Data Collection

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/

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

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

Dorsey, G, Kamya, M, Greenhouse, B, Arinaitwe, E, Kilama, M, Nankabirwa, J, Rek, J, Nsobya, S, Mawejje, H, Nzarubara, B, Lavoy, G, Kizza, T, Musiime, A, Kigozi, S, Ssewanyana, I, Rosenthal, P, Rodriguez-Barraquer, I, Clark, T, Conrad, M, Staedke, SG, Drakeley, C, Donnelly, M, Lindsay, S, Smith, D, Bousema, T and Andolina, C (2023). Dataset: PRISM2 ICEMR Cohort. [Data Collection]. ClinEpiDB. https://clinepidb.org/ce/app/workspace/analyses/DS_51b40fe2e2/new

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

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

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

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

Holt, KE (2023). Global Typhoid Genomics Consortium 2022 - Genome Assemblies. [Data Collection]. Monash University. https://doi.org/10.26180/21431883.v1

London School of Hygiene & Tropical Medicine (2023). Data for: "Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana". [Data Collection]. NCBI Sequence Read Archive. https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA1052100

London School of Hygiene & Tropical Medicine (2023). Phylogenetic inference of pneumococcal transmission from cross-sectional data, a pilot study. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB60532

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

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

Sanderson, T (2023). Processed INSDC dataset for MOV analysis. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8252387

Sanderson, T, Bileschi, M and Belanger, D (2023). google-research/proteinfer. [Data Collection]. Github. https://github.com/google-research/proteinfer

Sanderson, T and Ruis, C (2023). theosanderson/molnupiravir. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.8101002

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.

Soremekun, S, Källander, K, Lingam, R, Branco, AC, Batura, N, Strachan, DL, Muiambo, A, Salomao, N, Condoane, J, Benhane, F, Kasteng, F, Vassall, A, Hill, Z, ten Asbroek, G, Meek, S, Tibenderana, J and Kirkwood, B (2023). Restricted Randomisation Procedure and codes–inSCALE Mozambique. [Data Collection]. PLOS Digital Health. https://doi.org/10.1371/journal.pdig.0000235.s003

Soremekun, S, Källander, K, Lingam, R, Branco, AC, Batura, N, Strachan, DL, Muiambo, A, Salomao, N, Condoane, J, Benhane, F, Kasteng, F, Vassall, A, Hill, Z, ten Asbroek, G, Meek, S, Tibenderana, J and Kirkwood, B (2023). inSCALE data collection forms. [Data Collection]. PLOS Digital Health. https://doi.org/10.1371/journal.pdig.0000235.s002

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

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

Wang, L (2023). linfeng-wang/GMM4TB. [Data Collection]. Github. https://github.com/linfeng-wang/GMM4TB

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