Microbial RNA Analysis

✅ : recommended readings

0. Virome

2024 Genome Biology - VirRep: a hybrid language representation learning framework for identifying viruses from human gut metagenomes
✅ 2024 Cell - Using artificial intelligence to document the hidden RNA virosphere
✅ 2023 Cell - Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs

✅ 2025 Nature Biotechnology - Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes

✅ 2025 Nature Genetics - Blood DNA virome associates with autoimmune diseases and COVID-19
2025 Nature Biotechnology - Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
2022 eLife - Cancer type classification using plasma cell-free RNAs derived from human and microbes
2020 Nature - Microbiome analyses of blood and tissues suggest cancer diagnostic approach
2020 Microbiome - Separating the signal from the noise in metagenomic cell-free DNA sequencing
2019 PNAS - A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection

2024 Cell Host and Microbe - The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization
2024 Science - Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage
2023 Science - Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering
✅ 2021 Genome Biology - Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes
2019 Cell - Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes
2017 Science - Protein structure determination using metagenome sequence data
2019 Molecular Systems Biology - Unraveling the hidden universe of small proteins in bacterial genomes
2009 Nature - Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column.

✅ 2024 Cell - A pan-cancer analysis of the microbiome in metastatic cancer
[Review] 2022 Science - Engineering bacteria as interactive cancer therapies
2022 Nature - Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer
✅ 2022 Cell - Pan-cancer analyses reveal cancer-type-speciﬁc fungal ecologies and bacteriome interactions
2022 Cell - A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors
[Review] 2021 Cancer Cell - Microbiome and cancer
[Review] 2021 Science - The microbiome and human cancer
2020 Science - The human tumor microbiome is composed of tumor type–specific intracellular bacteria
2020 Cell - A Viral Exposure Signature Defines Early Onset of Hepatocellular Carcinoma

✅ 2022 Nature Microbe - Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration
2020 EMBO J. - Mouse circulating extracellular vesicles contain virus-derived siRNAs active in antiviral immunity
2018 Cell Host & Microbe - Plant-Derived Exosomal MicroRNAs Shape the Gut Microbiota.
2016 Cell Host & Microbe - The Host Shapes the Gut Microbiota via Fecal MicroRNA