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
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.
PMID 16381948 · PMC1347397 · Nucleic acids research · 2006 · 6 claims · 2 setups
CAGE Basic and Analysis Databases together form a comprehensive resource for promoter analysis using CAGE tag data from human and mouse
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Full-text index only
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
PMID 15980513 · PMC1160219 · Nucleic acids research · 2005 · 8 claims · 1 setups
AUGUSTUS web server allows users to impose constraints (splice sites, translation start/stop, known exons, exonic/intronic intervals) on predicted gene structures
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Has reproduction · 94
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells.
PMID 32770939 · PMC7430845 · BMC genomics · 2020 · 6 claims · 6 setups
SOX10 binds proximal promoters genome-wide in Schwann cells, with ChIP-seq signal concentrated directly over TSSs that are also marked by H3K4me3
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Has reproduction · 95
The archives are half-empty: an assessment of the availability of microbial community sequencing data.
PMID 32859925 · PMC7455719 · Communications biology · 2020 · 8 claims · 6 setups
A large proportion of 16S rRNA amplicon sequencing studies contain data that is not available or not reusable despite being reported as deposited.
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Has reproduction · 84
Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.
PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups
Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures
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Has reproduction · 64
Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism.
PMID 31825657 · PMC7099524 · American journal of physiology. Cell physiology · 2020 · 8 claims · 8 setups
C2C12 myotubes show enriched mRNA expression of genes coding for actin and myosin compared with L6 and HSMC.
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Has reproduction
Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.
PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 7 setups
Rap1 represses divergent noncoding transcription at highly expressed RP gene promoters (e.g., IRT2 at RPL43B, iMLP1 at RPL40B)
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups
TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene
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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 · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups
Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution
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Has reproduction · 68
Cell-type annotation with accurate unseen cell-type identification using multiple references.
PMID 37379341 · PMC10335708 · PLoS computational biology · 2023 · 8 claims · 4 setups
mtANN integrates multiple reference datasets and eight gene selection methods via ensemble learning (multiple deep classification models + majority voting) to improve cell-type annotation accuracy
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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
196 R. leguminosarum sv. trifolii strains form a five-species complex (gsA-gsE) with generally little recent between-species gene transfer, aside from a few highly mobile genetic regions
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Has reproduction · 71
Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.
PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups
Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments
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Has reproduction · 59
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.
PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering
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Has reproduction · 51
A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.
PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups
An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73
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Has reproduction · 96
Hypoxia-associated genes as predictors of outcomes in gastric cancer: a genomic approach.
PMID 40129974 · PMC11931070 · Frontiers in immunology · 2025 · 8 claims · 8 setups
A prognostic model built from five H1-specific hypoxia-associated transcription factors (EHF, EIF1AD, GLA, KEAP1, MAGED2) predicts overall survival in STAD, with high-risk patients showing significantly worse OS.
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Has reproduction · 23
Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.
PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups
COPD GWAS risk loci are statistically more clustered across the genome than expected by chance, with chromosome 4q containing a notably dense cluster of five loci within 70Mb.
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Has reproduction · 24
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.
PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups
MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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Has reproduction · 54
Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection.
PMID 34145026 · PMC8321655 · Life science alliance · 2021 · 8 claims · 6 setups
ATAC-seq reveals unique neutrophil chromatin architecture changes in response to different stimuli before transcriptional activation, possibly regulating downstream gene expression.