update

use_case_examples/use-case-examples.md

@@ -19,6 +19,8 @@ Here, we explore how we can use YACHT for contaminant detection with the followi
 * Cross Contamination Detection 
 * Contamination in Low-biomass Datasets 
 
+Lou YC, Hoff J, Olm MR, West-Roberts J, Diamond S, Firek BA, Morowitz MJ, Banfield JF. Using strain-resolved analysis to identify contamination in metagenomics data. Microbiome. 2023 Mar 2;11(1):36. doi: 10.1186/s40168-023-01477-2. PMID: 36864482; PMCID: PMC9979413.
+
 ### Contaminant Detection Examples
 
 #### External Contamination Detection
@@ -49,5 +51,9 @@ Methods for pathogen detection include PCR, multiplex PCR, broad-range PCR, anti
 
 Using clinical metagenomic data, we can detect any pathogenic infection (i.e. respiratory, bloodstream, central nervous system infections) without prior knowledge from millions of reads produced by shot gun metagenomic sequencing. 
 
+Gu W, Deng X, Lee M, Sucu YD, Arevalo S, Stryke D, Federman S, Gopez A, Reyes K, Zorn K, Sample H, Yu G, Ishpuniani G, Briggs B, Chow ED, Berger A, Wilson MR, Wang C, Hsu E, Miller S, DeRisi JL, Chiu CY. Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids. Nat Med. 2021 Jan;27(1):115-124. doi: 10.1038/s41591-020-1105-z. Epub 2020 Nov 9. PMID: 33169017; PMCID: PMC9020267.
+
+Batool M, Galloway-Peña J. Clinical metagenomics-challenges and future prospects. Front Microbiol. 2023 Jun 28;14:1186424. doi: 10.3389/fmicb.2023.1186424. PMID: 37448579; PMCID: PMC10337830.
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 ### Pathogenic Detection Examples