I attempt to keep this reverse-chronological list up-to-date (last updated: 8 August 2023). More recent publications may be on Google Scholar. Articles are nearly all open access; links to preprints are included where they exist. (+) denotes equal contribution (joint-first or joint-last authorship).


Visualizing and quantifying structural diversity around mobile AMR genes
L.P. Shaw and R.A. Neher. biorxvi (2023)
preprint: 10.1101/2023.08.07.551646

Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients
J. Diaz Caballero, R.M. Wheatley, N. Kapel, C. López-Causapé, T. Van der Schalk, A. Quinn, L.P. Shaw, L. Ogunlana, C. Recanatini, B. Britto Xavier, L. Timbermont, J. Kluytmans, A. Ruzin, M. Esser, S. Malhotra-Kumar, A. Oliver, R.C. MacLean. Nature Communications 14:4083 (2023)
doi: 10.1038/s41467-023-39416-2

Diverse Durham collection phages demonstrate complex BREX defence responses
A. Kelly, S. Went, G. Mariano, L.P. Shaw, D. Picton, S. Duffner, I. Coates, R. Herdman-Grant, J. Gordeeva, A. Drobiazko, A. Isaev, Y.-J. Lee, Y. Luyten, R. Morgan, P. Weigele, K. Severinov, N. Wenner, J. Hinton, and T.R. Blower. Applied and Environmental Microbiology (in press)

Restriction-modification systems have shaped the evolution and distribution of plasmids across bacteria
L.P. Shaw, E. P. C. Rocha, R. C. MacLean. Nucleic Acids Research (2023)
doi: 10.1093/nar/gkad452
preprint: 10.1101/2022.12.15.520556

PanGraph: scalable bacterial pan-genome graph construction
N. Noll(+), M. Molari(+), L.P. Shaw, R.A. Neher. Microbial Genomics (2023) doi: 10.1099/mgen.0.001034
preprint: 10.1101/2022.02.24.481757

Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK
W. Matlock(+), S. Lipworth(+), …, L.P. Shaw(+), N. Stoesser(+). eLife 85302 (2023)
doi: 10.7554/eLife.85302
preprint: 10.1101/2022.05.06.490774

The evolution of colistin resistance increases bacterial resistance to host antimicrobial peptides and virulence
P.K. Jangir, L. Ogunlana, P. Szili, M. Czikkely, L.P. Shaw, E.J. Stevens, Y. Yang, Q. Yang, Y. Wang, C. Pál, T. R. Walsh, R.C. MacLean, eLife (2023)
doi: 10.7554/eLife.84395

A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone
R.P, Smith, H.E. May, M. AbuOun, E. Stubberfield, D. Gilson, K.K. Chau, D.W. Crook, L.P. Shaw, D.S. Read, N. Stoesser, M. Jose Vilar, M.F. Anjum Frontiers in Microbiology (2023)
doi: 10.3389/fmicb.2023.1070340


Gut to lung translocation and antibiotic mediated selection shape the dynamics of Pseudomonas aeruginosa in an ICU patient
R. M. Wheatley, J. D. Caballero, T. E. van der Schalk, F.H.R. De Winter, L. P Shaw, N. Kapel, C. Recanatini, L. Timbermont, J. Kluytmans, M. Esser, A. Lacoma, C. Prat-Aymerich, A. Oliver, S. Kumar-Singh, S. Malhotra-Kumar, R. C. MacLean. Nature Communications (2022)
doi: 10.1038/s41467-022-34101-2

Regulatory fine-tuning and horizontal gene transfer stabilize mobile colistin resistance
L. Ogunlana, L.P. Shaw, D. Kuar, P. Jangir, T. Walsh, S. Uphoff, C. MacLean. biorxiv (2022)
preprint: 10.1101/2022.11.04.515217

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study
S. Lipworth(+), W. Matlock(+), L.P. Shaw, et al. medrxiv (2022)
preprint: 10.1101/2022.04.03.22273290

Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition
P. K. Jangir(+), Q. Yang(+), L.P. Shaw et al. eLife (2022)
doi: 10.7554/eLife.78834
preprint: 10.1101/2022.02.20.481192

Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM
M. Acman, R. Wang, L. van Dorp, L.P. Shaw, Q. Wang, N. Luhmann, Y. Yin, S. Sun, H. Chen, H. Wang, F. Balloux Nature Communications (2022)
doi: 10.1038/s41467-022-28819-2
preprint: 10.1101/2021.01.14.426698

Hospital outbreak of carbapenem-resistant Enterobacterales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399
A. Ledda, M. Cummins, L.P. Shaw, E. Jauneikaite, K. Cole, F. Lasalle, D. Barry, C. Rosmarin, S. Anaraki, D. Wareham, N. Stoesser, J. Paul, R. Manuel, B. Cherian, X. Didelot Microbial Genomics (2022)
doi: 10.1099/mgen.0.000675 preprint: 10.1101/2020.06.15.148189


A genomic epidemiological study shows prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage
M. AbuOun, H. Jones, E. Stubberfield, D. Gilson, L.P. Shaw, A. Hubbard, K. Chau, R. Sebra, T. Peto, D. Crook, D. Read, H. S. Gweon, A. S. Walker, N. Stoesser, R. P. Smith, M. Anjum Microbial Genomics (2021)
doi: 10.1099/mgen.0.000630
accepted version: here

Flanker: a tool for comparative genomics of gene flanking regions
W. Matlock(+), S. Lipworth(+), B. Constantinides, T. E. A. Peto, A. S. Walker, D. Crook, S. Hopkins, L.P. Shaw(+), N. Stoesser(+) Microbial Genomics (2021)
doi: 10.1099/mgen.0.000634
preprint: 10.1101/2021.02.22.432255

A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2
D. Richard, L. P Shaw, R. Lanfear, M. Acman, C. Owen, C. C. S. Tan, L. van Dorp, F. Balloux biorxiv (2021)
preprint: 10.1101/2021.05.06.442903

Drivers of methicillin resistant Staphylococcus aureus (MRSA) lineage replacement in China
H. Chen(+), Y. Yin(+), L. van Dorp, L.P. Shaw, H. Gao, M. Acman, J. Yuan F. Chen, S. Sun, X. Wang, S. Li, Y. Zhang, R. A. Farrer, H. Wang, F. Balloux Genome Medicine (2021) doi: 10.1186/s13073-021-00992-x

Letter: Null models for gene enrichment in plasmids
L.P. Shaw PNAS (2021)
doi: 10.1073/pnas.2103665118

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
L.P. Shaw et al. on behalf of the REHAB consortium Science Advances (2021)
doi: 10.1126/sciadv.abe3868
preprint: 10.1101/2020.07.23.215756

Genomic network analysis of an environmental and livestock IncF plasmid population
W. Matlock, …, A. S. Walker(+), N. Stoesser(+), L.P. Shaw(+) on behalf of the REHAB consortium The ISME Journal
doi: 10.1038/s41396-021-00926-w
preprint: 10.1101/2020.07.24.215889

Electronic application to improve management of infections in low-income neonatal units: pilot implementation of the NeoTree beta app in a public sector hospital in Zimbabwe
H. Gannon, … [12 authors inc. L.P. Shaw], F. C. Fitzgerald BMJ Open Quality (2021)
doi: 10.1136/bmjoq-2020-001043


No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
L. van Dorp(+), D. Richard(+), C. CS. Tan, L.P. Shaw, M. Acman, F. Balloux Nature Communications
doi: 10.1038/s41467-020-19818-2
preprint: 10.1101/2020.05.21.108506v5

STROBE-Metagenomics: A STROBE/STROME-ID extension statement to guide the reporting of studies applying metagenomics
T. Bharucha, C. Oeser, [alphabetical: 23 authors inc. L.P. Shaw], J. Breuer, N. Field Lancet Infectious Diseases 20:e251–60
doi: 10.1016/S1473-3099(20)30199-7

The phylogenetic range of bacterial and viral pathogens of vertebrates
L.P. Shaw(+), A. Wang(+), et al. Molecular Ecology 29:3361–3379
doi: 10.1111/mec.15463
preprint: 10.1101/670315v3

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
L. van Dorp, M. Acman(+), D. Richard(+), L.P. Shaw(+), C. E. Ford, L. Ormond, C. J. Owen, J. Pang, C. CS. Tan, F. AT. Boshier, A. Torres Ortiz, F. Balloux Infection, Genetics and Evolution 104351
doi: 10.1016/j.meegid.2020.104351

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study
R. M. Doyle, D. M. O’Sullivan, [alphabetical: 16 authors inc. L.P. Shaw] et al. Microbial Genomics 6(2)
doi: 10.1099/mgen.0.000335
preprint: 10.1101/793885v2

Genomic diversity affects the accuracy of bacterial SNP calling pipelines
S. J. Bush, D. Foster, D. W. Eyre, E. L. Clark, N. De Maio, L.P. Shaw et al. GigaScience 9(2):giaa007
doi: 10.1093/gigascience/giaa007
preprint: 10.1101/653774v1


The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
H. G. Soon, L.P. Shaw et al. on behalf of the REHAB consortium. Environmental Microbiome 14:7
doi: 10.1186/s40793-019-0347-1
preprint: 10.1101/593301v1

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
N. De Maio(+), L.P. Shaw(+) et al. on behalf of the REHAB consortium. Microbial Genomics 5(9)
doi: 10.1099/mgen.0.000294
preprint: 10.1101/530824v2

Representing antibiotic relationships using measurements of efficacy against clinical isolates [version 3; peer review: 2 approved]
L.P. Shaw. Wellcome Open Research 4:86
doi: 10.12688/wellcomeopenres.15304.3

Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
C. Nimmo, L.P. Shaw, et al. BMC Genomics 20:389
doi: 10.1186/s12864-019-5782-2
preprint: 10.1101/446849v3

Modelling microbiome recovery after antibiotics using a stability landscape framework
L.P. Shaw, H. Bassam, C. P. Barnes, N. Klein, A. Sarah Walker, F. Balloux. The ISME Journal 13:1845
doi: 10.1038/s41396-019-0392-1
preprint: 10.1101/222398v3

Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles
L.P. Shaw, R. Doyle, E. Kavaliunaite, H. Spencer, F. Balloux, G. Dixon, K. Harris. Clinical Infectious Diseases 69(10):1678
doi: 10.1093/cid/ciz069
preprint: 10.1101/436261v1

Review: The microbiome — the explanation for (almost) everything?
L.P. Shaw and N. Klein. The Pediatric Infectious Disease Journal 38(4):e69
doi: 10.1097/INF.0000000000002261


Microbial translocation does not drive immune activation in Ugandan children with HIV
F. C. Fitzgerald, E. L’homme, K. Harris, J. Kenny, R. Doyle, C. Kityo, L.P. Shaw et al. Journal of Infectious Diseases 219(1):89
doi: 10.1093/infdis/jiy495

Review: From theory to practice: translating whole-genome sequencing (WGS) into the clinic
F. Balloux(+), O. B. Brynildsrud(+), L. van Dorp(+), L.P. Shaw et al. Trends in Microbiology 26(12):P1035
doi: 10.1016/j.tim.2018.08.004

The global distribution and spread of the mobilized colistin resistance gene mcr-1
R. Wang(+), L. van Dorp(+), L.P. Shaw(+) et al. Nature Communications 9:1179
doi: 10.1038/s41467-018-03205-z
preprint: 10.1101/220921

Periapical infection may affect birth outcomes via systemic inflammation
U. Harjunmaa, R. Doyle, J. Jornstedt, S. Kamiz, J.M. Jorgensen, C.P. Stewart, L.P. Shaw, et al. Oral Diseases 24(5):847
doi: 10.1111/odi.12817

Deep sequencing of oral microbiomes from hunter-gatherers and traditional agriculturalists reveals shifts in commensal taxon balance and pathogen load linked to subsistence strategy
F. Lassalle(+), M. Spagnoletti(+), M. Fumagalli, L.P. Shaw, et al. Molecular Ecology 27(1):182
doi: 10.1111/mec.14435


The human salivary microbiome is shaped by shared environment rather than genetics: evidence from a large family of closely related individuals
L.P. Shaw(+), A. Ribeiro(+), A. Levine, N. Pontikos, F. Balloux, A. Segal, A. Roberts, A. Smith. mBio 8:e01237
doi: 10.1128/mBio.01237-17

Review: The oral microbiome
L.P. Shaw, A. Smith, A. Roberts. Emerging Topics in Life Sciences 1(4):287
doi: 10.1042/ETLS20170040

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast
D. Jeffares, C. Jolly, M. Hoti, D. Speed, C. Rallis, L.P. Shaw, F. Balloux, C. Dessimoz, J. Bahler, F. Sedlazeck. Nature Communications 8:14061
doi: 10.1038/ncomms14061
preprint: 10.1101/047266


Distinguishing the signals of gingivitis and periodontitis in supragingival plaque: a cross-sectional cohort study in Malawi
L.P. Shaw, U. Harjunmaa, R. Doyle et al. Applied and Environmental Microbiology 82:6057
doi: 10.1128/AEM.01756-16

Opinion: Claims made in scientific press releases need greater accountability
L.P. Shaw. BMJ 2016;353:i2728
doi: 10.1136/sbmj.i2728


DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization
J. Schreck, T. Ouldridge, F. Romano, P. Sulc, L.P. Shaw, A. Louis, J. Doye. Nucleic Acids Research 43(13):6181
doi: 10.1093/nar/gkv582

Other research

I have also published a few papers that fall broadly within the history and philosophy of science.

The logic of planetary combination in Vettius Valens
C. Hall, L.P. Shaw. ISAW Papers (2023) url: here preprint: pdf

The flying bomb and the actuary
L.P. Shaw, L. F. Shaw. Significance 16(5):12-17 (2019)
doi: 10.1111/j.1740-9713.2019.01315.x

Portable sequencing and the scales of genomic data in global EID surveillance
L.P. Shaw(+) and N. Sugden(+). Geo 5(2):e00066 (2018)
doi: 10.1002/geo2.66