Chou’s PseAAC

(2014) Jian Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets

(2014) Pufeng Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components

(2014) Wang-Ren Qiu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model

(2014) Wang-Ren Qiu et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition

(2014) Yan Xu et al.   PLoS One

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition

(2013) Yan Xu et al.   PLoS One

Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou's PseAAC

(2013) H.-L. Xie et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

(2013) Yan Xu et al.   PeerJ

PseAAC-Builder: A cross-platform stand-alone program for generating various special Chou’s pseudo-amino acid compositions

(2012) Pufeng Du et al.   ANALYTICAL BIOCHEMISTRY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein–protein interaction mechanism

(2011) Guo-Ping Zhou   JOURNAL OF THEORETICAL BIOLOGY

Predicting Functions of Proteins in Mouse Based on Weighted Protein-Protein Interaction Network and Protein Hybrid Properties

(2011) Lele Hu et al.   PLoS One

Graphic Rule for Drug Metabolism Systems

(2010) Kuo-Chen Chou   CURRENT DRUG METABOLISM

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

DNA motifs that sculpt the bacterial chromosome

(2010) Fabrice Touzain et al.   NATURE REVIEWS MICROBIOLOGY

An optimization approach to predicting protein structural class from amino acid composition

(2010) Chun-Ting Zhang et al.   PROTEIN SCIENCE