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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Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.
PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups
An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions
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An SVM-based system for predicting protein subnuclear localizations.
PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups
New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.
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Wiggle-predicting functionally flexible regions from primary sequence.
PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups
A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).
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Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines.
PMID 18005451 · PMC2216041 · BMC bioinformatics · 2007 · 8 claims · 5 setups
Parepro, an SVM-based method integrating three attribute sets (RD, MI, IE) derived from evolutionary and residue-property information, predicts whether an nsSNP is deleterious or neutral.
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Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.
PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups
Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments
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Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.
PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups
Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions
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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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SePaCS--a web-based application for classification of seroreactivity profiles.
PMID 17478503 · PMC1933220 · Nucleic acids research · 2007 · 8 claims · 4 setups
SePaCS is a freely available web-based tool that trains and applies multiple classification methods (4 Naive Bayes variants, SVM with RBF kernel, LDA, DLDA) to seroreactivity profiles and outputs results as a summary table plus a detailed PDF report
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Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.
PMID 18509521 · PMC2396875 · PloS one · 2008 · 7 claims · 6 setups
wKIERA combines a weighted-kernel discriminant (kernel perceptron) with an iterative stochastic probability estimation-of-distribution algorithm to estimate a relevance distribution over variables
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Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.
PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups
omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem
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All systems GO for understanding mouse gene function.
PMID 15610553 · PMC549721 · Journal of biology · 2004 · 7 claims · 4 setups
Quantitative, multivariate cross-tissue expression measurements are powerfully predictive of gene function
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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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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
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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.