(Q34579675)

3 August 2017

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

1 reference

3 August 2017

5

Kuo-Chen Chou

1 reference

3 August 2017

Hao Lin

1

1 reference

3 August 2017

En-Ze Deng

series ordinal

2

1 reference

3 August 2017

Hui Ding

series ordinal

3

1 reference

3 August 2017

Wei Chen

series ordinal

4

1 reference

3 August 2017

language of work or name

English

0 references

publication date

31 October 2014

1 reference

3 August 2017

12

1 reference

inferred from page(s)

published in

Nucleic Acids Research

1 reference

3 August 2017

42

1 reference

3 August 2017

21

1 reference

3 August 2017

12961-12972

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

3 August 2017

start time

3 May 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

iNitro-Tyr: prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition

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Prediction of protein structure classes by incorporating different protein descriptors into general Chou's pseudo amino acid composition.

7 July 2018

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PseAAC-General: fast building various modes of general form of Chou's pseudo-amino acid composition for large-scale protein datasets

7 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Predicting anticancer peptides with Chou's pseudo amino acid composition and investigating their mutagenicity via Ames test

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Some remarks on predicting multi-label attributes in molecular biosystems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

iNuc-PhysChem: a sequence-based predictor for identifying nucleosomes via physicochemical properties

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Recognition of prokaryotic promoters based on a novel variable-window Z-curve method

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

A rebuttal to the comments on the genome order index and the Z-curve

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Some remarks on protein attribute prediction and pseudo amino acid composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Predicting membrane protein types by the LLDA algorithm

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

DNA physical properties determine nucleosome occupancy from yeast to fly.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Generic eukaryotic core promoter prediction using structural features of DNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Determining promoter location based on DNA structure first-principles calculations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Recent progress in protein subcellular location prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Structural Basis of DNA Recognition by the Alternative Sigma-factor, σ54

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Using stacked generalization to predict membrane protein types based on pseudo-amino acid composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

The recognition and prediction of sigma70 promoters in Escherichia coli K-12.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Predicting subcellular localization of proteins in a hybridization space

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Support Vector Machines for Predicting Membrane Protein Types by Using Functional Domain Composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Prediction of protein cellular attributes using pseudo-amino acid composition

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Support vector machine classification and validation of cancer tissue samples using microarray expression data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Compilation and analysis of sigma(54)-dependent promoter sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

A transcriptional activator, FleQ, regulates mucin adhesion and flagellar gene expression in Pseudomonas aeruginosa in a cascade manner

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Molecular approaches applied to the epidemiology of leishmaniasis in Venezuela.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Prediction of protein structural classes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Compilation and analysis ofEscherichia colipromoter DNA sequences

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Structure and function of bacterial sigma factors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Neural network optimization for E. coli promoter prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

The sigma 70 family: sequence conservation and evolutionary relationships

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

Alginate synthesis in Pseudomonas aeruginosa: environmental regulation of the algC promoter

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4245931

sigma54-promoter discrimination and regulation by ppGpp and DksA.

7 July 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

The sigma54 regulon (sigmulon) of Pseudomonas putida.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Eukaryotic and prokaryotic promoter prediction using hybrid approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

An Improved Position Weight Matrix method based on an entropy measure for the recognition of prokaryotic promoters.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

DNA duplex stability as discriminative characteristic for Escherichia coli σ(54)- and σ(28)- dependent promoter sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Predicting promoters by pseudo-trinucleotide compositions based on discrete wavelets transform.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Prediction of Golgi-resident protein types by using feature selection technique

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Boosting classifier for predicting protein domain structural class.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

iCDI-PseFpt: identify the channel-drug interaction in cellular networking with PseAAC and molecular fingerprints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

SLLE for predicting membrane protein types.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

A key driving force in determination of protein structural classes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

DNAlive: a tool for the physical analysis of DNA at the genomic scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Using subsite coupling to predict signal peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Identification of mycobacterial membrane proteins and their types using over-represented tripeptide compositions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Prediction of the types of ion channel-targeted conotoxins based on radial basis function network

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

BacPP: bacterial promoter prediction--a tool for accurate sigma-factor specific assignment in enterobacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

The effect of regions flanking target site on siRNA potency.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

The maximum information principle and the evolution of nucleotide sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Minimal model for genome evolution and growth.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Identification and annotation of promoter regions in microbial genome sequences on the basis of DNA stability.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

The History of the Cluster Heat Map

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKU1019

Protein-length distributions for the three domains of life

21 January 2018

1 reference

12 December 2020

Predicting protein fold pattern with functional domain and sequential evolution information

1 reference

12 December 2020

Distance conservation of transcription regulatory motifs in human promoters

1 reference

12 December 2020

Codon-pair usage and genome evolution

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKU1019

1 reference

3 August 2017

1 reference

3 August 2017

1 reference