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 · 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 · 8 setups
S100A3 is a robust candidate biomarker showing consistent discriminatory performance across the acute sleep deprivation training cohort, an independent sleep deprivation cohort, and a chronic insomnia cohort.
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Has reproduction · 75
ResnetAge: A Resnet-Based DNA Methylation Age Prediction Method.
PMID 38247911 · PMC10813502 · Bioengineering (Basel, Switzerland) · 2023 · 8 claims · 4 setups
ResnetAge, a ResNet-based neural network using 22,278 shared Illumina 27K/450K CpG sites, predicts DNA methylation age from beta values.
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Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.
PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups
ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.
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Has reproduction · 90
Cell Specific eQTL Analysis without Sorting Cells.
PMID 25955312 · PMC4425538 · PLoS genetics · 2015 · 5 claims · 3 setups
A genome-environment interaction meta-analysis on whole blood can predict neutrophil- and lymphocyte-specific cis-eQTLs without sorting cells.
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Has reproduction · 71
Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.
PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 7 claims · 6 setups
An 18-gene mitophagy-related prognostic signature was identified by machine learning and used to build a prognostic risk score model for ALS.
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Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.
PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups
A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets
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Has reproduction · 83
Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.
PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups
188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways
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Has reproduction · 83
Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.
PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups
A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.
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Has reproduction · 68
Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing.
PMID 31443728 · PMC6708158 · Genome medicine · 2019 · 8 claims · 6 setups
The proportion of variance in chronological age explained by all DNA methylation probes is close to 1, so a near-perfect age predictor is in principle achievable with sufficient training data.
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Has reproduction · 100
Gene signature discovery and systematic validation across diverse clinical cohorts for TB prognosis and response to treatment.
PMID 37471455 · PMC10393163 · PLoS computational biology · 2023 · 8 claims · 8 setups
A network-based meta-analysis across studies identifies a common 45-gene signature specific to active TB disease that accounts for cohort/population heterogeneity
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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Has reproduction · 68
Machine learning algorithm predicts fibrosis-related blood diagnosis markers of intervertebral disc degeneration.
PMID 37915003 · PMC10619283 · BMC medical genomics · 2023 · 7 claims · 7 setups
CEP120 and SPDL1 are fibrosis-related diagnostic genes for IDD, identified via a random forest model from 29 differentially expressed fibrosis-related genes
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Has reproduction · 96
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.
PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups
Data-driven, high-dimensional ML approaches that learn multivariate signatures directly from genome-wide transcriptomic data (no prior gene selection) yield accurate and robust AML classifiers.
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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 · 89
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups
miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification
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Has reproduction · 58
Investigating epigenetic biomarkers of age, sex, and disease in captive South African cheetahs (Acinonyx jubatus jubatus).
PMID 41528985 · PMC12798976 · PloS one · 2026 · 8 claims · 7 setups
A cheetah-specific epigenetic age clock using 52 CpG sites predicts chronological age across blood and liver with r=0.97 and MAE=0.86 years
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Predicting failure rate of PCR in large genomes.
PMID 18492719 · PMC2441781 · Nucleic acids research · 2008 · 7 claims · 8 setups
The number of predicted primer-binding sites in genomic DNA is the most important factor determining PCR failure.
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Has reproduction · 83
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.
PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups
The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.
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Has reproduction · 81
Macrophages on the run: Exercise balances macrophage polarization for improved health.
PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups
Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.
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Has reproduction · 63
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.
PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups
Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA