Genomic Epidemiology Papers

Comprehensive database of pathogen genomic epidemiology research from PubMed, automatically updated daily

10,733 papers from PubMed

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10,733
Papers
18
Years Covered
0
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Publications Over Time

Annual counts use the selected publication year. 2026 is a partial year.

Methods: PubMed Search Query

Search Strategy:

Papers were retrieved from PubMed using the following query, which requires papers to have (1) genomic methods AND (2) pathogens AND (3) epidemiological context:

("Whole Genome Sequencing"[MeSH] OR "Genomics"[MeSH] OR "Bacterial Typing Techniques"[MeSH] OR "Molecular Typing"[MeSH])
AND
("Bacteria"[MeSH] OR "Viruses"[MeSH] OR "Fungi"[MeSH] OR "Parasites"[MeSH] OR "Communicable Diseases"[MeSH] OR "Bacterial Infections"[MeSH] OR "Virus Diseases"[MeSH] OR "Genome, Bacterial"[MeSH] OR "Genome, Viral"[MeSH] OR "Genome, Fungal"[MeSH])
AND
("Epidemiology"[MeSH] OR "Disease Outbreaks"[MeSH] OR "Public Health Surveillance"[MeSH] OR "Contact Tracing"[MeSH] OR "Disease Transmission, Infectious"[MeSH] OR "Infection Control"[MeSH] OR "Cross Infection"[MeSH])
NOT
("Genome-Wide Association Study"[MeSH] OR "Polymorphism, Single Nucleotide"[MeSH] OR "Genetic Predisposition to Disease"[MeSH] OR "Pharmacogenetics"[MeSH] OR "Neoplasms"[MeSH])

Date Range:

Search coverage starts in 2010 (updated daily). Earlier online publication years can appear for papers assigned to later issues.

Publication dates:

When two sources agree on the same year and month, that date is used without review. Both online and issue dates are compared, with each source counted once per month; OpenAlex contributes its reported publication date. If several dates are corroborated, online dates take priority, followed by dates with a known month, then the earliest date. Verified manual corrections take precedence. Without agreement, the earliest valid date across the three sources is used automatically. Differences in day are ignored. Within the earliest year, the earliest known month is used; if no month is known, only the year is shown. Each paper is counted once, using the same year as its listing and year filter. Future issue years are included when present; the current year is incomplete.

Exclusions:

Human genome-wide association studies (GWAS), single nucleotide polymorphism studies, genetic predisposition studies, pharmacogenetics, and cancer genomics are excluded to focus specifically on pathogen genomic epidemiology.

To Reproduce:

Visit PubMed and paste the query above into the search box. Add date filter: AND 2010:3000[PDAT]

Note: Papers are fetched automatically via PubMed E-utilities API and cached daily. Total retrieved: 10,733 papers.

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