ArticleNature computational science2023
Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues.
Article in Nature computational science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 21 citations in OpenAlex.
- scH16S-Seq Maps Klebsiella pneumoniae-Associated Myeloid States and Reveals a CD38-NAD Immunometabolic Axis That Impairs Lysosomal Acidification in Sepsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- Single-cell analyses of tissue regeneration in two true jellyfish.Molecular biology and evolution · 2026Article
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.Journal of translational medicine · 2026Article
- Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.Microorganisms · 2026Review
- Escherichia coli promotes colorectal cancer metastasis by maintaining enhancer-promoter loops through releasing neutrophil extracellular traps.Nature communications · 2026Article
- Stenotrophomonas promotes gastrointestinal tumor progression via STING degradation in tumour cells and mitigated immune response.Nature communications · 2026Article
- Intratumoral microbiome: the double-edged sword in remodeling cancer immunotherapy.Molecular cancer · 2026Review
- Article
- The High-Altitude Adaptation Characteristics of Microbiota-Host Cross-Talk in Yak Gastrointestinal Track.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- HGMT: a database of human gut microbiota for tumors and immunotherapy response.Genome biology · 2025Article
- Dissection of intratumor microbiome-host interactions at the single-cell level in lung cancer.hLife · 2025Article
- Polybacterial intracellular macromolecules shape single-cell inflammatory profiles in upper airway epithelia.NPJ biofilms and microbiomes · 2025Article
- Analyses of single-cell RNA sequencing uncover the role of intratumoral Helicobacter pylori in shaping tumor progression and immunity in gastric cancer.Cancer immunology, immunotherapy : CII · 2025Article
- Polybacterial Intracellular Macromolecules Shape Single-Cell Epikine Profiles in Upper Airway Mucosa.bioRxiv : the preprint server for biology · 2024Article
- Could the tumor-associated microbiota be the new multi-faceted player in the tumor microenvironment?Frontiers in oncology · 2023Review
- Article
- The Gastric Microbiota Invade the Lamina Propria in Helicobacter pylori-Associated Gastritis and Precancer.HelicobacterArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Existing genomic sequencing data can be used to study host-microbiome ecosystems, however distinguishing signals originating from truly present microbes versus contaminating species and artifacts is a substantial and often prohibitive challenge. Here we show that emerging sequencing technologies definitely capture reads from present microbes. We developed SAHMI, a computational resource to identify truly present microbial nucleic acids and filter contaminants and spurious false-positive taxonomic assignments from standard transcriptomic sequencing of mammalian tissues. In benchmark studies, SAHMI correctly identifies known microbial infections present in diverse tissues, and we validate SAHMI's enrichment for correctly classified, truly present species using multiple orthogonal computational experiments. The application of SAHMI to single-cell and spatial genomic data thus enables co-detection of somatic cells and microorganisms and joint analysis of host-microbiome ecosystems.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.