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Phenotypic, functional and taxonomic features predict host-pathogen interactions

https://doi.org/10.1101/508762
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What this work says

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

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Mouse genetic and phenotypic resources for human genetics
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The Informatics of Developmental Phenotypes
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Kaufman's Atlas of Mouse Development Supplement
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Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies
inferredcites →https://doi.org/10.1016/j.ajhg.2015.07.004openalex-snapshot
Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling
inferredcites →https://doi.org/10.1016/j.dnarep.2004.03.018openalex-snapshot
Interactions of viruses with the cellular DNA repair machinery
inferredcites →https://doi.org/10.1016/j.patrec.2005.10.010openalex-snapshot
An introduction to ROC analysis
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/emi.2016.141openalex-snapshot
Zika virus genome biology and molecular pathogenesis
inferredcites →https://doi.org/10.1038/ng.3901openalex-snapshot
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium
inferredcites →https://doi.org/10.1038/s41467-018-04776-7openalex-snapshot
The TRPV4 channel links calcium influx to DDX3X activity and viral infectivity
inferredcites →https://doi.org/10.1093/bib/bbv011openalex-snapshot
The role of ontologies in biological and biomedical research: a functional perspective
inferredcites →https://doi.org/10.1093/bib/bbv083openalex-snapshot
The digital revolution in phenotyping
inferredcites →https://doi.org/10.1093/bib/bbx035openalex-snapshot
The anatomy of phenotype ontologies: principles, properties and applications
inferredcites →https://doi.org/10.1093/bioinformatics/bts042openalex-snapshot
Literature mining of host–pathogen interactions: comparing feature-based supervised learning and language-based approaches
inferredcites →https://doi.org/10.1093/bioinformatics/bts375openalex-snapshot
Techniques to cope with missing data in host–pathogen protein interaction prediction
inferredcites →https://doi.org/10.1093/bioinformatics/btt613openalex-snapshot
Mouse model phenotypes provide information about human drug targets
inferredcites →https://doi.org/10.1093/bioinformatics/bty933openalex-snapshot
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
inferredcites →https://doi.org/10.1093/database/baw103openalex-snapshot
HPIDB 2.0: a curated database for host–pathogen interactions
inferredcites →https://doi.org/10.1093/hmg/ddw143openalex-snapshot
Targeted inactivation of murineDdx3x: essential roles ofDdx3xin placentation and embryogenesis
inferredcites →https://doi.org/10.1093/nar/gkh073openalex-snapshot
Database resources of the National Center for Biotechnology Information: update
inferredcites →https://doi.org/10.1093/nar/gkn741openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gkr538openalex-snapshot
PhenomeNET: a whole-phenome approach to disease gene discovery
inferredcites →https://doi.org/10.1093/nar/gkw1108openalex-snapshot
Expansion of the Gene Ontology knowledgebase and resources
inferredcites →https://doi.org/10.1093/nar/gkx1006openalex-snapshot
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse
inferredcites →https://doi.org/10.1093/nar/gkx1037openalex-snapshot
DrugBank 5.0: a major update to the DrugBank database for 2018
inferredcites →https://doi.org/10.1093/nar/gky1105openalex-snapshot
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
inferredcites →https://doi.org/10.1098/rstb.2011.0354openalex-snapshot
Human viruses: discovery and emergence
inferredcites →https://doi.org/10.1101/489971openalex-snapshot
PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research
inferredcites →https://doi.org/10.1126/science.276.5313.718openalex-snapshot
Exploitation of Mammalian Host Cell Functions by Bacterial Pathogens
inferredcites →https://doi.org/10.1186/1471-2105-15-245openalex-snapshot
Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens
inferredcites →https://doi.org/10.1186/1471-2105-15-26openalex-snapshot
Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach
inferredcites →https://doi.org/10.1186/gb-2004-6-1-r7openalex-snapshot
The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information
inferredcites →https://doi.org/10.1186/s12859-015-0456-9openalex-snapshot
Aber-OWL: a framework for ontology-based data access in biology
inferredcites →https://doi.org/10.1186/s12859-015-0535-yopenalex-snapshot
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs
inferredcites →https://doi.org/10.1186/s13326-017-0167-4openalex-snapshot
Integrating phenotype ontologies with PhenomeNET
inferredcites →https://doi.org/10.1371/journal.pone.0010840openalex-snapshot
Prevention of Catheter-Related Bacteremia with a Daily Ethanol Lock in Patients with Tunnelled Catheters: A Randomized, Placebo-Controlled Trial
inferredcites →https://doi.org/10.1371/journal.pone.0012089openalex-snapshot
The Human-Bacterial Pathogen Protein Interaction Networks of Bacillus anthracis, Francisella tularensis, and Yersinia pestis
inferredcites →https://doi.org/10.1371/journal.pone.0054583openalex-snapshot
Positive Outcomes Influence the Rate and Time to Publication, but Not the Impact Factor of Publications of Clinical Trial Results
inferredcites →https://doi.org/10.1371/journal.pone.0060847openalex-snapshot
Systematic Analysis of Experimental Phenotype Data Reveals Gene Functions
inferredcites →https://doi.org/10.1371/journal.pone.0079606openalex-snapshot
Probability Weighted Ensemble Transfer Learning for Predicting Interactions between HIV-1 and Human Proteins
inferredcites →https://doi.org/10.1371/journal.ppat.0040032openalex-snapshot
The Landscape of Human Proteins Interacting with Viruses and Other Pathogens
inferredcites →https://doi.org/10.1371/journal.ppat.1000092openalex-snapshot
Temperature, Viral Genetics, and the Transmission of West Nile Virus by Culex pipiens Mosquitoes
inferredcites →https://doi.org/10.1371/journal.ppat.1004691openalex-snapshot
Antibiotic Modulation of Capsular Exopolysaccharide and Virulence in Acinetobacter baumannii
inferredcites →https://doi.org/10.1371/journal.ppat.1005321openalex-snapshot
Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity
inferredcites →https://doi.org/10.3389/fmicb.2015.00094openalex-snapshot
Computational approaches for prediction of pathogen-host protein-protein interactions

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41597-019-0090-xopenalex-snapshot
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research
inferred← citeshttps://doi.org/10.1101/2020.04.23.057117openalex-snapshot
Self-normalizing learning on biomedical ontologies using a deep Siamese neural network
inferred← citeshttps://doi.org/10.1186/s13326-019-0208-2openalex-snapshot
Ontology based mining of pathogen–disease associations from literature
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