Browse by Faculty
Up a level |
- LSHTM Organisational Structure (3227)
- Faculty of Infectious and Tropical Diseases (827)
- Department of Infection Biology (94)
- Faculty of Infectious and Tropical Diseases (827)
A
Allen, DJ (2022). The impact of cognate strategy training on guessing accuracy for unknown visually-presented words: The case of Japanese learners of English. [Data Collection]. SAGE Journals. https://doi.org/10.25384/SAGE.c.6089659.v1
Ashall, J, Shah, S, Biggs, JR, Chang, JR, Jafari, Y, Brady, OJ, Mai, HK, Lien, LT, Do Thai, H, Nguyen, HAT, Anh, DD, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Rasschaert, F, Van Wesenbeeck, L, Yoshida, L, Hafalla, JCR, Hue, S and Hibberd, ML (2023). Dengue virus type 4 isolate DET-P-0428-1 polyprotein (POLY) gene, complete cds; and sfRNA2 lncRNA gene, partial sequence. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/OQ427062
Ashall, J, Shah, S, Biggs, JR, Chang, JR, Jafari, Y, Brady, OJ, Mai, HK, Lien, LT, Do Thai, H, Nguyen, HAT, Anh, DD, Iwasaki, C, Kitamura, N, Van Loock, M, Herrera-Taracena, G, Rasschaert, F, Van Wesenbeeck, L, Yoshida, L, Hafalla, JCR, Hue, S and Hibberd, ML (2023). Dengue virus type I isolate DEN-P-1098-1 polyprotein (POLY) gene, partial cds. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/nuccore/OQ426566.1/
C
Cerdeira, L, Dyson, ZA and Holt, KE (2023). typhoidgenomics/TyphiNET: New release. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.5281/zenodo.5338903
Cerdeira, L, Sharma, V, Maranga, M, Carey, M, Dyson, ZA and Holt, KE (2024). amrnet/amrnet: AMRnet-v1.0. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10810218
Chung The, H, Rabaa, MA, Pham Thanh, D, Ruekit, S, Wangchuk, S, Dorji, T, Pem Tshering, K, Nguyen Thi Nguyen, T, Voong Vinh, P, Ha Thanh, T, Nguyen Ngoc Minh, C, Turner, P, Sar, P, Thwaites, G, Holt, KE, Thomson, NR, Bodhidatta, L, Mason, CJ and Baker, S (2015). The introduction and establishment of fluoroquinolone resistant Shigella sonnei into Bhutan. [Data Collection]. Figshare.
Churcher, TS, Bousema, T, Walker, M, Drakeley, C, Schneider, P, Ouédraogo, AL and Basáñez, M (2013). Data from: Predicting mosquito infection from Plasmodium falciparum gametocyte density and estimating the reservoir of infection. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.0k402
Churcher, T, Stopard, I, Hamlet, A, Dee, D, Sanou, A, Rowland, M, Guelbeogo, M, Emidi, B, Mosha, J, Challenger, J, Denz, A, Charles, G, Russell, E, Fitzjohn, R, Winskill, P, Fornadel, C, Mclean, T, Digre, P, Wagman, J, Mosha, F, Cook, J, Akogbéto, M, Djogbenou, L, Ranson, H, Manjurano, A, N'fale, S, Protopopoff, N, Accrombessi, M, Ngufor, C, Foster, G and Sherrard-Smith, E (2023). MINT-data-v20230208. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8344311
Cleghorn, LAT, Wall, RJ, Albrecht, S, MacGowan, SA, Norval, S, De Rycker, M, Woodland, A, Spinks, D, Thompson, S, Patterson, S, Corpas Lopez, V, Dey, G, Collie, IT, Hallyburton, I, Kime, R, Simeons, FRC, Stojanovski, L, Frearson, JA, Wyatt, PG, Read, KD, Gilbert, IH and Wyllie, S (2023). Development of a 2,4-Diaminothiazole Series for the Treatment of Human African Trypanosomiasis Highlights the Importance of Static–Cidal Screening of Analogues. [Data Collection]. ACS Publications. https://doi.org/10.1021/acs.jmedchem.3c00509.s002
Coll, F (2022). francesccoll/powerbacgwas. [Data Collection]. Github. https://github.com/francesccoll/powerbacgwas/
D
Dyson, ZA (2022). zadyson/SNV_Stats_Generator. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6581275
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Accession numbers and data for S. Typhi sequences used in this study. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s005
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Excluded repeat and phage regions in PNG MDUST348 2.1.7.2 completed reference sequence. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s006
Dyson, ZA, Malau, E, Horwood, PF, Ford, R, Siba, V, Yoannes, M, Pomat, W, Passey, M, Judd, LM, Ingle, DJ, Williamson, DA, Dougan, G, Greenhill, AR and Holt, KE (2022). Outgroups used for phylogenetic tree rooting. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0010306.s007
d-j-e, Holt, KE and Wyres, KL (2022). katholt/RedDog. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6460229
E
Eccleston, RC, Manko, E, Campino, S, Clark, TG and Furnham, N (2022). A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6122329
Eckold, C, van Doorn, CL, Dockrell, H, Ottenhoff, TH, Vianello, E and Cliff, JM (2023). Impaired resolution of blood transcriptomes through tuberculosis treatment with diabetes comorbidity. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193978
F
Fombah, AE, Chen, H, Owusu-Kyei, K, Quinto, L, Gonzalez, R, Williams, J, Berne, ML, Wassenaar, M, Jalloh, A, Sunders, J, Ramirez, M, Bertran-Cobo, C, Saute, F, Ekouevi, DK, Briand, V, Kamara, AR, Sesay, T, Samai, M and Menéndez, C (2023). MULTIPLY - Baseline household survey, Sierra Leone. [Data Collection]. CORA.Repositori de Dades de Recerca. https://doi.org/10.34810/data603
Foster-Nyarko, E, Holt, KE, Cottingham, H, Wick, R, Judd, LM, Lam, M, Wyres, KL, Stanton, T, Tsang, KK, David, S, Bridel, S, Palma, F, Aanensen, DM and Brisse, S (2023). Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19745608.v2
G
Garcia, KKS, Soremekun, S, Bottomley, C, Abrahão, AA, de Miranda, CB, Drakeley, C, Ramalho, WM and Siqueira, AM (2023). Additional file 2 of Assessing the impact of the “malaria supporters project” intervention to malaria control in the Brazilian Amazon: an interrupted time-series analysis. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.24151173.v1
Garcia, KKS, Soremekun, S, Bottomley, C, Abrahão, AA, de Miranda, CB, Drakeley, C, Ramalho, WM and Siqueira, AM (2023). Additional file 3 of Assessing the impact of the “malaria supporters project” intervention to malaria control in the Brazilian Amazon: an interrupted time-series analysis. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.24151176.v1
Gibson, AJ, Stiens, J, Passmore, IJ, Faulkner, V, Miculob, J, Willcocks, S, Coad, M, Berg, S, Werling, D, Wren, BW, Nobeli, I, Villarreal-Ramos, B and Kendall, SL (2022). Defining the genes required for survival of Mycobacterium bovis in the bovine host offers novel insights into the genetic basis of survival of pathogenic mycobacteria. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6598445
Gomes, MC, Brokatzky, D, Bielecka, MK, Wardle, FC and Mostowy, S (2023). Shigella induces epigenetic reprogramming of zebrafish neutrophils. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217063
Guevara, PD, Maes, M, Thanh, DP, Duarte, C, Rodriguez, EC, Montaño, LA, Dan, THN, Nguyen, TNT, Carey, ME, Campos, J, Chinen, I, Perez, E and Baker, S (2021). Profile of the organisms selected for sequencing. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009755.s001
H
Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 1 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579653.v1
Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 3 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579659.v1
Hawkey, J, Wyres, KL, Judd, LM, Harshegyi, T, Blakeway, L, Wick, RR, Jenney, AWJ and Holt, KE (2022). Additional file 4 of ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.20579662.v1
Holt, KE (2016). Acinetobacter baumannii GC1 recombination analysis. [Data Collection]. University of Melbourne. https://doi.org/10.4225/49/5690B341A0FDB
Holt, KE (2023). Global Typhoid Genomics Consortium 2022 - Genome Assemblies. [Data Collection]. Monash University. https://doi.org/10.26180/21431883.v1
Holt, KE, Gorrie, C and Wyres, K (2021). Genome assemblies and pan-genome data for 328 clinical isolates of Klebsiella pneumoniae species complex, representing one year of infections diagnosed in a hospital diagnostic lab. [Data Collection]. Monash University. https://doi.org/10.26180/16811344
I
Ijaz, UZ, Gundogdu, O, Keating, C, Eekert, Mv, Gibson, W, Parkhill, J, Abilahi, F, Liseki, B, Nguyen, V, Sudgen, S, Quince, C, Ensink, JHJ, Torondel, B and Walker, AW (2022). Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate. [Data Collection]. Frontiers. https://doi.org/10.3389/fmicb.2022.960747.s008
Inouye, M, Dashnow, H, Pope, B, Wick, R and Holt, KE (2021). katholt/srst2. [Data Collection]. Github. https://github.com/katholt/srst2
K
Kane, L (2022). Investigation of Vibrio cholerae pathogenesis using a novel human intestinal model of infection. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/PUBS.04670346
Keegan, S, Pedersen, A and Fenton, A (2024). The impact of within-host coinfection interactions on between-host parasite transmission dynamics varies with spatial scale. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.tdz08kq68
Keegan, S, Pedersen, A and Fenton, A (2024). The impact of within-host coinfection interactions on between-host parasite transmission dynamics varies with spatial scale. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10777557
L
London School of Hygiene & Tropical Medicine (2022). CDC50 interacting partners of Plasmodium falcipraum. [Data Collection]. PRIDE: PRoteomic IDEntifications Database. https://www.ebi.ac.uk/pride/archive/projects/PXD033834
London School of Hygiene & Tropical Medicine (2019). Dual RNA-seq of zebrafish larvae infected with Shigella sonnei. [Data Collection]. NIH National Library of Medicine. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA590152
London School of Hygiene & Tropical Medicine (2022). Environmental detection of vector larvae. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/bioproject/PRJEB56414
London School of Hygiene & Tropical Medicine (2016). Mus musculus. [Data Collection]. NIH National Library of Medicine. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA348679
London School of Hygiene & Tropical Medicine (2010). Proteromonas lacertae. [Data Collection]. NCBI BioProject. https://www.ncbi.nlm.nih.gov/bioproject/50831
London School of Hygiene & Tropical Medicine (2010). Proteromonas lacertae strain:LA. [Data Collection]. NCBI BioProject. https://www.ncbi.nlm.nih.gov/bioproject/43423
López-Jiménez, AT, Brokatzky, D, Pillay, K, Williams, T, Özbaykal Güler, G and Mostowy, S (2024). High-content high-resolution microscopy and deep learning assisted analysis reveals host and bacterial heterogeneity during Shigella infection. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.10766626
López-jiménez, AT (2024). ATLopezJimenez/Toolset-high-content-analysis-of-Shigella-infection. [Data Collection]. Github. https://github.com/ATLopezJimenez/Toolset-high-content-analysis-of-Shigella-infection
López-jiménez, AT, Brokatzky, D, Pillay, K, Williams, T, Özbaykal Güler, G and Mostowy, S (2024). High-content high-resolution microscopy and deep learning assisted analysis reveals host and bacterial heterogeneity during Shigella infection. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.6wwpzgn5z
M
Maier, AG and Van ooij, C (2022). Table 1 - The role of cholesterol in invasion and growth of malaria parasites. [Data Collection]. Frontiers. https://doi.org/10.3389/fcimb.2022.984049.s001
Matos, GM, Lewis, MD, Talavera-López, C, Yeo, M, Grisard, EC, Messenger, LA, Miles, MA and Andersson, B (2021). Comparative genomic analyses of Trypanosoma cruzi experimental hybrids. [Data Collection]. NCBI BioProject. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA748998
McKenna, A, Ijaz, UZ, Kelly, C, Linton, M, Sloan, WT, Green, BD, Lavery, U, Dorrell, N, Wren, BW, Richmond, A, Corcionivoschi, N and Gundogdu, O (2020). Additional file 11 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.12936381.v1
Mowbray, CE, Braillard, S, Glossop, PA, Whitlock, GA, Jacobs, RT, Speake, J, Pandi, B, Nare, B, Maes, L, Yardley, V, Freund, Y, Wall, RJ, Carvalho, S, Bello, D, Van den Kerkhof, M, Caljon, G, Gilbert, IH, Corpas-Lopez, V, Lukac, I, Patterson, S, Zuccotto, F and Wyllie, S (2021). DNDI-6148: A Novel Benzoxaborole Preclinical Candidate for the Treatment of Visceral Leishmaniasis. [Data Collection]. ACS Publications, Washington, DC, USA. https://doi.org/10.1021/acs.jmedchem.1c01437.s004
N
Nair, M, Kumar, P, Pandey, S, Kazmi, S, Moreto-Planas, L, Ranjan, A and Burza, S (2020). Quality of life perceptions amongst patients co-infected with Visceral Leishmaniasis and HIV: A qualitative study from Bihar, India. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0227911.s003
Nasher, F, Lehri, B, Horney, M, Stabler, R and Wren, BW (2022). Campylobacter jejuni interactions with Acanthamoeba castellanii. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206909
O
Oresegun, DR, Thorpe, P, Benavente, ED, Campino, S, Muh, F, Moon, RW, Clark, TG and Cox-Singh, J (2022). De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. [Data Collection]. Frontiers. https://doi.org/10.3389/fgene.2022.855052.s001
Oulton, T, Obiero, J, Rodriguez, I, Ssewanyana, I, Dabbs, RA, Bachman, CM, Greenhouse, B, Drakeley, C, Felgner, PL, Stone, WJR and Tetteh, KKA (2022). Correlation coefficient results for all protein pairs. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0273106.s005
Oulton, T, Obiero, J, Rodriguez, I, Ssewanyana, I, Dabbs, RA, Bachman, CM, Greenhouse, B, Drakeley, C, Felgner, PL, Stone, WJR and Tetteh, KKA (2022). Detail of expressed protein targets. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0273106.s004
P
Patel, A, Nofal, SD, Blackman, MJ and Baker, DA (2022). Supplementary information, CDC50 orthologues in Plasmodium falciparum have distinct roles in merozoite egress and trophozoite maturation. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6619340
Phelan, J (2023). jodyphelan/host-pathogen. [Data Collection]. Github. https://github.com/jodyphelan/host-pathogen
Phelan, JE and Menzel, P (2023). jodyphelan/tbdb. [Data Collection]. Github. https://github.com/jodyphelan/tbdb
Phelan, J and Manko, E (2023). jodyphelan/malaria-db. [Data Collection]. GitHub. https://github.com/jodyphelan/malaria-db
Phelan, J and Thorpe, J (2023). jodyphelan/malaria-profiler. [Data Collection]. GitHub. https://github.com/jodyphelan/Malaria-Profiler
Pietersen, E, Anderson, K, Cox, H, Dheda, K, Bian, A, Shepherd, BE, Sterling, TR, Warren, RM and van der Heijden, YF (2023). Data for: "Variation in missed doses and reasons for discontinuation of anti-tuberculosis drugs during hospital treatment for drug-resistant tuberculosis in South Africa". [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0281097.s001
R
Racané, L, Ptiček, L, Kostrun, S, Raić-Malić, S, Taylor, MC, Delves, M, Alsford, S, Olmo, F, Francisco, AF and Kelly, JM (2023). Bis-6-amidino-benzothiazole Derivative that Cures Experimental Stage 1 African Trypanosomiasis with a Single Dose. [Data Collection]. ACS Publications. https://doi.org/10.1021/acs.jmedchem.3c01051.s002
Raghavan, M, Kalantar, K, Duarte, E, Teyssier, N, Takahashi, S, Kung, A, Rajan, JU, Rek, J, Tetteh, KKA, Drakeley, C, Ssewanyana, I, Rodriguez-Barraquer, I, Greenhouse, B and DeRisi, J (2023). Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum. [Data Collection]. Dryad. https://doi.org/10.7272/Q69S1P9G
Ramaprasad, A, Burda, P, Koussis, K, Thomas, JA, Pietsch, E, Calvani, E, Howell, SA, MacRae, JI, Snijders, AP, Gilberger, T and Blackman, MJ (2023). Label-free quantitation of proteins detected in SUB1-null schizonts in the presence or absence of C2. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1011449.s007
Ramaprasad, A, Burda, P, Koussis, K, Thomas, JA, Pietsch, E, Calvani, E, Howell, SA, MacRae, JI, Snijders, AP, Gilberger, T and Blackman, MJ (2023). Raw peak intensities of various lipid species measured before and after egress in RAP-treated (+RAP) and mock-treated (-RAP) LCAT:2loxPint parasites. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1011449.s009
Ramaprasad, A, Burda, P, Koussis, K, Thomas, JA, Pietsch, E, Calvani, E, Howell, SA, MacRae, JI, Snijders, AP, Gilberger, T and Blackman, MJ (2023). Raw peak intensities of various lipid species measured in LCAT:2loxPint egress-stalled schizonts following mock-or RAP-treatment at ring stages. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1011449.s008
Ramaprasad, A, Burda, P, Koussis, K, Thomas, J, Pietsch, E, Calvani, E, Howell, SA, MacRae, JI, Snijders, AP, Gilberger, T and Blackman, MJ (2023). Sequences of oligonucleotides and other synthetic DNA used in this study. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1011449.s006
Reuter, S, Corander, J, de Been, M, Harris, S, Cheng, L, Hall, M, Thomson, NR and McNally, A (2015). Directional gene flow and ecological separation in Yersinia enterocolitica. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.1482060.v1
Ruiz Cuenca, P, Key, S, Lindblade, KA, Vythilingam, I, Drakeley, C and Fornace, K (2022). Additional file 3 of Is there evidence of sustained human-mosquito-human transmission of the zoonotic malaria Plasmodium knowlesi? A systematic literature review. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.19380996.v1
Ruiz Cuenca, P, Key, S, Lindblade, KA, Vythilingam, I, Drakeley, C and Fornace, K (2022). Is there evidence of sustained human-mosquito-human transmission of the zoonotic malaria Plasmodium knowlesi? A systematic literature review. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.5902668.v1
Ruiz Cuenca, P, Key, S, Lindblade, KA, Vythilingam, I, Drakeley, C and Fornace, K (2022). Is there evidence of sustained human-mosquito-human transmission of the zoonotic malaria Plasmodium knowlesi? A systematic literature review. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.c.5902668.v1
S
Schneider, P, Bousema, T, Gouagna, LC, Otieno, S, van de Vegte-Bolmer, M, Omar, SA and Sauerwein, RW (2013). Data from: Submicroscopic Plasmodium falciparum gametocyte densities frequently result in mosquito infection. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.589ft
Schwalb, A (2023). Data for: "Travel and tuberculosis in migrants". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00003534.
Slater, HC, Ross, A, Felger, I, Hofmann, NE, Robinson, L, Cook, J, Gonçalves, BP, Björkman, A, Ouedraogo, AL, Morris, U, Msellem, M, Koepfli, C, Mueller, I, Tadesse, F, Gadisa, E, Domingo, G, Kapulu, M, Midega, J, Owusu-Agyei, S, Nabet, C, Piarroux, R, Doumbo, O, Doumbo, SN, Koram, K, Lucchi, N, Udhayakumar, V, Mosha, J, Tiono, A, Chandramohan, D, Gosling, R, Mwingira, F, Sauerwein, R, Riley, EM, White, NJ, Nosten, F, Imwong, M, Bousema, T, Drakeley, C and Okell, LC (2019). Data from: The temporal dynamics and infectiousness of subpatent Plasmodium falciparum infections in relation to parasite density. [Data Collection]. Dryad. https://doi.org/10.5061/dryad.75t5382
Smith, A, Wall, RJ, Patterson, S, Rowan, T, Rico Vidal, E, Stojanovski, L, Huggett, M, Hampton, SE, Thomas, MG, Corpas Lopez, V, Gillingwater, K, Duke, J, Napier, G, Peter, R, Vitouley, HS, Harrison, JR, Milne, R, Jeacock, L, Baker, N, Davis, SH, Simeons, F, Riley, J, Horn, D, Brun, R, Zuccotto, F, Witty, MJ, Wyllie, S, Read, KD and Gilbert, IH (2022). Repositioning of a Diaminothiazole Series Confirmed to Target the Cyclin-Dependent Kinase CRK12 for Use in the Treatment of African Animal Trypanosomiasis. [Data Collection]. ACS Publications. https://doi.org/10.1021/acs.jmedchem.1c02104.s003
Spadar, A (2022). AntonS-bio/entropy. [Data Collection]. GitHub. https://github.com/AntonS-bio/entropy
Spadar, A, Perdigão, J, Campino, S and Clark, TG (2023). Additional file 2 of Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.22611932.v1
T
Tawaraishi, T, Ochida, A, Akao, Y, Itono, S, Kamaura, M, Akther, T, Shimada, M, Canan, S, Chowdhury, S, Cao, Y, Condroski, K, Engkvist, O, Francisco, A, Ghosh, S, Kaki, R, Kelly, JM, Kimura, C, Kogej, T, Nagaoka, K, Naito, A, Pairaudeau, G, Radu, C, Roberts, I, Shum, D, Watanabe, N, Xie, H, Yonezawa, S, Yoshida, O, Yoshida, R, Mowbray, C and Perry, B (2023). Collaborative Virtual Screening Identifies a 2‑Aryl-4-aminoquinazoline Series with Efficacy in an In Vivo Model of Trypanosoma cruzi Infection. [Data Collection]. ACS Publications. https://doi.org/10.1021/acs.jmedchem.2c00775.s002
Torraca, V, Kaforou, M, Watson, J, Duggan, GM, Guerrero-Gutierrez, H, Krokowski, S, Hollinshead, M, Clarke, TB, Mostowy, RJ, Tomlinson, GS, Sancho-Shimizu, V, Clements, A and Mostowy, S (2019). Shigella sonnei infection of zebrafish reveals that O-antigen mediates neutrophil tolerance and dysentery incidence. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1008006.s007
Torraca, V, Sommer, F, In 't Veld, AE, Willemse, J and Meijer, AH (2021). RNAseq expression analysis of FACS-sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149942
Tsang, KK (2020). karatsang/rulesbased_logisticregression. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.3988479
V
Verboven, L, Phelan, J, Heupink, TH and Van Rie, A (2022). TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. S1 File. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0279644.s002
Verboven, L, Phelan, J, Heupink, TH and Van Rie, A (2022). TBProfiler for automated calling of the association with drug resistance of variants in Mycobacterium tuberculosis. S2 File. [Data Collection]. Github. https://doi.org/10.1371/journal.pone.0279644.s003
W
Wang, L (2023). linfeng-wang/GMM4TB. [Data Collection]. Github. https://github.com/linfeng-wang/GMM4TB
Wick, RR and Holt, KE (2022). Genome details for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s015
Wick, RR and Holt, KE (2022). Assembly and polishing details for the real-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s020
Wick, RR and Holt, KE (2022). Confusion matrices for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s017
Wick, RR and Holt, KE (2022). Predictors of assembly quality. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s018
Wick, RR and Holt, KE (2022). Raw results for the real-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s019
Wick, RR and Holt, KE (2022). Raw results for the simulated-read tests. [Data Collection]. PLOS Computational Biology. https://doi.org/10.1371/journal.pcbi.1009802.s016
Wick, R, kelwyres and Holt, KE (2022). katholt/Kaptive. [Data Collection]. Github. https://github.com/katholt/Kaptive
Wick, R, kelwyres, Pan, A, Stanton, T, Watts, S and Lee, T (2022). kelwyres/Kaptive-Web. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.7039364
Willcocks, S (2019). Genome-wide Assessment of Antimicrobial Tolerance in Yersinia pseudotuberculosis Under Ciprofloxacin Stress. [Data Collection]. NCBI Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135236
Wright, K, de Silva, K, Plain, KM, Purdie, AC, Blair, TA, Duggin, IG, Britton, WJ and Oehlers, SH (2021). Source data for graphs. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1009186.s008
Wright, K, de Silva, K, Plain, KM, Purdie, AC, Blair, TA, Duggin, IG, Britton, WJ and Oehlers, SH (2021). miR-206 target prediction results from TargetScan analysis. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1009186.s007
Z
Záhonová, K, Low, RS, Warren, CJ, Cantoni, D, Herman, EK, Yiangou, L, Ribeiro, CA, Phanprasert, Y, Brown, IR, Rueckert, S, Baker, NL, Tachezy, J, Betts, EL, Gentekaki, E, van der Giezen, M, Clark, CG, Jackson, AP, Dacks, JB and Tsaousis, AD (2023). Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis. [Data Collection]. Current Biology. https://doi.org/10.1016/j.cub.2023.05.025