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).

Publications 1.3k Datasets 392.5k Experiments 14

System / cell line: network ✕ Assay: direct ✕ Clear

Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

Has reproduction · 50

BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

bovine direct amplified synthetic
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
Indirect genomic effects on survival from gene expression data.

PMID 18358079 · PMC2397510 · Genome biology · 2008 · 7 claims · 6 setups

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A novel methodology (dynamic path analysis combined with additive hazard survival regression) can detect and quantify indirect effects of gene expression on survival mediated through transcription factor target genes.

dutch uppsala dlbcl gene gene literature permutation
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

user-submitted query genomes proteins domain profile-profile comparative
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

Has reproduction · 92

Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

post-mortem adra immunohistochemistry protein-protein pathway
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups

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CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad

pubmed ctd manual computational case-study
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 62

CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

cask ko1 day mature bulk qrt-pcr western
Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

Has reproduction · 64

Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

heart degs dgat2 mitodegs microarray kegg protein-protein
Spinocerebellar ataxia type 23: a genetic update.

PMID 19089525 · PMC2694919 · Cerebellum (London, England) · 2009 · 8 claims · 6 setups

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The SCA23 disease locus maps to chromosome 20p13-12.3, spanning ~6 Mb and containing 97 known/predicted genes.

members post-mortem candidate coding genome-wide neuropathological southern
The dystrobrevin-binding protein 1 gene: features and networks.

PMID 18663367 · PMC2859304 · Molecular psychiatry · 2009 · 8 claims · 6 setups

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DTNBP1 gene structure, protein-coding sequence, and dysbindin domain are conserved across 13 vertebrate species, while noncoding sequence is diverse.

vertebrate dtnbp1 comparative cross-species molecular
Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

PMID 35269470 · PMC8909161 · Cells · 2022 · 7 claims · 7 setups

Has reproduction · 88

COVID-19 and HLH share immunological pathways, yielding 237 common up-regulated DEGs dominated by cytokine/chemokine signaling and neutrophil-mediated immune responses.

peripheral leukocytes plasma degs bulk single-cell plasma
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

Has reproduction · 63

More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes

melanogaster dgrp drosophila genes bulk locomotor gene
Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.

PMID 28097058 · PMC5228507 · PeerJ · 2017 · 8 claims · 8 setups

Has reproduction · 95

Similar virus-host interactions and glycerol metabolism gene associations (notably dihydroxyacetone kinase with Haloquadratum/Halorubrum) exist across geographically diverse solar salterns

solar saltern combined individual metagenomic taxonomic functional

Experiments

Detection of venous thromboembolism by proteomic serum biomarkers.

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

Evolutionary origins of human apoptosis and genome-stability gene networks.

Indirect genomic effects on survival from gene expression data.

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

Spinocerebellar ataxia type 23: a genetic update.

The dystrobrevin-binding protein 1 gene: features and networks.

Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States.

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics.