Publications where the CRyPTIC Consortium was an author are listed below. If the consortium is the sole author this indicates that this publication is a primary output of the research project.


14. The CRyPTIC Consortium
A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics
PLoS Biology doi:10.1371/journal.pbio.3001721
bioRxiv preprint doi:10.1101/2021.09.14.460274

13. The CRyPTIC Consortium
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
PLoS Biology doi:10.1371/journal.pbio.3001755
bioRxiv preprint doi:10.1101/2021.09.14.460272

12. Fowler PW, Wright C, Spiers H, Zhu T, Baeten EML, Hoosdally SW, Gibertoni Cruz AL, Roohi A, Kouchaki S, Walker TM, Peto TEA, Miller G, Lintott C, Clifton D, Crook DW, Walker AS, The CRyPTIC Consortium
BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates
eLife 11:e75046 doi:10.7554/eLife.75046
bioRxiv preprint doi:10.1101/2021.07.20.453060

11. The CRyPTIC Consortium
Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.
Eur Resp J doi:10.1183/13993003.00239-2022
medRxiv preprint doi:10.1101/2021.02.24.21252386.

10. Walker TM, Miotto P, Köser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey JE, Omar SV, Peto TEA, Suresh A, Uplekar S, Laurent S, Colman
R, Nathanson CM, Zignol M, Walker AS, the CRyPTIC Consortium, the Seq&Treat Consortium,
Crook DW, Ismail N, Rodwell TC
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A new global standard for molecular diagnostics
Lancet Microbe 3:E265


9. Sonnenkalb L, Carter JJ, Spitaleri A, Iqbal Z, Hunt M, Malone K, Utpatel C, Cirrillo DM, Rodrigues C, Nilgiriwala KS, the CRyPTIC Consortium, Fowler PW, Merker M, Niemann S.
Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach
bioRxiv preprint doi:10.1101/2021.02.24.21252386

8. Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues C, Crook DW, the CRyPTIC Consortium, Mistry N, Niemann S
Transmission of pre-XDR and XDR-TB in the Mumbai Metropolitan Region, India
bioRxiv preprint: doi:10.1101/2021.02.02.429364

7. Adams O, Deme JC, Parker JL, the CRyPTIC Consortium, Fowler PW, Lea SM, Newstead S
Cryo-EM Structure and Resistance Landscape of M. tuberculosis MmpL3: An Emergent Therapeutic Target
Structure 29:1


6. Wilson DJ, CRyPTIC Consortium
GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes.
Mol Biol Evol msaa0699
doi: 10.1093/molbev/msaa069


5. Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Shamout F, the CRyPTIC Consortium, Zhu T, Clifton DA
DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis
Bioinformatics 35:3240
doi: 10.1093/bioinformatics/btz067

4. Kouchaki S, Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, CRyPTIC Consortium, Clifton DA
Application of machine learning techniques to tuberculosis drug resistance analysis
Bioinformatics 35:2276
doi: 10.1093/bioinformatics/bty949


3. The CRyPTIC Consortium and the 100,000 Genomes Project
Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing
N Eng J Med 379:1403
doi: 10.1056/NEJMoa1800474

2. Rancoita PMV, Cugnata F, Gibertoni-Cruz AL, Borroni E, Hoosdally SJ, Walker TM, Grazian C, 2018 12 Davies TJ, Peto TEA, Crook DW, Fowler PW, Cirillo DM and the CRyPTIC Consortium
Validating a 14-Drug Microtiter Plate Containing Bedaquiline and Delamanid for Large-Scale Research Susceptibility Testing of Mycobacterium tuberculosis
Antimicrob Agent Chemo 62:e00344
doi: 10.1128/AAC.00344-18

1. Fowler PW, Gibertoni-Cruz AL, Hoosdally S, Jarrett L, Borroni E, Chiacchiaretta M, Rathod P, Lehmann S, Molodtsov N, Grazian C, Walker TM, Robinson E, Hoffmann H, Peto TEA, Cirillo DM, Smith EG, Crook DW
Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis
Microbiology 164:1522
doi: 10.1099/mic.0.000733