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Number of items: 27.

Data Collection

Aibana, O, Acharya, X, Huang, C, Becerra, MC, Galea, JT, Chiang, SS, Contreras, C, Calderon, R, Yataco, R, Velásquez, GE, Tintaya, K, Jimenez, J, Lecca, L and Murray, MB (2016). Data for prospective cohort study. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0166333.s001

Andreu, N, Phelan, J, de Sessions, PF, Cliff, JM, Clark, T and Hibberd, M (2017). Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. [Data Collection]. Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88801

Arnvig, KB, Comas, I, Thomson, NR, Houghton, J, Boshoff, HI, Croucher, NJ, Rose, G, Perkins, TT, Parkhill, J, Dougan, G and Young, DB (2011). Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis. [Data Collection]. Figshare. https://doi.org/10.1371/journal.ppat.1002342

Coll, F, Mallard, K, Preston, M, Bentley, S, Parkhill, J, Mcnerney, R, Martin, N and Clark, T (2012). In Silico Spoligotyping. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://pathogenseq.lshtm.ac.uk/

Coll, F, Preston, M, Guerra-Assunção, JA, Hill-Cawthorn, G, Harris, D, Perdigão, J, Viveiros, M, Portugal, I, Drobniewski, F, Gagneux, S, Glynn, JR, Pain, A, Parkhill, J, McNerney, R, Martin, N and Clark, T (2014). PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://pathogenseq.lshtm.ac.uk/#tuberculosis

Cortes, T and Carvalho, L (2018). Whole genome sequencing of Mycobacterium tuberculosis strains resistant to D-cycloserine. [Data Collection]. ArrayExpress. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5935/

Cortes, T, Schubert, OT, Banaei-Esfahani, A, Collins, BC, Aebersold, R and Young, DB (2017). Time course RNA-seq of Mycobacterium tuberculosis exposed to nitric oxide. [Data Collection]. ArrayExpress. http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5557/

Hanifa, Y, Fielding, K, Chihota, VN, Adonis, L, Charalambous, S, Karstaedt, A, McCarthy, K, Nicol, MP, Ndlovu, NT, Sahid, F, Churchyard, G and Grant, AD (2016). Diagnostic Accuracy of Lateral Flow Urine LAM Assay for TB Screening of Adults with Advanced Immunosuppression Attending Routine HIV Care in South Africa. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0156866.

Kaswaswa, K, MacPherson, P, Kumwenda, M, Mpunga, J, Thindwa, D, Nliwasa, M, Mwapasa, M, Odland, J, Tomoka, T, Chipungu, G, Mukaka, M and Corbett, EL (2022). Effect of patient-delivered household contact tracing and prevention for tuberculosis: A household cluster-randomised trial in Malawi. Data. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.1371/journal.pone.0269219.s002

London School of Hygiene & Tropical Medicine (2018). Methylation and transcription analysis of Mycobacterium tuberculosis. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/data/view/PRJEB29197

London School of Hygiene & Tropical Medicine (2021). Sequencing of M/XDR isoaltes from Pakistan. [Data Collection]. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB43284

McCarthy, K, Fielding, K, Churchyard, GJ and Grant, AD (2018). Empiric tuberculosis treatment in South African primary health care facilities - for whom, where, when and why: Implications for the development of tuberculosis diagnostic tests. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pone.0191608.s001

McCreesh, N (2021). NickyMcC/WithinClinics. [Data Collection]. Github. https://github.com/NickyMcC/WithinClinics

Meier, S, Seddon, JA, Maasdorp, E, Kleynhans, L, du Plessis, N, Loxton, AG, Malherbe, ST, Zak, DE, Thompson, E, Duffy, FJ, Kaufmann, SHE, Ottenhoff, THM, Scriba, TJ, Suliman, S, Sutherland, JS, Winter, J, Kuivaniemi, H, Walzl, G and Tromp, G (2022). Gene ontology (GO) enrichment analysis results for significantly upregulated genes at all time points. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0278295.s003

Meier, S, Seddon, JA, Maasdorp, E, Kleynhans, L, du Plessis, N, Loxton, AG, Malherbe, ST, Zak, DE, Thompson, E, Duffy, FJ, Kaufmann, SHE, Ottenhoff, THM, Scriba, TJ, Suliman, S, Sutherland, JS, Winter, J, Kuivaniemi, H, Walzl, G and Tromp, G (2022). KEGG and gene ontology (GO) enrichment analyses for significantly differentially expressed genes between low and high PET score groups for the terms and pathways identified in the main analyses. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0278295.s005

Meier, S, Seddon, JA, Maasdorp, E, Kleynhans, L, du Plessis, N, Loxton, AG, Malherbe, ST, Zak, DE, Thompson, E, Duffy, FJ, Kaufmann, SHE, Ottenhoff, THM, Scriba, TJ, Suliman, S, Sutherland, JS, Winter, J, Kuivaniemi, H, Walzl, G and Tromp, G (2022). KEGG pathway enrichment analysis results for significantly differentially expressed genes at all time points. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0278295.s004

Meier, S, Seddon, JA, Maasdorp, E, Kleynhans, L, du Plessis, N, Loxton, AG, Malherbe, ST, Zak, DE, Thompson, E, Duffy, FJ, Kaufmann, SHE, Ottenhoff, THM, Scriba, TJ, Suliman, S, Sutherland, JS, Winter, J, Kuivaniemi, H, Walzl, G and Tromp, G (2022). List of differentially expressed genes at all time points. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0278295.s002

Meier, S, Seddon, JA, Maasdorp, E, Kleynhans, L, du Plessis, N, Loxton, AG, Malherbe, ST, Zak, DE, Thompson, E, Duffy, FJ, Kaufmann, SHE, Ottenhoff, THM, Scriba, TJ, Suliman, S, Sutherland, JS, Winter, J, Kuivaniemi, H, Walzl, G and Tromp, G (2022). PET scores for the catalysis study specimens. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0278295.s001

Nliwasa, M, MacPherson, P, Chisala, P, Kamdolozi, M, Khundi, MJ, Kaswaswa, K, Mwapasa, M, Msefula, C, Sohn, H, Flach, C and Corbett, E (2016). LAMP minimal dataset. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0155101.s001

Ofori-Anyinam, B, Dolganov, G, Van, T, Davis, JL, Walter, ND, Garcia, BJ, Voskuil, M, Fissette, K, Diels, M, Driesen, M, Meehan, CJ, Yeboah-Manu, D, Coscolla, M, Gagneux, S, Antonio, M, Schoolnik, G, Gehre, F and de Jong, BC (2017). Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum. [Data Collection]. Tuberculosis. https://doi.org/10.1016/j.tube.2017.03.001

Palittapongarnpim, P, Ajawatanawong, P, Viratyosin, W, Smittipat, N, Disratthakit, A, Mahasirimongkol, S, Yanai, H, Yamada, N, Nedsuwan, S, Imasanguan, W, Kantipong, P, Chaiyasirinroje, B, Wongyai, J, Toyo-oka, L, Phelan, J, Parkhill, J, Clark, TG, Hibberd, ML, Ruengchai, W, Palittapongarnpim, P, Juthayothin, T, Tongsima, S and Tokunaga, K (2018). Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. [Data Collection]. Scientific Reports. https://doi.org/10.1038/s41598-018-29986-3

Phelan, JE, Coll, F, Bergval, I, Anthony, RM, Warren, R, Sampson, SL, Gey van Pittius, NC, Glynn, JR, Crampin, AC, Alves, A, Bessa, TB, Campino, S, Dheda, K, Grandjean, L, Hasan, R, Hasan, Z, Miranda, A, Moore, D, Panaiotov, S, Perdigao, J, Portugal, I, Sheen, P, de Oliveira Sousa, E, Streicher, EM, van Helden, PD, Viveiros, M, Hibberd, ML, Pain, A, Mcnerney, R and Clark, TG (2016). Data for: "Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom.

Scriba, TJ, Kimuda, SG, Biraro, IA, Bagaya, BS, Raynes, JG and Cose, S (2018). S1 Data File for: "Characterising antibody avidity in individuals of varied Mycobacterium tuberculosis infection status using surface plasmon resonance". [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0205102.s007

Sobkowiak, B, Glynn, JR, Houben, Rein M. G. J., Mallard, K, Phelan, JE, Guerra-Assunção, JA, Banda, L, Mzembe, T, Viveiros, M, McNerney, R, Parkhill, J, Crampin, AC and Clark, TG (2018). Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6968636.v1

Tientcheu, L, Haks, MC, Agbla, S, Sutherland, J, Adetifa, I, Donkor, S, Quinten, E, Daramy, M, Antonio, M, Kampmann, B, Ottenhoff, THM, Dockrell, H and Ota, MO (2016). Host Immune Responses Differ between M. africanum- and M. tuberculosis-Infected Patients following Standard Anti-tuberculosis Treatment. [Data Collection]. PLoS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0004701

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

This list was generated on Fri Jun 9 03:09:52 2023 BST.