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).
-
Has reproduction · 79
Contribution of retrotransposition to developmental disorders.
PMID 31604926 · PMC6789007 · Nature communications · 2019 · 7 claims · 8 setups
De novo retrotransposition events, though rare, can be diagnostic causes of severe developmental disorders
-
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)
-
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
-
Has reproduction · 75
Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.
PMID 34143800 · PMC8213194 · PloS one · 2021 · 8 claims · 7 setups
306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified from three independent GEO microarray datasets comparing EOC and adjacent normal ovarian tissue
-
Has reproduction · 62
The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.
PMID 38537644 · PMC11063626 · Cell reports · 2024 · 8 claims · 8 setups
The natural (non-sterilized) Clue Field soil microbiome reduces Striga attachment to sorghum roots compared to gamma-sterilized soil
-
Has reproduction · 94
A Deluge of Complex Repeats: The Solanum Genome.
PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 8 setups
~50–60% of the genomes of S. tuberosum and S. lycopersicum are composed of repetitive elements
-
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
-
Has reproduction · 69
Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance.
PMID 39009986 · PMC11247842 · Genetics, selection, evolution : GSE · 2024 · 5 claims · 8 setups
Meta-analysis of GWAS across six dairy cattle breeds identifies 58 lead markers associated with clinical mastitis and somatic cell score
-
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
-
Has reproduction · 66
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.
PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups
A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons
-
Has reproduction · 82
Reusable building blocks in biological systems.
PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 5 setups
Biological systems can be decomposed into phenotypic building blocks (PBBs) whose reusability ranges from single-use (condition-specific) to constitutive
-
Has reproduction · 90
Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle.
PMID 36057548 · PMC9441065 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 6 setups
Commercially available genotyping arrays are not effective at capturing variants that segregate among African indicine cattle compared to African and European taurine cattle.
-
Has reproduction · 80
Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.
PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups
α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination
-
Has reproduction · 73
Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions.
PMID 31681245 · PMC6813237 · Frontiers in microbiology · 2019 · 5 claims · 5 setups
S. aureus COL (MRSA) survives and grows well under acidic (pH5) and alkaline (pH9) conditions, both planktonically and as a biofilm
-
Has reproduction · 100
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 8 claims · 7 setups
Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p, Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic CRC sites compared to primary CRC.
-
Has reproduction · 63
RummaGEO: Automatic mining of human and mouse gene sets from GEO.
PMID 39569206 · PMC11573963 · Patterns (New York, N.Y.) · 2024 · 8 claims · 7 setups
RummaGEO is a gene expression signature search engine built from automatically mined human and mouse RNA-seq perturbation studies in GEO
-
Has reproduction · 84
Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.
PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups
Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).
-
Has reproduction · 67
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.
PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups
PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons
-
Has reproduction · 59
Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer.
PMID 40197136 · PMC11974128 · BMC cancer · 2025 · 8 claims · 8 setups
High γδT cell infiltration is associated with favorable prognosis in TNBC but not in HR-positive or HER2-positive breast cancer
-
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.