{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T23:09:38Z","timestamp":1780441778057,"version":"3.54.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,26]],"date-time":"2018-06-26T00:00:00Z","timestamp":1529971200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The South African Research Chairs Initiatives"},{"DOI":"10.13039\/501100006143","name":"Department of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006143","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Research Foundation of South Africa"},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Triplet amino acids have successfully been included in feature selection to predict human-HPV protein-protein interactions (PPI). The utility of supervised learning methods is curtailed due to experimental data not being available in sufficient quantities. Improvements in machine learning techniques and features selection will enhance the study of PPI between host and pathogen.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a comparison of a neural network model versus SVM for prediction of host-pathogen PPI based on a combination of features including: amino acid quadruplets, pairwise sequence similarity, and human interactome properties. The neural network and SVM were implemented using Python Sklearn library. The neural network model using quadruplet features and other network features outperformance the SVM model. The models are tested against published predictors and then applied to the human-B.anthracis case. Gene ontology term enrichment analysis identifies immunology response and regulation as functions of interacting proteins. For prediction of Human-viral PPI, our model (neural network) is a significant improvement in overall performance compared to a predictor using the triplets feature and achieves a good accuracy in predicting human-B.anthracis PPI.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All code can be downloaded from ftp:\/\/ftp.sanbi.ac.za\/machine_learning\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty504","type":"journal-article","created":{"date-parts":[[2018,6,24]],"date-time":"2018-06-24T19:09:27Z","timestamp":1529867367000},"page":"4159-4164","source":"Crossref","is-referenced-by-count":33,"title":["Prediction of human-<i>Bacillus anthracis<\/i> protein\u2013protein interactions using multi-layer neural network"],"prefix":"10.1093","volume":"34","author":[{"given":"Ibrahim","family":"Ahmed","sequence":"first","affiliation":[{"name":"South African National Bioinformatics Institute, South African MRC Bioinformatics Unit"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Witbooi","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Applied Mathematics, University of the Western Cape, Bellville, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0420-2916","authenticated-orcid":false,"given":"Alan","family":"Christoffels","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, South African MRC Bioinformatics Unit"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,6,26]]},"reference":[{"key":"2023012712253232400_bty504-B1","author":"Ahmed","year":"2017"},{"key":"2023012712253232400_bty504-B2","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network biology: understanding the cell\u2019s functional organization","volume":"5","author":"Barab\u00e1si","year":"2004","journal-title":"Nat. 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