Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Has reproduction · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life
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Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
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Has reproduction · 100
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning.
PMID 35118380 · PMC8808542 · NAR genomics and bioinformatics · 2022 · 8 claims · 7 setups
nf-core/mag is a Nextflow/nf-core pipeline for hybrid metagenome assembly, binning and taxonomic classification of MAGs.
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Has reproduction
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.
PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups
Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph
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Has reproduction · 75
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.
PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups
AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles
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Has reproduction · 50
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.
PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups
GAL08 is a dominant bacterial clade in a neutral hot spring, comprising up to 29.2% of the community by relative read abundance and up to 4.7 × 10^5 16S rRNA gene copies per gram sediment.
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Has reproduction · 99
Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.
PMID 36242054 · PMC9563170 · Microbiome · 2022 · 8 claims · 8 setups
Three MAGs from a stratified salt crust represent a novel order, Nucleotidisoterales, within Ca. Nanohaloarchaeota
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Has reproduction · 83
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.
PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups
MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences
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Has reproduction · 89
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.
PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups
MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa
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Has reproduction · 84
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.
PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 6 claims · 7 setups
DeepProg, an ensemble of deep-learning and machine-learning models, robustly predicts patient survival subtypes from multi-omics data and explicitly models survival as the objective while predicting new patient risks