John A. Lees

8.8k total citations · 1 hit paper
50 papers, 2.1k citations indexed

About

John A. Lees is a scholar working on Molecular Biology, Epidemiology and Microbiology. According to data from OpenAlex, John A. Lees has authored 50 papers receiving a total of 2.1k indexed citations (citations by other indexed papers that have themselves been cited), including 24 papers in Molecular Biology, 24 papers in Epidemiology and 14 papers in Microbiology. Recurrent topics in John A. Lees's work include Genomics and Phylogenetic Studies (20 papers), Pneumonia and Respiratory Infections (19 papers) and Bacterial Infections and Vaccines (12 papers). John A. Lees is often cited by papers focused on Genomics and Phylogenetic Studies (20 papers), Pneumonia and Respiratory Infections (19 papers) and Bacterial Infections and Vaccines (12 papers). John A. Lees collaborates with scholars based in United Kingdom, United States and Finland. John A. Lees's co-authors include Stephen D. Bentley, Jukka Corander, Gerry Tonkin‐Hill, Simon D. W. Frost, Jeffrey N. Weiser, Julian Parkhill, Rebecca A. Gladstone, Stephanie W. Lo, Nicholas J. Croucher and Neil MacAlasdair and has published in prestigious journals such as Nucleic Acids Research, Journal of Clinical Investigation and Nature Communications.

In The Last Decade

John A. Lees

45 papers receiving 2.0k citations

Hit Papers

align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Producing polished prokaryotic pangenomes with the Panaroo pipeline

2020 576 citations Gerry Tonkin‐Hill, Neil MacAlasdair et al. profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
John A. Lees United Kingdom	18	807	553	449	352	329	50	2.1k
Koji Yahara Japan	25	598 0.7×	321 0.6×	356 0.8×	369 1.0×	236 0.7×	95	2.0k
Vegard Eldholm Norway	26	797 1.0×	1.0k 1.9×	1.1k 2.4×	308 0.9×	218 0.7×	51	2.5k
Khalil Abudahab United Kingdom	9	543 0.7×	267 0.5×	749 1.7×	333 0.9×	274 0.8×	17	1.7k
Jorge E. Vidal United States	32	663 0.8×	983 1.8×	1.1k 2.6×	233 0.7×	456 1.4×	111	2.9k
Elizabeth M. Driebe United States	26	655 0.8×	805 1.5×	710 1.6×	582 1.7×	326 1.0×	41	2.4k
Mikeljon P. Nikolich United States	25	656 0.8×	325 0.6×	265 0.6×	500 1.4×	341 1.0×	72	1.9k
Huaiqi Jing China	24	522 0.6×	321 0.6×	753 1.7×	203 0.6×	469 1.4×	100	2.2k
Stephanie W. Lo United Kingdom	14	438 0.5×	730 1.3×	229 0.5×	274 0.8×	191 0.6×	54	1.5k
Luce Landraud France	18	874 1.1×	362 0.7×	430 1.0×	780 2.2×	644 2.0×	39	2.2k
Haijian Zhou China	24	408 0.5×	537 1.0×	353 0.8×	608 1.7×	638 1.9×	121	1.9k

Countries citing papers authored by John A. Lees

Since Specialization

Citations

This map shows the geographic impact of John A. Lees's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by John A. Lees with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites John A. Lees more than expected).

Fields of papers citing papers by John A. Lees

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by John A. Lees. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by John A. Lees. The network helps show where John A. Lees may publish in the future.

Co-authorship network of co-authors of John A. Lees

This figure shows the co-authorship network connecting the top 25 collaborators of John A. Lees. A scholar is included among the top collaborators of John A. Lees based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with John A. Lees. John A. Lees is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

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20 of 20 papers shown

McHugh, M., Samuel Horsfield, Kerry A. Pettigrew, et al.. (2025). Integrated population clustering and genomic epidemiology with PopPIPE. Microbial Genomics. 11(4).

Derelle, Romain, Kieran Madon, Joel Hellewell, et al.. (2025). Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA). Molecular Biology and Evolution. 42(4). 1 indexed citations

Horsfield, Samuel, et al.. (2025). Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm. Genome Research. 35(4). 1025–1040.

Kumar, Narender, Kate C. Mellor, Paulina A. Hawkins, et al.. (2024). Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae. Microbial Genomics. 10(8). 2 indexed citations

Horsfield, Samuel, Anna K. Pöntinen, Sergio Arredondo-Alonso, et al.. (2024). Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome Research. 34(7). 1081–1088.

Lees, John A., et al.. (2023). Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics Advances. 3(1). vbad027–vbad027. 3 indexed citations

Derelle, Romain, John A. Lees, Jody Phelan, et al.. (2023). fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing. Bioinformatics. 39(11). 3 indexed citations

Kremer, Philip H. C., Bart Ferwerda, Hester J. Bootsma, et al.. (2022). Pneumococcal genetic variability in age-dependent bacterial carriage. eLife. 11. 7 indexed citations

Kwambana-Adams, Brenda, Jia Mun Chan, Andrea Gori, et al.. (2022). Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis. Journal of Clinical Microbiology. 61(1). e0080222–e0080222. 3 indexed citations

10.

Lees, John A., William P. Hanage, Marc Lipsitch, et al.. (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME Journal. 15(5). 1523–1538. 16 indexed citations

11.

Hogan, Alexandra B., Peter Winskill, Oliver J. Watson, et al.. (2021). Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: A mathematical modelling analysis. Vaccine. 39(22). 2995–3006. 72 indexed citations

12.

Lehtinen, Sonja, Claire Chewapreecha, John A. Lees, et al.. (2020). Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae. Science Advances. 6(21). eaaz6137–eaaz6137. 16 indexed citations

13.

Kremer, Philip H. C., John A. Lees, Bart Ferwerda, et al.. (2020). Diversification in immunogenicity genes caused by selective pressures in invasive meningococci. Microbial Genomics. 6(9). 5 indexed citations

14.

Pensar, Johan, Santeri Puranen, Brian J. Arnold, et al.. (2019). Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Research. 47(18). e112–e112. 30 indexed citations

15.

Lees, John A., Simon R. Harris, Gerry Tonkin‐Hill, et al.. (2019). Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research. 29(2). 304–316. 220 indexed citations

16.

Lees, John A., Marco Galardini, Stephen D. Bentley, Jeffrey N. Weiser, & Jukka Corander. (2018). pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics. 34(24). 4310–4312. 172 indexed citations

17.

Puranen, Santeri, Maiju Pesonen, Johan Pensar, et al.. (2018). SuperDCA for genome-wide epistasis analysis. Microbial Genomics. 4(6). 17 indexed citations

18.

Lees, John A., Philip H. C. Kremer, Ana Sousa Manso, et al.. (2016). Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. Microbial Genomics. 3(1). e000103–e000103. 30 indexed citations

19.

David, Sophia, Christophe Rusniok, M. Mentasti, et al.. (2016). Multiple major disease-associated clones ofLegionella pneumophilahave emerged recently and independently. Genome Research. 26(11). 1555–1564. 65 indexed citations

20.

Barrett‐Bee, Keith, John A. Lees, & Walter Henderson. (1982). Variation in the activities of enzymes associated with cell wall metabolism during a growth cycle ofCandida albicans. FEMS Microbiology Letters. 15(4). 275–278. 10 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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