ArticleBioinformatics (Oxford, England)2018
Sipros Ensemble improves database searching and filtering for complex metaproteomics.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 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
24 citing papers in PubMed.
- Machine learning-based models for intraoperative blood loss of retroperitoneal laparoscopic adrenalectomy.Surgical endoscopy · 2026Article
- Aerith: Visualization and Annotation of Isotopic Enrichment Patterns of Peptides and Metabolites with Stable Isotope Labeling from Proteomics and Metabolomics.Analytical chemistry · 2025Article
- Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.Nature communications · 2025Article
- Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.Microbiome · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Absence of biofilm adhesin proteins changes surface attachment and cell strategy forJournal of bacteriology · 2025Article
- Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.Microbiome · 2024Article
- SEMQuant: Extending Sipros-Ensemble with Match-Between-Runs for Comprehensive Quantitative Metaproteomics.Bioinformatics research and applications : ... international symposium, ISBRA ... proceedings. ISBRA (Conference) · 2024Article
- CloudProteoAnalyzer: scalable processing of big data from proteomics using cloud computing.Bioinformatics advances · 2024Article
- Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia.The ISME journal · 2023Article
- Article
- A bibliometric analysis of the global impact of metaproteomics research.Frontiers in microbiology · 2023Article
- Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.Microbiome · 2022Article
- FineFDR: Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- MetaLP: An integrative linear programming method for protein inference in metaproteomics.PLoS computational biology · 2022Article
- Considerations for constructing a protein sequence database for metaproteomics.Computational and structural biotechnology journal · 2022Review
- Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Deep learning for peptide identification from metaproteomics datasets.Journal of proteomics · 2021Article
- Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost.Microbiome · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics. Results: Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers. Availability and implementation: Freely available under the GNU GPL license at http://sipros.omicsbio.org. Contact: cpan@utk.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
Indexed as
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.