Research map: High-precision binary trait association on phylogenetic trees

Back to the article

Papers in this map

  1. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing · Yoav Benjamini · 1995 · 112507 citations · Cited by this paper
  2. Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing · 2026 · Related
  3. Prokka: rapid prokaryotic genome annotation · Torsten Seemann · 2014 · 20457 citations · Cited by this paper
  4. Evolving strategies for virus discovery · 2026 · Related
  5. Evolutionary trees from DNA sequences: A maximum likelihood approach · Joseph Felsenstein · 1981 · 14970 citations · Cited by this paper
  6. Integrated poultry production as a reservoir of tet(X4) and mcr-1.1 encoding Escherichia coli in Pakistan · 2026 · Related
  7. The control of the false discovery rate in multiple testing under dependency · Yoav Benjamini · 2001 · 10974 citations · Cited by this paper
  8. Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium · 2026 · Related
  9. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters · 1994 · 1981 citations · Cited by this paper
  10. Genomic analysis of intrahospital transmission of carbapenem-resistant Gram-negative bacteria: a multicentre study in Japan · 2026 · Related
  11. Genome-wide association studies · Emil Uffelmann · 2021 · 1878 citations · Cited by this paper
  12. Downregulation is the dominant effect of new regulatory mutations in a fungal pathogen · 2026 · Related
  13. clinker & clustermap.js: automatic generation of gene cluster comparison figures · Cameron L. M. Gilchrist · 2021 · 1755 citations · Cited by this paper
  14. Reproducible profiling of the gut microbiota using surplus clinical faecal immunochemical test samples · 2026 · Related
  15. Producing polished prokaryotic pangenomes with the Panaroo pipeline · Gerry Q. Tonkin‐Hill · 2020 · 1440 citations · Cited by this paper
  16. Phylogenetically diverse Mucorales–Mycetohabitans endosymbiotic interactions identified from whole-genome sequencing using a targeted metagenomic assembly pipeline · 2026 · Related
  17. FaST linear mixed models for genome-wide association studies · Christoph Lippert · 2011 · 1403 citations · Cited by this paper
  18. A standardized core genome multilocus sequence typing and life identification number barcoding framework for global Pasteurella multocida surveillance and outbreak investigation · 2026 · Related
  19. Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary · Ola Brønstad Brynildsrud · 2016 · 789 citations · Cited by this paper
  20. Efficient ancestry and mutation simulation with msprime 1.0 · Franz Baumdicker · 2021 · 544 citations · Cited by this paper
  21. panX: pan-genome analysis and exploration · Wei Ding · 2017 · 342 citations · Cited by this paper
  22. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance · Abigail L. Manson · 2017 · 304 citations · Cited by this paper
  23. A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination · Caitlin Collins · 2018 · 293 citations · Cited by this paper
  24. A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios · Sohta A. Ishikawa · 2019 · 287 citations · Cited by this paper
  25. Variance of the Number of False Discoveries · Art B. Owen · 2005 · 152 citations · Cited by this paper
  26. Bacterial defense systems exhibit synergistic anti-phage activity · Yi Hsuan Wu · 2024 · 140 citations · Cited by this paper
  27. Epistasis and evolution: recent advances and an outlook for prediction · Milo S. Johnson · 2023 · 125 citations · Cited by this paper
  28. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls · James Emmanuel San · 2020 · 97 citations · Cited by this paper
  29. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants · Danielle J. Ingle · 2016 · 83 citations · Cited by this paper
  30. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes · Morteza Mahmoudi Saber · 2020 · 82 citations · Cited by this paper
  31. Coinfinder: detecting significant associations and dissociations in pangenomes · Fiona Jane Whelan · 2020 · 81 citations · Cited by this paper
  32. Interactions and evolutionary relationships among bacterial mobile genetic elements · Andrew S. I. D. Lang · 2025 · 78 citations · Cited by this paper
  33. Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population · Frédéric Auvray · 2021 · 57 citations · Cited by this paper
  34. Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes · Thomas Röder · 2024 · 40 citations · Cited by this paper
  35. Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility · Rebecca J Hall · 2021 · 39 citations · Cited by this paper
  36. Fast and flexible bacterial genomic epidemiology with PopPUNK · John A. Lees · 2018 · 27 citations · Cited by this paper
  37. Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning · The CRyPTIC consortium · 2024 · 12 citations · Cited by this paper
  38. Beware of counter-intuitive levels of false discoveries in datasets with strong intra-correlations · Chakravarthi Kanduri · 2025 · 11 citations · Cited by this paper
  39. Evo‐Scope : Fully automated assessment of correlated evolution on phylogenetic trees · Maxime Godfroid · 2023 · 8 citations · Cited by this paper

Source: OpenAlex (CC0)