To date CRyPTIC has published
- five primary publications (consortium is sole author)
- twelve secondary publications (consortium is listed as a co-author)
2024
The CRyPTIC Consortium
Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning
PLoS Comp Biol doi: 10.1371/journal.pcbi.1012260
bioRxiv preprint. doi: 10.1101/2021.09.14.458035
The CRyPTIC Consortium
Quantitative measurement of antibiotic resistance in M. tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach.
Nature Comms 15:488 doi:10.1038/s41467-023-44325-5
bioRxiv preprint doi:10.1101/2021.09.14.460353
2023
The CRyPTIC Consortium
Reply: “Epidemiological cut-off values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.”
Eur Resp J 61:2300426 doi:10.1183/13993003.00426-2023
Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues K, Crook DW, The CRyPTIC Consortium, Rasigade JP, Wirth T, Mistry N, Niemann S
High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region
Genome Med 22:14 doi:10.1186/s13073-022-01076-0
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
Lancet Microbe 54:e358 doi:10.1016/S2666-5247(23)00002-2
bioRxiv preprint doi:10.1101/2021.03.19.436148.
2022
Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz M, Ramakrishnan S, The CRyPTIC Consortium, Iqbal Z
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Genome Biology 23:147
doi:10.1186/s13059-022-02714-x
bioRxiv preprint: doi:10.1101/2021.09.15.460475
The CRyPTIC Consortium
A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics
PLoS Biology 20(8):e3001721 doi:10.1371/journal.pbio.3001721
bioRxiv preprint doi:10.1101/2021.09.14.460274
The CRyPTIC Consortium
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
PLoS Biology 20(8):e3001755 doi:10.1371/journal.pbio.3001755
bioRxiv preprint doi:10.1101/2021.09.14.460272
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
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 60:2200239 doi:10.1183/13993003.00239-2022
medRxiv preprint doi:10.1101/2021.02.24.21252386.
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
doi:10.1016/S2666-5247(21)00301-3
Yang Y, Walker TM, Kouchaki S, Wang C, Peto TEA, Crook DW, CRYPTIC Consortium, Clifton DA
An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction
Briefings in Bioinformatics 22:bbab299
doi: 10.1093/bib/bbab299
2021
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 29:1182
doi:10.1016/j.str.2021.06.013
2020
Kouchaki S,Yang Y, Lachapelle A, Walker TM, Walker AS, CRyPTIC Consortium, Peto TEA, Crook DW, Clifton DA
Multi-label random forest model for tuberculosis drug resistance classification and mutation ranking.
Frontiers in Microbiology 11:667
doi: 10.3389/fmicb.2020.00667
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 and biorXiv preprint doi: 10.1101/523316
2019
Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Shamout F, CRyPTIC Consortium, Zhu T, Clifton DA
DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis
Bioinformatics 35:3240
doi: 10.1093/bioinformatics/btz067
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
2018
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
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 and biorXiv preprint doi: 10.1101/244731