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DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines
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SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
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Augmented cell-graphs for automated cancer diagnosis
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Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
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CD-HIT Suite: a web server for clustering and comparing biological sequences
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Deep architectures for protein contact map prediction
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Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles
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Deep learning of the tissue-regulated splicing code
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Curation, integration and visualization of bacterial virulence factors in PATRIC
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Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors
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Deep learning improves antimicrobial peptide recognition
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Random forest based similarity learning for single cell RNA sequencing data
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ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides
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Bastion3: a two-layer ensemble predictor of type III secreted effectors
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Identifying antimicrobial peptides using word embedding with deep recurrent neural networks
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DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network
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Deep learning on chaos game representation for proteins
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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
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VFDB 2019: a comparative pathogenomic platform with an interactive web interface
inferredcites →https://doi.org/10.1093/nar/gky999openalex-snapshot
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On Position-Specific Scoring Matrix for Protein Function Prediction
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Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information
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XGBoost
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inferredcites →https://doi.org/10.1186/cc7127openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0042517openalex-snapshot
A Comparison of Computational Methods for Identifying Virulence Factors
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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RVFScan Predicts Virulence Factor Genes and Hypervirulence of Clinical Metagenome
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Protein-level representations outperform nucleotide foundation models for virulence-factor classification in an organism-level holdout benchmark
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NEPTUNE: A novel computational approach for accurate and large-scale identification of tumor homing peptides
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SAPPHIRE: A stacking-based ensemble learning framework for accurate prediction of thermophilic proteins
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PSRTTCA: A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning
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VF-Pred: Predicting virulence factor using sequence alignment percentage and ensemble learning models
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Identifying virulence factors using graph transformer autoencoder with ESMFold-predicted structures
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Computational prediction of phosphorylation sites of SARS-CoV-2 infection using feature fusion and optimization strategies
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inferred← citeshttps://doi.org/10.1093/bib/bbaf271openalex-snapshot
VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts
inferred← citeshttps://doi.org/10.1093/bib/bbaf481openalex-snapshot
VF-Fuse: a dual-path feature fusion and iterative update architecture for virulence factor prediction
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Structure-based virulence factor classification using a dual-driven graph transformer with a pretrained language model
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SEVA: structural and evolutionary feature integration for predicting virulence factors and antibiotic resistance genes
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TROLLOPE: A novel sequence-based stacked approach for the accelerated discovery of linear T-cell epitopes of hepatitis C virus
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Bag-of-words is competitive with sum-of-embeddings language-inspired representations on protein inference
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BLSAM-TIP: Improved and robust identification of tyrosinase inhibitory peptides by integrating bidirectional LSTM with self-attention mechanism
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Empirical comparison and analysis of machine learning-based predictors for predicting and analyzing of thermophilic proteins
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Empirical comparison and analysis of machine learning-based approaches for druggable protein identification
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RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome
inferred← citeshttps://doi.org/10.21203/rs.3.rs-6554281/v1openalex-snapshot
In Silico Structural and Functional Characterization of Hypothetical Protein WP_000477209.1 from Hypervirulent Klebsiella aerogenes G7 Reveals a Potential Epigenetic Regulator
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PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods
inferred← citeshttps://doi.org/10.2174/1574893618666230908092847openalex-snapshot
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features
inferred← citeshttps://doi.org/10.3390/bioengineering10070858openalex-snapshot
StackDPP: Stacking-Based Explainable Classifier for Depression Prediction and Finding the Risk Factors among Clinicians
inferred← citeshttps://doi.org/10.3390/genes15091170openalex-snapshot
DTVF: A User-Friendly Tool for Virulence Factor Prediction Based on ProtT5 and Deep Transfer Learning Models
inferred← citeshttps://doi.org/10.3390/ijms222313124openalex-snapshot
UMPred-FRL: A New Approach for Accurate Prediction of Umami Peptides Using Feature Representation Learning
inferred← citeshttps://doi.org/10.3390/ijms231911026openalex-snapshot
DLm6Am: A Deep-Learning-Based Tool for Identifying N6,2′-O-Dimethyladenosine Sites in RNA Sequences
inferred← citeshttps://doi.org/10.3390/microorganisms13071635openalex-snapshot
Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein–Protein Interaction Networks
inferred← citeshttps://doi.org/10.3934/mbe.2022622openalex-snapshot
SPREAD: An ensemble predictor based on DNA autoencoder framework for discriminating promoters in Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.6084/m9.figshare.24180897openalex-snapshot
Additional file 1 of TIPred: a novel stacked ensemble approach for the accelerated discovery of tyrosinase inhibitory peptides
inferred← citeshttps://doi.org/10.6084/m9.figshare.26607256openalex-snapshot
Additional file 1 of StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens
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