{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T13:47:17Z","timestamp":1785937637488,"version":"3.56.0"},"reference-count":14,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"2","license":[{"start":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T00:00:00Z","timestamp":1785888000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,5]]},"abstract":"<jats:title>ABSTRACT.<\/jats:title>\n                  <jats:p>\n                    Major advances in\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    sequencing approaches, bioinformatic pipelines, and data analysis tools have provided valuable insights into malaria epidemiology from parasite genomic data. However, translating genetic data into actionable information for decision-makers remains a challenge. Significant barriers limit the integration of these advances into a functional data analysis ecosystem that produces standardized, interpretable results for use by national malaria control programs. The\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    Genomic Epidemiology network convened 18 subject matter experts across 15 institutions at the Reproducibility, Accessibility, Documentation, and Interoperability Standards Hackathon in 2023 to identify available analysis tools, evaluate software standards, improve documentation, and outline workflows. Eight use cases for genomic data were identified, and a subset was developed into analysis workflows comprising a series of connected functionalities. Software tools were then mapped against functionalities to outline a modular approach to data analysis for these use cases. In addition to outlining workflows, a set of objective criteria was developed for evaluating software standards. A total of 40\n                    <jats:italic>Plasmodium<\/jats:italic>\n                    genomic analysis tools were identified, 22 of which were prioritized for software standards evaluation. Additional tutorials were developed for 10 tools in the form of reproducible code applied to shared datasets. These resources are available on PGEforge (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/mrc-ide.github.io\/PGEforge\" xlink:type=\"simple\">mrc-ide.github.io\/PGEforge<\/jats:ext-link>\n                    ), a new community resource that serves as a central, open repository for current and future resources for malaria genomic data analysis.\n                  <\/jats:p>","DOI":"10.4269\/ajtmh.25-0418","type":"journal-article","created":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T16:58:27Z","timestamp":1782233907000},"page":"216-228","source":"Crossref","is-referenced-by-count":0,"title":["Toward an Open Analysis Ecosystem for Plasmodium Genomic Epidemiology"],"prefix":"10.4269","volume":"115","author":[{"given":"Shazia","family":"Ruybal-Pes\u00e1ntez","sequence":"first","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom;"},{"name":"Instituto de Microbiolog\u00eda, Universidad San Francisco de Quito, Quito, Ecuador;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Amaya-Romero","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"B\u00e9rub\u00e9","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Florida, Gainesville, Florida, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas F.","family":"Brazeau","sequence":"additional","affiliation":[{"name":"Physician-Scientist Training Program, Duke University Hospital, Durham, North Carolina, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mouhamadou F.","family":"Diop","sequence":"additional","affiliation":[{"name":"The Gambia at London School of Hygiene and Tropical Medicine, Medical Research Council Unit, Fajara, The Gambia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Hathaway","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason A.","family":"Hendry","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Infection Biology, Berlin, Germany;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsty","family":"McCann","sequence":"additional","affiliation":[{"name":"Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Australia;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Murie","sequence":"additional","affiliation":[{"name":"EPPIcenter Program, Division of HIV, ID, and Global Medicine, University of California, San Francisco, California, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxwell","family":"Murphy","sequence":"additional","affiliation":[{"name":"EPPIcenter Program, Division of HIV, ID, and Global Medicine, University of California, San Francisco, California, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karamoko","family":"Niar\u00e9","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody","family":"Phelan","sequence":"additional","affiliation":[{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen F.","family":"Schaffner","sequence":"additional","affiliation":[{"name":"Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, USA;"},{"name":"Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred","family":"Simkin","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aimee R.","family":"Taylor","sequence":"additional","affiliation":[{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9, Paris, France;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Greenhouse","sequence":"additional","affiliation":[{"name":"EPPIcenter Program, Division of HIV, ID, and Global Medicine, University of California, San Francisco, California, USA;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amy","family":"Wesolowski","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Verity","sequence":"additional","affiliation":[{"name":"MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2795","reference":[{"issue":"6906","key":"b1","series-title":"Nature","first-page":"498","article-title":"Genome sequence of the human malaria parasite Plasmodium falciparum.","volume":"419","author":"Gardner","year":"2002"},{"issue":"1","key":"b2","series-title":"Sci Data","first-page":"622","article-title":"Introducing the FAIR Principles for research 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