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 · 57
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.
PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups
About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.
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Has reproduction · 51
Construction and Validation of an Immune Infiltration-Related Gene Signature for the Prediction of Prognosis and Therapeutic Response in Breast Cancer.
PMID 33986754 · PMC8110914 · Frontiers in immunology · 2021 · 7 claims · 8 setups
A 15-gene immune infiltration-related signature (IRS) predicts overall survival in breast cancer, with higher IRS indicating worse prognosis
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Has reproduction · 86
Screening of core genes prognostic for sepsis and construction of a ceRNA regulatory network.
PMID 36855106 · PMC9976425 · BMC medical genomics · 2023 · 8 claims · 7 setups
RNA-seq of peripheral blood from 23 sepsis patients and 10 healthy controls identifies 1,044 DEmRNAs, 66 DEmiRNAs and 155 DElncRNAs.
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Has reproduction · 83
FAM3C/ILEI protein is elevated in psoriatic lesions and triggers psoriasiform hyperproliferation in mice.
PMID 37226685 · PMC10331587 · EMBO molecular medicine · 2023 · 8 claims · 8 setups
ILEI protein, but not mRNA, is elevated in psoriatic skin and correlates with disease severity
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Has reproduction · 64
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data.
PMID 37180100 · PMC10172660 · Frontiers in immunology · 2023 · 7 claims · 7 setups
VIGET is a web portal that lets users select vaccines/ImmPort studies, run differential gene expression analysis, and perform Reactome-based pathway enrichment and functional interaction network construction
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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 · 88
Constructing an APOBEC-related gene signature with predictive value in the overall survival and therapeutic sensitivity in lung adenocarcinoma.
PMID 37954334 · PMC10637964 · Heliyon · 2023 · 8 claims · 8 setups
APOBEC family genes are aberrantly expressed across cancers, with APOBEC3B the most consistently upregulated, and APOBEC3B/APOBEC3A are markedly altered in LUAD
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Has reproduction · 94
iBRIDGE: A Data Integration Method to Identify Inflamed Tumors from Single-cell RNA-Seq Data and Differentiate Cell Type-Specific Markers of Immune-Cell Infiltration.
PMID 37023414 · PMC10236149 · Cancer immunology research · 2023 · 8 claims · 8 setups
Malignant cells cluster by patient in scRNA-seq data while immune and stromal cells cluster by cell type, making malignant cells uniquely suited to carry patient-level inflamed/cold signal
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Has reproduction · 71
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.
PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups
DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue
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Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.
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Has reproduction · 90
Stemness genes and miR-1247-3p expression associate with clinicopathological parameters and prognosis in lung adenocarcinoma.
PMID 37948380 · PMC10637681 · PloS one · 2023 · 6 claims · 7 setups
Three stem cell-related genes (ORC1L, KIF20A, DLGAP5) are differentially expressed in LUAD and correlate with altered immune infiltration and reduced patient survival.
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Has reproduction · 77
Representing and querying disease networks using graph databases.
PMID 27462371 · PMC4960687 · BioData mining · 2016 · 7 claims · 8 setups
Graph databases are well suited for representing biological information that is highly connected, semi-structured, and unpredictable.
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Has reproduction · 70
Spatial transcriptomics reveals the molecular signatures of prodromal and advanced α-synucleinopathy.
PMID 41736854 · PMC12927100 · iScience · 2026 · 8 claims · 6 setups
Induction of aSyn pathology in rodent brainstem at the early/prodromal stage triggers upregulation of energy metabolism pathways (glycolysis, oxidative phosphorylation, fatty acid metabolism)
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Has reproduction · 85
A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.
PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups
EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)
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Has reproduction · 82
Landscape of allele-specific transcription factor binding in the human genome.
PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups
A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.
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Has reproduction · 95
A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.
PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups
RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae.
PMID 37240377 · PMC10218906 · International journal of molecular sciences · 2023 · 7 claims · 8 setups
HyperTRIBE was successfully established in S. cerevisiae by fusing an RBP to the hyper-active catalytic domain of human ADAR2 (E488Q), marking target transcripts with A-to-G editing events detectable by high-throughput sequencing
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Has reproduction · 89
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.
PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups
Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM
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Computational comparison of two mouse draft genomes and the human golden path.
PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups
The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)