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VIDHOP, viral host prediction with Deep Learning

https://doi.org/10.1101/575571
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What this work says

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

inferredcites →https://doi.org/10.1016/j.chom.2010.05.009openalex-snapshot
Influenza Virus Evolution, Host Adaptation, and Pandemic Formation
inferredcites →https://doi.org/10.1016/j.ijpara.2007.05.011openalex-snapshot
Tick genomics: The Ixodes genome project and beyond
inferredcites →https://doi.org/10.1016/j.vetmic.2009.08.028openalex-snapshot
Zoonotic aspects of rotaviruses
inferredcites →https://doi.org/10.1016/j.virol.2011.11.020openalex-snapshot
Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses
inferredcites →https://doi.org/10.1038/s41598-018-28308-xopenalex-snapshot
Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btx383openalex-snapshot
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
inferredcites →https://doi.org/10.1093/femsre/fuv048openalex-snapshot
Computational approaches to predict bacteriophage–host relationships
inferredcites →https://doi.org/10.1093/gigascience/giy037openalex-snapshot
Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning
inferredcites →https://doi.org/10.1093/nar/gkw1002openalex-snapshot
Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
inferredcites →https://doi.org/10.1109/5.58337openalex-snapshot
Backpropagation through time: what it does and how to do it
inferredcites →https://doi.org/10.1109/icnn.1994.374611openalex-snapshot
Truncated backpropagation through time and Kalman filter training for neurocontrol
inferredcites →https://doi.org/10.1128/jvi.00601-10openalex-snapshot
Use of Nucleotide Composition Analysis To Infer Hosts for Three Novel Picorna-Like Viruses
inferredcites →https://doi.org/10.1146/annurev-animal-022516-022811openalex-snapshot
Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species
inferredcites →https://doi.org/10.1162/neco.1997.9.8.1735openalex-snapshot
Long Short-Term Memory
inferredcites →https://doi.org/10.1186/1755-8794-7-s3-s1openalex-snapshot
Predicting host tropism of influenza A virus proteins using random forest
inferredcites →https://doi.org/10.1186/s12859-017-1473-7openalex-snapshot
Prediction of virus-host infectious association by supervised learning methods
inferredcites →https://doi.org/10.1371/journal.ppat.1004395openalex-snapshot
The Evolution and Genetics of Virus Host Shifts
inferredcites →https://doi.org/10.1371/journal.ppat.1004604openalex-snapshot
Dengue Virus RNA Structure Specialization Facilitates Host Adaptation
inferredcites →https://doi.org/10.15252/emmm.201404792openalex-snapshot
Investigating the zoonotic origin of the West African Ebola epidemic
inferredcites →https://doi.org/10.24963/ijcai.2018/369openalex-snapshot
Online Deep Learning: Learning Deep Neural Networks on the Fly

What points at this work

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

inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20995-3openalex-snapshot
Database and Analytical Resources for Viral Research Community
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2024.108114openalex-snapshot
Prediction of viral families and hosts of single-stranded RNA viruses based on K-Mer coding from phylogenetic gene sequences
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.12.007openalex-snapshot
SARS-CoV-2 virus classification based on stacked sparse autoencoder
inferred← citeshttps://doi.org/10.1016/j.jbi.2021.103736openalex-snapshot
Reservoir hosts prediction for COVID-19 by hybrid transfer learning model
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab585openalex-snapshot
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac495openalex-snapshot
Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
inferred← citeshttps://doi.org/10.1093/nargab/lqab004openalex-snapshot
Interpretable detection of novel human viruses from genome sequencing data
inferred← citeshttps://doi.org/10.1101/2021.01.26.428301openalex-snapshot
Deep learning-based real-time detection of novel pathogens during sequencing
inferred← citeshttps://doi.org/10.1101/2021.10.14.464414openalex-snapshot
Deep learning based on stacked sparse autoencoder applied to viral genome classification of SARS-CoV-2 virus
inferred← citeshttps://doi.org/10.1101/2024.03.30.587436openalex-snapshot
ViRNN: A Deep Learning Model for Viral Host Prediction
inferred← citeshttps://doi.org/10.1109/cits49457.2020.9232598openalex-snapshot
Pathogenic virus detection method based on multi-model fusion
inferred← citeshttps://doi.org/10.1109/ijcnn52387.2021.9534430openalex-snapshot
A Novel Training Strategy for Deep Learning Model Compression Applied to Viral Classifications
inferred← citeshttps://doi.org/10.12785/ijcds/120101openalex-snapshot
Deep Learning based analysis of Covid-19 mortality risk
inferred← citeshttps://doi.org/10.17520/biods.2020156openalex-snapshot
Verification of virus identity and host association using genomics technology
inferred← citeshttps://doi.org/10.3390/s22155730openalex-snapshot
Convolutional Neural Network Applied to SARS-CoV-2 Sequence Classification
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