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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Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase.
PMID 17316440 · PMC1852407 · Genome biology · 2007 · 8 claims · 6 setups
CDK consensus motifs are frequently clustered (closely spaced) in known CDK substrate proteins rather than uniformly distributed
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Has reproduction · 87
CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.
PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups
CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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Large-scale structural analysis of the core promoter in mammalian and plant genomes.
PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups
DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.
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Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.
PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups
A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.
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RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.
PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups
Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.
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Has reproduction · 67
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.
PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups
Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies
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Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.
PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups
A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)
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The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.
PMID 15608288 · PMC540018 · Nucleic acids research · 2005 · 8 claims · 8 setups
The TIGR Gene Indices (TGI) are a collection of 77 species-specific databases that cluster and assemble EST and known gene sequences into tentative consensus (TC) sequences to identify and characterize expressed transcripts.
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Has reproduction · 67
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups
An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.
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Has reproduction
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.
PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 6 claims · 8 setups
A deep learning WSI cluster (three-class mini batch K-means on Inception V3 features) is associated with overall survival (P<0.001) and is an independent prognostic predictor (P=0.031) in BLCA.
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Has reproduction · 100
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.
PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups
44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.
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Has reproduction · 77
Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.
PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups
457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis
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The MAPPER database: a multi-genome catalog of putative transcription factor binding sites.
PMID 15608292 · PMC540057 · Nucleic acids research · 2005 · 8 claims · 6 setups
Built a library of 1134 HMM models (359 matrix-derived, 718 factor-derived, 57 JASPAR-derived), corresponding to 863 distinct TF names, from TRANSFAC and JASPAR binding site data
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Has reproduction · 52
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups
epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome
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Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.
PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups
A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome