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 · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Has reproduction · 49
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.
PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups
ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 8 claims · 8 setups
PARP1, PTPN1, and ITGA4 are core PAH protein targets identified via PPI network analysis and XGBoost feature selection from AD-associated DEGs
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Has reproduction · 49
Integration of Transcriptomics With Interpretable Artificial Intelligence for Identifying Molecular Signatures of Physiological Stress in Sleep Deprivation.
PMID 42216239 · PMC13240488 · Journal of cellular and molecular medicine · 2026 · 8 claims · 7 setups
S100A3 shows consistent discriminatory performance across the training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort
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Has reproduction · 84
Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.
PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups
Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.
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Has reproduction · 90
Inferring a spatial code of cell-cell interactions across a whole animal body.
PMID 36395331 · PMC9714814 · PLoS computational biology · 2022 · 8 claims · 6 setups
cell2cell computes cell-cell interaction (CCI) potential using a novel modified Bray-Curtis score based on complementary coexpression of ligand-receptor pairs between cells
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Has reproduction · 66
Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.
PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups
Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.
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Has reproduction · 81
Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.
PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups
SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains
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Has reproduction · 90
A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.
PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups
A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.
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Rapid detection, cloning and molecular cytogenetic characterisation of sequences from an MRP-encoding amplicon by chromosome microdissection.
PMID 8018546 · PMC2033297 · British journal of cancer · 1994 · 7 claims · 6 setups
Chromosome microdissection can be used to rapidly detect, clone and cytogenetically characterise amplified sequences from hsrs/dmins in drug-resistant cells
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Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).
PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups
The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.
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Incidence of mutation and deletion in topoisomerase II alpha mRNA of etoposide and mAMSA-resistant cell lines.
PMID 11676865 · PMC5926608 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 6 setups
Acquired mutations of the topoisomerase IIα gene are an important and frequent mechanism of resistance to topoisomerase II inhibitors, independent of the degree of resistance.
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Comparative genomics.
PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups
Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences
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Microarray analysis: genome-scale hypothesis scanning.
PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups
Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.
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GoMiner: a resource for biological interpretation of genomic and proteomic data.
PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups
GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).
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Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.
PMID 15743496 · PMC1064127 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups
A common BRCA1 haplotype (haplotype 2, C A G G) is associated with a modest increase in sporadic breast cancer risk
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Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.
PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups
New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach
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Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.
PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups
The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.
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Has reproduction
Genome-wide signatures of convergent evolution in echolocating mammals.
PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups
Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.