A

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]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1002342.s008

G

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). 99% credible set SNPs for leprosy association at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s016

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Analysis of pleiotropy at the leprosy association at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s018

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Association statistics for imputed classical HLA alleles and leprosy risk in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s022

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Chromatin state at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s020

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Genome-wide association study of leprosy in Malawi and Mali. S2 Table. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s015

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Leprosy association statistics for suggestive associations in Malawi. S1 Table. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s014

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Regulatory function at the chromosome 10q24 leprosy association. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s021

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Replication of previously-published leprosy associated non-HLA SNPs in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s023

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Replication of previously-published leprosy associated non-HLA SNPs in Malawi and Mali stratified by multibacillary and paucibacillary disease. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s024

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). SNP quality control summary in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s026

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Sample quality control summary in Malawi and Mali. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s025

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Selection signatures at chromosome 10q24. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s019

Gilchrist, JJ, Auckland, K, Parks, T, Mentzer, AJ, Goldblatt, L, Naranbhai, V, Band, G, Rockett, KA, Toure, OB, Konate, S, Sissoko, S, Djimdé, AA, Thera, MA, Doumbo, OK, Sow, S, Floyd, S, Pönnighaus, JM, Warndorff, DK, Crampin, AC, Fine, PEM, Fairfax, BP and Hill, AVS (2022). Study populations and leprosy association statistics at rs2015583 in the Chinese replication analysis. [Data Collection]. PLOS Pathogens. https://doi.org/10.1371/journal.ppat.1010312.s017

Gliddon, HD, Kaforou, M, Alikian, M, Habgood-Coote, D, Zhou, C, Oni, T, Anderson, ST, Brent, AJ, Crampin, AC, Eley, B, Heyderman, R, Kern, F, Langford, PR, Ottenhoff, THM, Hibberd, ML, French, N, Wright, VJ, Dockrell, HM, Coin, LJ, Wilkinson, RJ and Levin, M (2021). Identification of Reduced Host Transcriptomic Signatures for Tuberculosis Disease and Digital PCR-Based Validation and Quantification. [Data Collection]. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2021.637164.s001

J

Joshua, G (2014). Transcription profiling by array of Caenorhabditis elegans with biofilm compared to without biofilm. [Data Collection]. ArrayExpress. http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2981/

M

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

N

Namulondo, J, Nyangiri, OA, Kimuda, MP, Nambala, P, Nassuuna, J, Egesa, M, Nerima, B, Biryomumaisho, S, Mugasa, CM, Nabukenya, I, Kato, D, Elliott, A, Noyes, H, Tweyongyere, R, Matovu, E and Mulindwa, J (2023). RNA Sequence data analysis using DESeq2 pipeline. [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0011455.s009

O

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

P

Pumirat, P, Cuccui, J, Stabler, R, Stevens, JM, Muangsombut, V, Singsuksawat, E, Stevens, MP, Wren, B and Korbsrisate, S (2014). Transcription profiling of Burkholderia pseudomallei under salt stress and the effect on a type III secretion system. [Data Collection]. ArrayExpress. http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2302/

T

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.s005

W

Watkins, NA, Gusnanto, A, de Bono, B, De, S, Miranda-Saavedra, D, Hardie, DL, Angenent, WGJ, Attwood, AP, Ellis, PD, Erber, W, Foad, NS, Garner, SF, Isacke, CM, Jolley, J, Koch, K, Macaulay, IC, Morley, SL, Rendon, A, Rice, KM, Taylor, N, Thijssen-Timmer, DC, Tijssen, MR, van der Schoot, CE, Wernisch, L, Winzer, T, Dudbridge, F, Buckley, CD, Langford, CF, Teichmann, S, Göttgens, B and Ouwehand, WH (2009). A HaemAtlas: characterizing gene expression in differentiated human blood cells. [Data Collection]. Blood. https://doi.org/10.1182/blood-2008-06-162958

Wright, M, Smed, MK, Nelson, JL, Olsen, J, Hetland, ML, Jewell, NP, Zoffmann, V and Jawaheer, D (2024). Additional file 3 of Pre-pregnancy gene expression signatures are associated with subsequent improvement/worsening of rheumatoid arthritis during pregnancy. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26622631.v1

X

Xie, J, Chen, P, Zhang, J, Gao, Z, Neves, H, Zhang, S, Wen, Q, Chen, W, Kwok, HF and Lin, Y (2017). The prognostic significance of DAPK1 in bladder cancer. [Data Collection]. PLOS One. https://doi.org/10.1371/journal.pone.0175290.s004