Authors: Doran, James W.G., Thompson, Robin N., Yates, Christian A., Bowness, Ruth

Superior Title: In Epidemics December 2023 45

Authors: Lasri Doukkali, Anas, Lorenzi, Tommaso, Parcell, Benjamin J., Rohn, Jennifer L., Bowness, Ruth

Superior Title: Lasri Doukkali , A , Lorenzi , T , Parcell , B J , Rohn , J L & Bowness , R 2023 , ' A hybrid individual-based mathematical model to study bladder infections ' , Frontiers in Applied Mathematics and Statistics , vol. 9 , 1090334 . https://doi.org/10.3389/fams.2023.1090334

Subject Terms: bladder, Escherichia coli, individual-based, infection, mathematical, model, simulation, /dk/atira/pure/subjectarea/asjc/2600/2613, name=Statistics and Probability, /dk/atira/pure/subjectarea/asjc/2600/2604, name=Applied Mathematics

File Description: application/pdf

Relation: https://discovery.dundee.ac.uk/en/publications/30462fbe-9303-4997-9347-fb7803a20bc6

Availability: https://doi.org/10.3389/fams.2023.1090334
https://discovery.dundee.ac.uk/en/publications/30462fbe-9303-4997-9347-fb7803a20bc6
https://discovery.dundee.ac.uk/ws/files/97623443/fams_09_1090334.pdf
http://www.scopus.com/inward/record.url?scp=85148359934&partnerID=8YFLogxK

Authors: Hammond, Robert J. H.^{Aff1, IDs41598022226716_cor1}, Falconer, Kerry, Powell, Thomas, Bowness, Ruth, Gillespie, Stephen H.

Superior Title: Scientific Reports. 12(1)

Authors: Karr, Jonathan, Malik-Sheriff, Rahuman S., Osborne, James, Gonzalez-Parra, Gilberto, Forgoston, Eric, Bowness, Ruth, Liu, Yaling, Thompson, Robin, Garira, Winston, Barhak, Jacob, Rice, John, Torres, Marcella, Dobrovolny, Hana M., Tang, Tingting, Waites, William, Glazier, James A., Faeder, James R., Kulesza, Alexander

Subject Terms: Electronic computers. Computer science, Mathematics, Immunology, Biology

File Description: text

Relation: https://strathprints.strath.ac.uk/79975/1/Karr_etal_FSB_2022_Model_integration_in_computational_biology_the_role_of_reproducibility_credibility_utility.pdf; Karr, Jonathan and Malik-Sheriff, Rahuman S. and Osborne, James and Gonzalez-Parra, Gilberto and Forgoston, Eric and Bowness, Ruth and Liu, Yaling and Thompson, Robin and Garira, Winston and Barhak, Jacob and Rice, John and Torres, Marcella and Dobrovolny, Hana M. and Tang, Tingting and Waites, William and Glazier, James A. and Faeder, James R. and Kulesza, Alexander (2022 ) Model integration in computational biology : the role of reproducibility, credibility and utility. Frontiers in Systems Biology , 2. 822606. ISSN 2674-0702

Availability: https://doi.org/10.3389/fsysb.2022.822606
https://strathprints.strath.ac.uk/79975/
https://strathprints.strath.ac.uk/79975/1/Karr_etal_FSB_2022_Model_integration_in_computational_biology_the_role_of_reproducibility_credibility_utility.pdf

Authors: Rowlatt, Christopher F, Chaplain, Mark Andrew Joseph, Hughes, David John, Gillespie, Stephen Henry, Dockrell, David, johannessen , Ingolfur, Bowness, Ruth

Superior Title: Rowlatt , C F , Chaplain , M A J , Hughes , D J , Gillespie , S H , Dockrell , D , johannessen , I & Bowness , R 2022 ' Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages ' bioRxiv . https://doi.org/10.1101/2022.05.06.490883

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-withinhost-spread-of-sarscov2-infection-and-the-subsequent-immune-response-using-a-hybrid-multiscale-individualbased-model-part-i-macrophages(90d76e08-9dbe-4134-8f5a-0f308d53a8bd).html

Availability: https://doi.org/10.1101/2022.05.06.490883
https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-withinhost-spread-of-sarscov2-infection-and-the-subsequent-immune-response-using-a-hybrid-multiscale-individualbased-model-part-i-macrophages(90d76e08-9dbe-4134-8f5a-0f308d53a8bd).html

Authors: Sabiiti, Wilber, Azam, Khalide, Farmer, Eoghan, Kuchaka, Davis, Mtafya, Bariki, Bowness, Ruth, Oravcova, Katarina, Honeyborne, Isobella, Evangelopoulos, Dimitrios, McHugh, Timothy D, Khosa, Celso, Rachow, Andrea, Heinrich, Norbert, Kampira, Elizabeth, Davies, Geraint, Bhatt, Nilesh, Ntinginya, Elias N, Viegas, Sofia, Jani, Ilesh, Kamdolozi, Mercy, Mdolo, Aaron, Khonga, Margaret, Boeree, Martin J, Phillips, Patrick PJ, Sloan, Derek James, Hoelscher, Michael, Kibiki, Gibson, Gillespie, Stephen Henry

Superior Title: Sabiiti , W , Azam , K , Farmer , E , Kuchaka , D , Mtafya , B , Bowness , R , Oravcova , K , Honeyborne , I , Evangelopoulos , D , McHugh , T D , Khosa , C , Rachow , A , Heinrich , N , Kampira , E , Davies , G , Bhatt , N , Ntinginya , E N , Viegas , S , Jani , I , Kamdolozi , M , Mdolo , A , Khonga , M , Boeree , M J , Phillips , P PJ ....

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/tuberculosis-bacillary-load-an-early-marker-of-disease-severity-and-treatment-response(c88bae49-dbb3-4734-9213-aba07b287e41).html

Availability: https://doi.org/10.1136/thoraxjnl-2019-214238
https://research-portal.st-andrews.ac.uk/en/researchoutput/tuberculosis-bacillary-load-an-early-marker-of-disease-severity-and-treatment-response(c88bae49-dbb3-4734-9213-aba07b287e41).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/19881/1/Sabiiti_2020_Tuberculosis_bacillary_load_Thorax_CC.pdf

Authors: Pitcher, Michael John, Dobson, Simon Andrew, Kelsey, Tom, Chaplain, Mark Andrew Joseph, Sloan, Derek James, Gillespie, Stephen Henry, Bowness, Ruth

Superior Title: Pitcher , M J , Dobson , S A , Kelsey , T , Chaplain , M A J , Sloan , D J , Gillespie , S H & Bowness , R 2020 , ' How mechanistic in silico modelling can improve our understanding of TB disease and treatment ' , International Journal of Tuberculosis and Lung Disease , vol. 24 , no. 11 , pp. 1145-1150 . https://doi.org/10.5588/ijtld.20.0107

Subject Terms: TB modelling, Disease models, Statistical modelling, Within-host mechanistic model

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/how-mechanistic-in-silico-modelling-can-improve-our-understanding-of-tb-disease-and-treatment(c847b1ec-88e1-4f6a-96c3-cfabc7b7c89c).html

Availability: https://doi.org/10.5588/ijtld.20.0107
https://research-portal.st-andrews.ac.uk/en/researchoutput/how-mechanistic-in-silico-modelling-can-improve-our-understanding-of-tb-disease-and-treatment(c847b1ec-88e1-4f6a-96c3-cfabc7b7c89c).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20951/1/Pitcher_2020_How_mechanistic_in_silico_IJTLD_1145_CCBY.pdf

Authors: Pitcher, Michael John, Bowness, Ruth, Dobson, Simon Andrew, Eftimie, Raluca, Gillespie, Stephen Henry

Superior Title: Pitcher , M J , Bowness , R , Dobson , S A , Eftimie , R & Gillespie , S H 2020 , ' Modelling the effects of environmental heterogeneity within the lung on the tuberculosis life-cycle ' , Journal of Theoretical Biology , vol. 506 , 110381 . https://doi.org/10.1016/j.jtbi.2020.110381

Subject Terms: Tuberculosis, Computational biology, Within-host model, Bacteria, Metapopulation, Lung, Localisation

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-effects-of-environmental-heterogeneity-within-the-lung-on-the-tuberculosis-lifecycle(59412098-18f9-4883-a6f3-a3fbfbe60eb4).html

Availability: https://doi.org/10.1016/j.jtbi.2020.110381
https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-effects-of-environmental-heterogeneity-within-the-lung-on-the-tuberculosis-lifecycle(59412098-18f9-4883-a6f3-a3fbfbe60eb4).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/20596/1/Pitcher_2020_JEB_Environmental_CC.pdf

Authors: Sabiiti, Wilber, Azam, Khalide, Farmer, Eoghan Charles William, Kuchaka, Davis, Mtafya, Bariki, Bowness, Ruth, Oravcova, Katarina, Honeyborne, Isobella, Evangelopoulos, Dimitrios, McHugh, Timothy Daniel, Khosa, Celso, Rachow, Andrea, Heinrich, Norbert, Kampira, Elizabeth, Davies, Geraint, Bhatt, Nilesh, Ntinginya, Elias N, Viegas, Sofia, Jani, Ilesh, Kamdolozi, Mercy, Mdolo, Aaron, Khonga, Margaret, Boeree, Martin J, Phillips, Patrick P J, Sloan, Derek, Hoelscher, Michael, Kibiki, Gibson, Gillespie, Stephen H

File Description: text

Relation: https://eprints.gla.ac.uk/215891/1/215891.pdf; Sabiiti, W. et al. (2020) Tuberculosis bacillary load, an early marker of disease severity: the utility of tuberculosis Molecular Bacterial Load Assay. Thorax , 75(7), pp. 606-608. (doi:10.1136/thoraxjnl-2019-214238 ) (PMID:32354738) (PMCID:PMC7361026)

Availability: https://doi.org/10.1136/thoraxjnl-2019-214238
https://eprints.gla.ac.uk/215891/
https://eprints.gla.ac.uk/215891/1/215891.pdf

Authors: Pitcher, Michael J.^Aff1, Bowness, Ruth^Aff2, Dobson, Simon^Aff1, Gillespie, Stephen H.^Aff2

Superior Title: Applied Network Science. 3(1)

Authors: Donald, Iain, Meyer, Karen A., Brengman, John, Gillespie, Stephen H., Bowness, Ruth

Superior Title: Journal of Computing in Higher Education: Research & Integration of Instructional Technology. :1-19

Authors: Bowness, Ruth, Chaplain, Mark A.J., Powathil, Gibin G., Gillespie, Stephen H.

Superior Title: Bowness , R , Chaplain , M A J , Powathil , G G & Gillespie , S H 2018 , ' Modelling the effects of bacterial cell state and spatial location on tuberculosis treatment : insights from a hybrid multiscale cellular automaton model ' , Journal of Theoretical Biology , vol. 446 , pp. 87-100 . https://doi.org/10.1016/j.jtbi.2018.03.006

Subject Terms: Tuberculosis, Cellular automaton, Hybrid multiscale model, Antibiotics, Bacteria

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-effects-of-bacterial-cell-state-and-spatial-location-on-tuberculosis-treatment(9761399e-957c-4ab7-a262-eb5e946be073).html

Availability: https://doi.org/10.1016/j.jtbi.2018.03.006
https://research-portal.st-andrews.ac.uk/en/researchoutput/modelling-the-effects-of-bacterial-cell-state-and-spatial-location-on-tuberculosis-treatment(9761399e-957c-4ab7-a262-eb5e946be073).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/12983/1/Bowness_2018_JTB_BacterialCellState_CC.pdf

Authors: Bowness, Ruth

Contributors: Schmitz, Ulf, Wolkenhauer, Olaf

Superior Title: Bowness , R 2016 , Systems medicine and infection . in U Schmitz & O Wolkenhauer (eds) , Systems Medicine . Methods in Molecular Biology , vol. 1386 , Springer , pp. 107-118 . https://doi.org/10.1007/978-1-4939-3283-2_7

Subject Terms: Infection, Mathematical, Modeling, Epidemic, Tuberculosis, HIV

File Description: application/pdf

Availability: https://doi.org/10.1007/978-1-4939-3283-2_7
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/systems-medicine-and-infection(c39ed1f6-f88c-4ea4-93ac-9bdf1d431ff1).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/10036/1/Systems_Infection_Chapter_us090415.pdf

Authors: Sabiiti, Wilber, Ntinginya, Nyanda, Kuchaka, Davis, Azam, Khalide, Kampira, Elizabeth, Mtafya, Bariki, Bowness, Ruth, Bhatt, Nilesh, Davies, Gerry, Kibiki, Gibson, Gillespie, Stephen

Superior Title: BMJ Global Health ; volume 2, issue Suppl 2, page A8.1-A8 ; ISSN 2059-7908

Subject Terms: Public Health, Environmental and Occupational Health, Health Policy

Availability: https://doi.org/10.1136/bmjgh-2016-000260.16

Authors: Rowlatt, Christopher F., Chaplain, Mark A. J., Hughes, David J., Gillespie, Stephen H., Dockrell, David H., Johannessen, Ingolfur, Bowness, Ruth

Subject Terms: SARS-CoV-2, COVID-19, individual-based model, agent-based model, within-host modelling, viral infection, infectious diseases, immune response, type I interferon, macrophages

Relation: https://zenodo.org/record/6514656; https://doi.org/10.5281/zenodo.6514656; oai:zenodo.org:6514656

Availability: https://doi.org/10.5281/zenodo.6514656
https://doi.org/10.5281/zenodo.6514655
https://zenodo.org/record/6514656

Authors: Donald, Iain, Meyer, Karen, Gillespie, Stephen Henry, Bowness, Ruth, Brengman, John

Superior Title: Donald , I , Meyer , K , Gillespie , S H , Bowness , R & Brengman , J 2015 , Project Sanitarium : gaming TB - A serious game for a serious problem . in 7th International Conference on Games and Virtual Worlds for Serious Applications, VS-Games 2015 . , 7295782 , IEEE , Seventh International Conference on Virtual Worlds and Games for Serious Applications: VS-Games 2015 , University of Skövde , Sweden , 16/09/15 . https://doi.org/10.1109/VS-GAMES.2015.7295782

Subject Terms: Games with purpose, Games for change, Serious games, Games education, Educational games

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/project-sanitarium(dded4b08-8bd1-4dd1-bdd5-17c06eb1c47f).html; urn:ISBN:9781479981021

Availability: https://doi.org/10.1109/VS-GAMES.2015.7295782
https://research-portal.st-andrews.ac.uk/en/researchoutput/project-sanitarium(dded4b08-8bd1-4dd1-bdd5-17c06eb1c47f).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/7738/1/VS_Games_Final_Submit.pdf

Authors: Bowness, Ruth, Boeree, Martin J, Aarnoutse, Rob, Dawson, Rodney, Diacon, Andreas, Mangu, Chacha, Heinrich, Norbert, Ntinginya, Nyanda E, Kohlenberg, Anke, Mtafya, Bariki, Phillips, Patrick P J, Rachow, Andrea, Plemper van Balen, Georgette, Gillespie, Stephen H

Superior Title: Bowness , R , Boeree , M J , Aarnoutse , R , Dawson , R , Diacon , A , Mangu , C , Heinrich , N , Ntinginya , N E , Kohlenberg , A , Mtafya , B , Phillips , P P J , Rachow , A , Plemper van Balen , G & Gillespie , S H 2015 , ' The relationship between Mycobacterium tuberculosis MGIT time to positivity and cfu in sputum samples demonstrates changing bacterial phenotypes potentially reflecting the impact of chemotherapy on critical sub-populations ' , Journal of Antimicrobial Chemotherapy , ....

Subject Terms: TTP, M. tuberculosis, TB

File Description: application/pdf

Relation: https://research-portal.st-andrews.ac.uk/en/researchoutput/the-relationship-between-mycobacterium-tuberculosis-mgit-time-to-positivity-and-cfu-in-sputum-samples-demonstrates-changing-bacterial-phenotypes-potentially-reflecting-the-impact-of-chemotherapy-on-critical-subpopulations(604a7382-f89c-43ab-8255-da83fa3fdf50).html

Availability: https://doi.org/10.1093/jac/dku415
https://research-portal.st-andrews.ac.uk/en/researchoutput/the-relationship-between-mycobacterium-tuberculosis-mgit-time-to-positivity-and-cfu-in-sputum-samples-demonstrates-changing-bacterial-phenotypes-potentially-reflecting-the-impact-of-chemotherapy-on-critical-subpopulations(604a7382-f89c-43ab-8255-da83fa3fdf50).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/7686/1/bowness2014jantimicrobchemo_accepted.pdf
https://research-repository.st-andrews.ac.uk/bitstream/10023/7686/2/bowness2014jantimicrobchemo_accepted_supplement.pdf

Authors: Donald, Iain, Meyer, Karen A., Brengman, John, Gillespie, Stephen H., Bowness, Ruth

Superior Title: Journal of Computing in Higher Education: Research & Integration of Instructional Technology. :1-2

Authors: Bowness, Ruth, Boeree, Martin J., Aarnoutse, Rob, Dawson, Rodney, Diacon, Andreas, Mangu, Chacha, Heinrich, Norbert, Ntinginya, Nyanda E., Kohlenberg, Anke, Mtafya, Bariki, Phillips, Patrick P. J., Rachow, Andrea, Plemper van Balen, Georgette, Gillespie, Stephen H.

Subject Terms: Original research

File Description: text/html

Relation: http://jac.oxfordjournals.org/cgi/content/short/dku415v1; http://dx.doi.org/10.1093/jac/dku415

Availability: https://doi.org/10.1093/jac/dku415
http://jac.oxfordjournals.org/cgi/content/short/dku415v1

Authors: Bowness, Ruth, Hood, Alan William, Parnell, Clare Elizabeth

Superior Title: Bowness , R , Hood , A W & Parnell , C E 2013 , ' Coronal heating and nanoflares : current sheet formation and heating ' , Astronomy & Astrophysics , vol. 560 , A89 . https://doi.org/10.1051/0004-6361/201116652

Subject Terms: Magnetohydrodynamics (MHD), Magnetic reconnection, Corona

File Description: application/pdf

Availability: https://doi.org/10.1051/0004-6361/201116652
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/coronal-heating-and-nanoflares(1c3965ff-48dc-4711-a9ff-4128333bf70f).html
https://research-repository.st-andrews.ac.uk/bitstream/10023/4364/1/aa16652_11.pdf