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 29

System / cell line: candidate ✕ Assay: protein-protein ✕ Clear

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

medline annotated interactions consolidated conditional co-citation bayesian
Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

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Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection
Predicting candidate genes for human deafness disorders: a bioinformatics approach.

PMID 16854223 · PMC1564145 · BMC genomics · 2006 · 8 claims · 4 setups

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A bioinformatic approach combining expression databases and protein interaction data narrows ~2400 candidate genes across deafness loci to a manageable set of candidates.

genomic developing proteins positional expression protein-protein
Prioritization of candidate cancer genes--an aid to oncogenomic studies.

PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

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Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

genes cancer interpro interactome averaged cross-validation domain
The role of medical structural genomics in discovering new drugs for infectious diseases.

PMID 19855826 · PMC2756625 · PLoS computational biology · 2009 · 8 claims · 6 setups

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Structure-based drug design using X-ray/NMR protein structures has contributed to the development of numerous approved and improved therapeutics.

bacteria plasmodium candidate burkholderia high-throughput animal compound-target
Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

PMID 19779614 · PMC2745575 · PloS one · 2009 · 8 claims · 8 setups

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A protein-centric data integration approach (Master Protein Directory) enables integration and mining of heterogeneous pathogen-host omics data across multiple research centers

macrophage hela vaccinia bacillus gene protein-protein comparative
NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

Has reproduction · 83

170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

afb1 breast training candidate computational bulk weighted
Assembling a jigsaw puzzle with 20,000 parts.

PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

yeast caenorhabditis escherichia proteome-wide microarray yeast rnai
Update of the G2D tool for prioritization of gene candidates to inherited diseases.

PMID 17478516 · PMC1933178 · Nucleic acids research · 2007 · 8 claims · 4 setups

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G2D is a web server that prioritizes candidate genes for inherited diseases using three distinct algorithms based on different input information.

genome genomic etrb computational literature go-similarity
A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups

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A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability

hela candidate screen genome-wide propidium sirna
WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

PMID 20887964 · PMC2948809 · American journal of human genetics · 2010 · 5 claims · 3 setups

Has reproduction

WDR11 is a gene involved in human puberty, identified via the chromosomal breakpoint of a balanced t(10;12) translocation in a Kallmann syndrome subject.

kallmann unrelated wdr11 translocation mutation 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
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

jurkat computational immunoblotting structural protein-protein
Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.

PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 8 setups

Has reproduction · 56

ChickpeaOmicsR is the first comprehensive R package that integrates transcriptomic, genomic, and proteomic chickpea data, automates DEG/PPI/GWAS analyses, and standardizes fragmented chickpea gene nomenclature

cicer bulk gwas protein-protein
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
Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

cmt2c affected spinal drg genetic sanger quantitative
Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

PMID 39256359 · PMC11387733 · Nature communications · 2024 · 8 claims · 7 setups

Has reproduction · 87

Heterozygous missense or loss-of-function variants in LRRC7 cause a dominant neurodevelopmental disorder in 33 identified individuals

genomes genematcher affected 293t genetic exome phenotype
CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

PMID 41056017 · PMC12646653 · The Journal of clinical investigation · 2025 · 8 claims · 8 setups

Has reproduction · 67

Heterozygous CDKL1 missense variants (Cys143Arg, Ser206Leu, Thr135Met) were identified in 6 patients from 3 families with TAAD spectrum disorders

patients cohort cdkl1 aortic exome gene structural
Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups

Has reproduction · 58

EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD

pbmc intersected candidate wgcna differential kegg

Experiments

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

Predicting candidate genes for human deafness disorders: a bioinformatics approach.

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

The role of medical structural genomics in discovering new drugs for infectious diseases.

Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

Assembling a jigsaw puzzle with 20,000 parts.

Update of the G2D tool for prioritization of gene candidates to inherited diseases.

A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

WDR11, a WD protein that interacts with transcription factor EMX1, is mutated in idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

Spinocerebellar ataxia type 23: a genetic update.

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.

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

Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

CDKL1 variants affecting ciliary formation predispose to thoracic aortic aneurysm and dissection.

Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.