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 · 76
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.
PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 6 setups
DRW-GM evaluates gene topological importance by directed random walk on a global gene–metabolite pathway graph integrating gene expression and metabolomic profiles to infer pathway activities
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Has reproduction · 95
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.
PMID 32111840 · PMC7048732 · Nature communications · 2020 · 8 claims · 8 setups
SuSr-D1 encodes Med15b.D, a subunit of the Mediator complex
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 6 setups
A 120-gene transcriptomic fingerprint encoding defective decidualization is present in decidua of women who developed sPE in a prior pregnancy
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 69
Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.
PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups
Kidney xenografts show only modest/minimal growth after transplantation into NHP recipients
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Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups
CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue
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Has reproduction · 81
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.
PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL
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Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups
GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance
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Has reproduction · 40
PD-1 blockade potentiates neoadjuvant chemotherapy in NSCLC via increasing CD127(+) and KLRG1(+) CD8 T cells.
PMID 37231145 · PMC10213055 · NPJ precision oncology · 2023 · 8 claims · 5 setups
NAPC produces higher major pathological response (MPR) and pathological complete response (pCR) rates and longer DFS/OS than NAC alone
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 53
PulmonDB: a curated lung disease gene expression database.
PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 7 claims · 6 setups
PulmonDB is a curated, web-based relational database (plus R package) integrating microarray and RNA-seq gene expression data with controlled-vocabulary annotation for COPD and IPF.
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Has reproduction · 45
De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.
PMID 29451882 · PMC5815590 · PloS one · 2018 · 8 claims · 7 setups
This is the first de novo transcriptomic analysis of C. officinalis leaf and fruit tissue, performed using the Illumina HiSeq 4000 platform.
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Has reproduction · 63
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.
PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups
Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.
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Has reproduction · 90
Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart.
PMID 37012284 · PMC10070245 · Scientific reports · 2023 · 7 claims · 8 setups
Batch correction using sequencing platform as the correcting variable (via Combat-Seq) removes technical variability so that samples cluster by injury condition rather than dataset origin.
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Has reproduction · 65
A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.
PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups
A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC
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Has reproduction · 97
Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle.
PMID 32523568 · PMC7261829 · Frontiers in microbiology · 2020 · 6 claims · 6 setups
Photosynthesis-related and translational transcripts are upregulated at midday (high light) compared to night/darkness in the pond microeukaryotic community
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Has reproduction · 50
Wx: a neural network-based feature selection algorithm for transcriptomic data.
PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups
The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups
WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features
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Has reproduction · 89
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.
PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 7 setups
There is a general lack of global gene regulation across re-analyzed Wolbachia transcriptomes, with the exception of a weak transcriptional response upregulating ribosomal proteins in early larval stages.
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Has reproduction · 71
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.
PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups
TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.