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.

7. 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

6. 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

5. 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

4. 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

3. 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

2. 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.

1. 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