John A. Lees - Publications, H-index & Citations

John A. Lees

european bioinformatics institute

40H指数

207论文数

8.8K被引数

收录论文 60

发表时间

Kamino: fast proteome-wide variant calling for amino acid phylogenomics Kamino：用于氨基酸系统发育基因组学的快速全蛋白质组变异检测

Molecular Biology and Evolution

IF5.3

2026-09-28

OAAI

Romain Derelle; John A Lees; Leonid Chindelevitch; null

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions 泛基因组选择的可重用模型为疫苗引入期间的优化监测策略提供信息

Genome Medicine

IF11.2

2026-09-07

OAAI

Leonie J. Lorenz; Joel Hellewell; Samuel T. Horsfield; Matthew J. Russell; Shrijana Shrestha; Andrew J. Pollard; Stephen D. Bentley; Stephanie W. Lo; Caroline Colijn; Nicholas J. Croucher; John A. Lees

A comprehensive AMR genotype–phenotype database (CABBAGE)全面的AMR基因型-表型数据库（CABBAGE）

Nucleic Acids Research

IF13.1

2026-08-24

OAAI

Emily Dickens; Romain Derelle; Robert Beardmore; Anita Suresh; Swapna Uplekar; Andrey G Azov; Tatiana A Gurbich; Bilal El Houdaigui; Jon Keatley; Sofiia Ochkalova; Orges Koci; Nadim M Rahman; Anu Shivalikanjli; Andrea Winterbottom; Galabina Yordanova; Helen Parkinson; Andrew D Yates; Robert D Finn; John A Lees; Leonid Chindelevitch; null

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences SBMLtoOdin 和 Menelmacar：面向专家和非专家受众的系统生物学模型交互式可视化

BIOINFORMATICS

IF5.4

2025-09-01

OAAI

Lorenz, Leonie J.; Andreoletti, Antoine; Nguyen, Tung V. N.; Hermjakob, Henning; FitzJohn, Richard G.; Malik Sheriff, Rahuman S.; Lees, John A.

Colonization dynamics of Streptococcus pneumoniae are determined by polymorphisms in the BlpAB transporter 肺炎链球菌（Streptococcus pneumoniae）的定植动力学由BlpAB转运蛋白中的多态性决定。

INFECTION AND IMMUNITY

IF2.8

2025-06-10

OAAI

Aggarwal, Surya D.; Toussaint, Jacqueline; Lees, John A.; Weiser, Jeffrey N.

Integrated population clustering and genomic epidemiology with PopPIPE 集成人群聚类与基因组流行病学分析工具PopPIPE

MICROBIAL GENOMICS

IF4

2025-04-28

OAAI

McHugh, Martin P.; Horsfield, Samuel T.; von Wachsmann, Johanna; Toussaint, Jacqueline; Pettigrew, Kerry A.; Czarniak, Elzbieta; Evans, Thomas J.; Leanord, Alistair; Tysall, Luke; Gillespie, Stephen H.; Templeton, Kate E.; Holden, Matthew T. G.; Croucher, Nicholas J.; Lees, John A.

Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

GENOME RESEARCH

IF5.5

2024-10-15

OAAI

Derelle, Romain; von Wachsmann, Johanna; Maklin, Tommi; Hellewell, Joel; Russell, Timothy; Lalvani, Ajit; Chindelevitch, Leonid; Croucher, Nicholas J.; Harris, Simon R.; Lees, John A.

Comparison of gene- by- gene and genome- wide short nucleotide sequence- based approaches to define the global population structure of Streptococcus pneumoniae

MICROBIAL GENOMICS

IF4

2024-08-28

OAAI

King, Alannah C.; Kumar, Narender; Mellor, Kate C.; Hawkins, Paulina A.; Mcgee, Lesley; Croucher, Nicholas J.; Bentley, Stephen D.; Lees, John A.; Lo, Stephanie W.

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

GENOME RESEARCH

IF5.5

2024-08-12

OAAI

Kuronen, Juri; Horsfield, Samuel T.; Pontinen, Anna K.; Mallawaarachchi, Sudaraka; Arredondo-Alonso, Sergio; Thorpe, Harry; Gladstone, Rebecca A.; Willems, Rob J. L.; Bentley, Stephen D.; Croucher, Nicholas J.; Pensar, Johan; Lees, John A.; Tonkin-Hill, Gerry; Corander, Jukka

Recent approaches in computational modelling for controlling pathogen threats

LIFE SCIENCE ALLIANCE

IF2.9

2024-06-21

OAAI

Lees, John A.; Russell, Timothy W.; Shaw, Liam P.; Hellewell, Joel

Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae

MICROBIAL GENOMICS

IF4

2024-03-26

OAAI

Biffignandi, Gherard Batisti; Chindelevitch, Leonid; Corbella, Marta; Feil, Edward J.; Sassera, Davide; Lees, John A.

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

NATURE COMMUNICATIONS

IF15.7

2024-03-13

OAAI

Xie, Ouli; Morris, Jacqueline M.; Hayes, Andrew J.; Towers, Rebecca J.; Jespersen, Magnus G.; Lees, John A.; Ben Zakour, Nouri L.; Berking, Olga; Baines, Sarah L.; Carter, Glen P.; Tonkin-Hill, Gerry; Schrieber, Layla; McIntyre, Liam; Lacey, Jake A.; James, Taylah B.; Sriprakash, Kadaba S.; Beatson, Scott A.; Hasegawa, Tadao; Giffard, Phil; Steer, Andrew C.; Batzloff, Michael R.; Beall, Bernard W.; Pinho, Marcos D.; Ramirez, Mario; Bessen, Debra E.; Dougan, Gordon; Bentley, Stephen D.; Walker, Mark J.; Currie, Bart J.; Tong, Steven Y. C.; McMillan, David J.; Davies, Mark R.

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications

MICROBIAL GENOMICS

IF4

2023-12-12

OAAI

Timme, Ruth E.; Karsch-Mizrachi, Ilene; Waheed, Zahra; Arita, Masanori; Maccannell, Duncan; Maguire, Finlay; Petit III, Robert; Page, Andrew J.; Mendes, Catarina Ines; Nasar, Muhammad Ibtisam; Oluniyi, Paul; Tyler, Andrea D.; Raphenya, Amogelang R.; Guthrie, Jennifer L.; Olawoye, Idowu; Rinck, Gabriele; O'Cathail, Colman; Lees, John; Cochrane, Guy; Cummins, Carla; Brister, J. Rodney; Klimke, William; Feldgarden, Michael; Griffiths, Emma

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia

NATURE COMMUNICATIONS

IF15.7

2023-11-13

OAAI

Chapman, Lloyd A. C.; Aubry, Maite; Maset, Noemie; Russell, Timothy W.; Knock, Edward S.; Lees, John A.; Mallet, Henri-Pierre; Cao-Lormeau, Van-Mai; Kucharski, Adam J.

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

GENOME RESEARCH

IF5.5

2023-08-24

OAAI

Horsfield, Samuel T.; Tonkin-Hill, Gerry; Croucher, Nicholas J.; Lees, John A.

Dissemination of carbapenemase- producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study

MICROBIAL GENOMICS

IF4

2023-03-14

OAAI

Hadjirin, Nazreen F.; van Tonder, Andries J.; Blane, Beth; Lees, John A.; Kumar, Narender; Delappe, Niall; Brennan, Wendy; McGrath, Elaine; Parkhill, Julian; Cormican, Martin; Peacock, Sharon J.; Ludden, Catherine

Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis 用于表征链球菌种群多样性的新型多位点序列分型和全局序列聚类方案

JOURNAL OF CLINICAL MICROBIOLOGY

IF5.4

2023-01-26

OAAI

Kalizang'oma, Akuzike; Kwambana-Adams, Brenda; Chan, Jia Mun; Viswanath, Aishwarya; Gori, Andrea; Richard, Damien; Jolley, Keith A.; Lees, John; Goldblatt, David; Beleza, Sandra; Bentley, Stephen D.; Heyderman, Robert S.; Chaguza, Chrispin

Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

IF4.7

2022-08-22

OAAI

Lees, John A.; Tonkin-Hill, Gerry; Yang, Zhirong; Corander, Jukka

Pneumococcal genetic variability in age-dependent bacterial carriage

ELIFE

IF0

2022-07-26

OAAI

Kremer, Philip H. C.; Ferwerda, Bart; Bootsma, Hester J.; Rots, Nienke Y.; Wijmenga-Monsuur, Alienke J.; Sanders, Elisabeth A. M.; Trzcinski, Krzysztof; Wyllie, Anne L.; Turner, Paul; van der Ende, Arie; Brouwer, Matthijs C.; Bentley, Stephen D.; van de Beek, Diederik; Lees, John A.

Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae 通过肺炎链球菌中的移动遗传元件靶向控制肺炎球菌溶血素的产生

MICROBIAL GENOMICS

IF4

2022-04-26

OAAI

Stevens, Emily J.; Morse, Daniel J.; Bonini, Dora; Duggan, Seana; Brignoli, Tarcisio; Recker, Mario; Lees, John A.; Croucher, Nicholas J.; Bentley, Stephen; Wilson, Daniel J.; Earle, Sarah G.; Dixon, Robert; Nobbs, Angela; Jenkinson, Howard; van Opijnen, Tim; Thibault, Derek; Wilkinson, Oliver J.; Dillingham, Mark S.; Carlile, Simon; McLoughlin, Rachel M.; Massey, Ruth C.

研究方向