Below are a list of manuscripts that are available as a preprint but have not yet been accepted in a peer-reviewed journal. Once accepted they will be moved to the Publications page.

69. Hunt M, Swann J, Constantinides B, Fowler PW, Iqbal Z
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
bioRxiv preprint doi:10.1101/2022.01.21.477194

68. Constantinides B, Webster H, Gentry J, Bastable J, Dunn L, Oakley S, Swann J, Sanderson N, Fowler PW, Peto TEA, Stoesser N, Street T, Crook DW
Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance
medRxiv preprint doi:10.1101/2021.12.28.21268461

67. Brankin AE, Fowler PW
Predicting antibiotic resistance in complex protein targets using alchemical free energy methods
under review at J. Comp. Chem. & chemRxiv preprint doi:10.26434/chemrxiv-2021-shfgp

66. Davies TJ, Swann J, Sheppard AE, Pickford H, Lipworth S, AbuOun M, Ellington M, Fowler PW, Hopkins S, Hopkins KL, Crook DW, Peto TEA, Anjum MF, Walker AS, Stoesser N
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli
bioRxiv preprint doi:10.1101/2021.11.03.467004

65. 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
under review at Genome Biology & bioRxiv preprint doi:10.1101/2021.09.15.460475

64. The CRyPTIC Consortium
Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes
under review at eLife & bioRxiv preprint doi:10.1101/2021.09.14.460272

63. The CRyPTIC Consortium
Quantitative measurement of antibiotic resistance in M. tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach.
under review at Nature Comms & bioRxiv preprint. doi:10.1101/2021.09.14.460353

62. The CRyPTIC Consortium
A generalisable approach to drug susceptibility prediction for M. tuberculosis using machine learning and whole- genome sequencing.
under review at Nature Medicine & bioRxiv preprint. doi: 10.1101/2021.09.14.458035

61. The CRyPTIC Consortium
A data compendium of Mycobacterium tuberculosis antibiotic resistance
under review at eLife & bioRxiv preprint doi:10.1101/2021.09.14.460274

60. 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
under review at eLife & bioRxiv preprint doi:10.1101/2021.07.20.453060

59. The CRyPTIC Consortium
Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis.
under review at Eur Resp J & medRxiv preprint doi:10.1101/2021.02.24.21252386.

58. 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
under review at Nature Microbiology & bioRxiv preprint doi:10.1101/2021.03.19.436148.

57. Carter JJ, Walker TM, Waker AS, Whitfield M, Morlock GP, Peto TEA, Posey JE, Crook DW, Fowler PW.
Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches.
under review at Nature Communications & bioRxiv preprint doi:10.1101/518142