{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T20:14:43Z","timestamp":1782936883167,"version":"3.54.5"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T00:00:00Z","timestamp":1660089600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NVIDIA and Purdue Rosen Center for Advanced Computing"},{"name":"Purdue Department of Biological Sciences"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>As recently demonstrated by the COVID-19 pandemic, large-scale pathogen genomic data are crucial to characterize transmission patterns of human infectious diseases. Yet, current methods to process raw sequence data into analysis-ready variants remain slow to scale, hampering rapid surveillance efforts and epidemiological investigations for disease control. Here, we introduce an accelerated, scalable, reproducible, and cost-effective framework for pathogen genomic variant identification and present an evaluation of its performance and accuracy across benchmark datasets of Plasmodium falciparum malaria genomes. We demonstrate superior performance of the GPU framework relative to standard pipelines with mean execution time and computational costs reduced by 27\u00d7 and 4.6\u00d7, respectively, while delivering 99.9% accuracy at enhanced reproducibility.<\/jats:p>","DOI":"10.1093\/bib\/bbac314","type":"journal-article","created":{"date-parts":[[2022,8,10]],"date-time":"2022-08-10T01:58:12Z","timestamp":1660096692000},"source":"Crossref","is-referenced-by-count":15,"title":["A GPU-accelerated compute framework for pathogen genomic variant identification to aid genomic epidemiology of infectious disease: a malaria case study"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8137-6285","authenticated-orcid":false,"given":"Giovanna","family":"Carpi","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Purdue University , West Lafayette, IN, USA"},{"name":"Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University , West Lafayette, IN, USA"},{"name":"W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1877-009X","authenticated-orcid":false,"given":"Lev","family":"Gorenstein","sequence":"additional","affiliation":[{"name":"Rosen Center for Advanced Computing, Purdue University , West Lafayette IN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy T","family":"Harkins","sequence":"additional","affiliation":[{"name":"NVIDIA , 2788 San Tomas, Santa Clara, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehrzad","family":"Samadi","sequence":"additional","affiliation":[{"name":"NVIDIA , 2788 San Tomas, Santa Clara, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pankaj","family":"Vats","sequence":"additional","affiliation":[{"name":"NVIDIA , 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