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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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.
PMID 17868464 · PMC2375030 · Genome biology · 2007 · 8 claims · 8 setups
InSite predicts protein-pair-specific binding motifs ('Motif M on protein A binds to protein B') by integrating heterogeneous PPI and motif-motif interaction evidence within a Bayesian network trained by EM
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Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations.
PMID 19654296 · PMC2763410 · Cancer research · 2009 · 7 claims · 7 setups
CHASM, a Random Forest-based computational method, was developed to identify and prioritize missense mutations likely to be functional drivers of tumor cell proliferation.
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Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.
PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups
The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.
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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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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 · 59
Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.
PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups
The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance
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Has reproduction · 83
Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.
PMID 35953471 · PMC9372134 · Nature communications · 2022 · 8 claims · 8 setups
ATX1, ATX2, and ATXR7 redundantly mediate H3K4 monomethylation genome-wide
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Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.
PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups
A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures
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Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.
PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups
A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.
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Has reproduction · 94
Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.
PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups
HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)
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Has reproduction · 85
Digital sorting of complex tissues for cell type-specific gene expression profiles.
PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups
The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.
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High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.
PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups
Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse
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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.
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Has reproduction · 85
ScLRTC: imputation for single-cell RNA-seq data via low-rank tensor completion.
PMID 34844559 · PMC8628418 · BMC genomics · 2021 · 8 claims · 8 setups
scLRTC imputes dropout entries closest to the original expression values on simulated datasets, outperforming other state-of-the-art methods by SSE and PCC.