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

2. Six-year experience of Australia's first dedicated cancer of unknown primary clinic

3. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

4. SARS-CoV-2 evolution during treatment of chronic infection

5. Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae

6. Identifying the Resource Needs of Young People with Differences of Sex Development.

7. Genomic reconstruction of the SARS-CoV-2 epidemic in England

8. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

9. An integrated national scale SARS-CoV-2 genomic surveillance network

10. Genomic reconstruction of the SARS-CoV-2 epidemic in England

11. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

12. Recurrent SARS-CoV-2 mutations in immunodeficient patients

13. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

14. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

15. The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

16. Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

17. Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

18. Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonization using next-generation sequencing data.

19. Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study.

21. Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs.

22. Measuring changes in Plasmodium falciparum census population size in response to sequential malaria control interventions.

23. Detecting co-selection through excess linkage disequilibrium in bacterial genomes.

24. Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange.

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

26. Mutational spectra are associated with bacterial niche.

27. The relationship between commencement of continuous renal replacement therapy and urine output, fluid balance, mean arterial pressure and vasopressor dose.

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

29. Six-year experience of Australia's first dedicated cancer of unknown primary clinic.

30. Mge-cluster: a reference-free approach for typing bacterial plasmids.

31. Challenges in prokaryote pangenomics.

32. Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.

33. Pneumococcal within-host diversity during colonization, transmission and treatment.

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

35. Age-specific patterns of DBLα var diversity can explain why residents of high malaria transmission areas remain susceptible to Plasmodium falciparum blood stage infection throughout life.

36. Identifying the Resource Needs of Young People with Differences of Sex Development.

37. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci.

38. An accurate method for identifying recent recombinants from unaligned sequences.

39. Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae .

40. RCandy: an R package for visualizing homologous recombinations in bacterial genomes.

41. Patterns of within-host genetic diversity in SARS-CoV-2.

42. Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study.

43. Common virulence gene expression in adult first-time infected malaria patients and severe cases.

44. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.

45. Genomic epidemiology of COVID-19 in care homes in the east of England.

46. Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents.

47. A comprehensive and high-quality collection of Escherichia coli genomes and their genes.

48. Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.

49. Producing polished prokaryotic pangenomes with the Panaroo pipeline.

50. Genome-wide epistasis and co-selection study using mutual information.

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