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 · 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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Has reproduction
Identification of a novel 10 immune-related genes signature as a prognostic biomarker panel for gastric cancer.
PMID 34382341 · PMC8446556 · Cancer medicine · 2021 · 7 claims · 6 setups
A 10 immune-related gene signature (BMPR1B, GHR, IL11RA, INHBB, NPR3, OBP2A, PTN, R3HDML, TAC1, TPM2) was constructed via WGCNA combined with LASSO-Cox and predicts overall survival in gastric cancer
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Genome-wide identification of specific oligonucleotides using artificial neural network and computational genomic analysis.
PMID 17518996 · PMC1892811 · BMC bioinformatics · 2007 · 7 claims · 4 setups
The IAB algorithm (integration of ANN and BLAST) identifies genome-wide specific oligos much faster than pure BLAST search while maintaining comparable success rate and cross homology
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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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Discovery and identification of potential biomarkers of papillary thyroid carcinoma.
PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups
A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity
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Has reproduction · 100
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.
PMID 34654806 · PMC8519947 · Nature communications · 2021 · 7 claims · 4 setups
Pathway-based signatures derived from on-treatment tumor specimens (PASS-ON) are highly predictive of response to anti-PD1 blockade in metastatic melanoma, achieving validation AUCs of 0.85–0.89.
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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 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.
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Has reproduction · 71
Qualitative Transcriptional Signature for the Pathological Diagnosis of Pancreatic Cancer.
PMID 33173782 · PMC7538791 · Frontiers in molecular biosciences · 2020 · 8 claims · 7 setups
A 12-gene-pair (17-gene) REO-based signature discriminates PC and cancer-adjacent normal tissue from non-tumor (healthy/pancreatitis) pancreatic tissue.
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Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.
PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups
An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set
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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 · 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 · 4 setups
DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities
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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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MALDI profiling of human lung cancer subtypes.
PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups
PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes
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A genomic approach to improve prognosis and predict therapeutic response in chronic lymphocytic leukemia.
PMID 19861443 · PMC2783430 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups
A genomic signature derived from CLL patient leukemic cells significantly differentiates stable from progressive disease
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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 · 83
Macrel: antimicrobial peptide screening in genomes and metagenomes.
PMID 33384902 · PMC7751412 · PeerJ · 2020 · 8 claims · 8 setups
Macrel is an end-to-end pipeline that predicts high-quality AMP candidates from peptides, contigs, or reads of (meta)genomes
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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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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Constructing support vector machine ensembles for cancer classification based on proteomic profiling.
PMID 16689692 · PMC5173238 · Genomics, proteomics & bioinformatics · 2005 · 7 claims · 4 setups
CSVME, built by selecting a subset of base SVMs via SVM-RFE ranking and fusing them with a trained upper-layer SVM, achieves better classification performance than an ensemble of all base SVMs.
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Has reproduction · 53
Combining evidence of preferential gene-tissue relationships from multiple sources.
PMID 23950964 · PMC3741196 · PloS one · 2013 · 8 claims · 8 setups
A high-level integration approach combining three methods across four human microarray datasets, merged by consensus voting and a rule-based inner/total score, predicts preferentially expressed genes while reducing method- and study-specific bias.