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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Full-text index only
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups
FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data
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Has reproduction · 83
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.
PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 5 claims · 8 setups
A near-complete metagenome-assembled genome (MAG) of Dolichospermum lemmermannii (FEM_B0920) was recovered from a Lake Garda bloom and clarified the species' taxonomic position within the genus Dolichospermum and the ADA group.
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Has reproduction · 56
Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.
PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 4 setups
ChickpeaOmicsR is the first comprehensive/specialized R package integrating transcriptomic, genomic, and proteomic (RNA-seq, GWAS, PPI) data within a unified, reproducible framework and standardizing fragmented chickpea gene nomenclature.
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Has reproduction · 32
Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods.
PMID 34307679 · PMC8272456 · BioMed research international · 2021 · 7 claims · 2 setups
A pipeline combining Boruta and mRMR feature selection with incremental feature selection (IFS) was used to identify COVID-19-specific transcriptomic biomarkers from blood gene expression data.
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.
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Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
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Has reproduction · 58
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.
PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups
EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD
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Has reproduction · 84
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.
PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups
A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts
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Has reproduction · 93
Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.
PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups
5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)
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Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Has reproduction · 68
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs.
PMID 30542296 · PMC6277807 · Frontiers in physiology · 2018 · 8 claims · 8 setups
The complete genome of L. plantarum ZLP001 comprises a single 3,164,369 bp circular chromosome (GC 44.65%) plus seven plasmids (A–G), encoding 3,264 protein-coding sequences.
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups
lncRNA-mRNA ceRNA networks differ substantially between control and cytokine-treated islet exosomes, sharing lncRNAs more than mRNAs, implying state-dependent regulatory functions
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Has reproduction · 67
Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development.
PMID 33679890 · PMC7933673 · Frontiers in genetics · 2021 · 8 claims · 7 setups
Immune cell infiltration and abnormal gene expression are closely related to vitiligo pathogenesis
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Has reproduction
Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.
PMID 40276518 · PMC12018310 · Frontiers in immunology · 2025 · 7 claims · 6 setups
Intrinsic microbiota (chiefly genera Burkholderia and Ralstonia) reside in the heart and liver of SPF mice, with the heart having lower bacterial abundance than the liver
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Has reproduction · 74
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.
PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups
540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed
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Has reproduction · 55
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.
PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 6 claims · 6 setups
TYR, TYRP1, DCT and LARP7 are biomarkers associated with vitiligo
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Has reproduction · 70
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).
PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups
AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella
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Has reproduction · 84
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.
PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups
COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.