{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T08:29:38Z","timestamp":1768292978267,"version":"3.49.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T00:00:00Z","timestamp":1758844800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100016566","name":"Mohammed VI Polytechnic University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016566","id-type":"DOI","asserted-by":"publisher"}]},{"name":"African Supercomputing Center at UM6P"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic\/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GRUMB is freely available under the MIT License at: https:\/\/github.com\/SuleimanAminu\/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https:\/\/doi.org\/10.5281\/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf548","type":"journal-article","created":{"date-parts":[[2025,9,25]],"date-time":"2025-09-25T12:05:00Z","timestamp":1758801900000},"source":"Crossref","is-referenced-by-count":2,"title":["GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk"],"prefix":"10.1093","volume":"41","author":[{"given":"Suleiman","family":"Aminu","sequence":"first","affiliation":[{"name":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS) , Mohammed VI Polytechnic University (UM6P) , Benguerir, 43150, Morocco"},{"name":"Department of Biochemistry , Ahmadu Bello University , Zaria, Kaduna, 1096,","place":["Nigeria"]}]},{"given":"AbdulAziz","family":"Ascandari","sequence":"additional","affiliation":[{"name":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical 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