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 23

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

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

acid-extracted hela online offline
Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

PMID 20057903 · PMC2802291 · Molecular vision · 2009 · 7 claims · 8 setups

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BEST1 mutations are not correlated with the severity of functional and clinical data in Best VMD patients

genomic unrelated best1 best1-4 direct chromosome pathogenicity
Disease-specific proteins from rheumatoid arthritis patients.

PMID 16778393 · PMC2729955 · Journal of Korean medical science · 2006 · 8 claims · 6 setups

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Fibronectin, semaphorin 7A precursor, growth factor receptor-bound protein 7 (GRB7), and immunoglobulin µ chain specifically associate with antibodies purified from RA synovial fluid

synovium synovial synoviocytes western affinity antibody-affinity
A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

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Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

genomic hek293 hepg2 microsomes pcr site-directed luciferase
RIT1 controls actin dynamics via complex formation with RAC1/CDC42 and PAK1.

PMID 29734338 · PMC5937737 · PLoS genetics · 2018 · 8 claims · 8 setups

Has reproduction

PAK1 is a novel direct effector of RIT1

hek293t cos7 his-tagged western gst co-immunoprecipitation
Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

PMID 11710958 · PMC59832 · BMC genetics · 2001 · 7 claims · 6 setups

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DHPLC screening combined with direct sequencing detects likely disease-causative point mutations in the dystrophin gene missed by multiplexed PCR deletion/duplication testing

genomic muscle blood direct dhplc multiplexed
CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

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Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

PMID 17298666 · PMC1805452 · BMC neurology · 2007 · 8 claims · 8 setups

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Four unrelated NA patients show a novel erythrocyte membrane defect: 4.1R protein deficiency

erythrocyte genomic peripheral erythrocytes sds-page non-denaturing direct
Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

plasma ppp reference identification quantitative specimen
Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

PMID 19122847 · PMC2585750 · Circulation. Arrhythmia and electrophysiology · 2008 · 7 claims · 5 setups

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A missense R99H mutation in KCNE3 was identified in a Brugada Syndrome proband and cosegregates with the phenotype in the family (4/4 phenotype-positive, 0/3 phenotype-negative members carried it)

genomic cho-k1 left ventricular sscp whole-cell co-immunoprecipitation
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
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

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Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.

PMID 35624178 · PMC9142503 · Nature communications · 2022 · 7 claims · 5 setups

Has reproduction · 84

pcSecYeast, a proteome-constrained genome-scale model integrating metabolism, translation, and detailed secretory pathway processing (translocation, PTMs, folding, misfolding, degradation), was constructed for S. cerevisiae

cerevisiae genome-scale unit expression
Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

PMID 8879195 · PMC2192830 · The Journal of experimental medicine · 1996 · 6 claims · 8 setups

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The patient is a compound heterozygote for a p67-phox gene mutation: an in-frame deletion of lysine 58 on one allele and an 11-13 kb genomic deletion on the other allele.

granulocytes granulocyte mononuclear leukocyte nbt cell-free western
From genomes to systems.

PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr
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
Systematic prediction of human membrane receptor interactions.

PMID 19798668 · PMC3076061 · Proteomics · 2009 · 7 claims · 6 setups

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Predicting interactions specifically for membrane receptors, rather than deriving them from a general human interactome model, improves prediction performance for these proteins

cos-1 um-22a hep3b gst-egfr co-immunoprecipitation pulldown binding
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

Experiments

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

Functional and clinical data of Best vitelliform macular dystrophy patients with mutations in the BEST1 gene.

Disease-specific proteins from rheumatoid arthritis patients.

A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

RIT1 controls actin dynamics via complex formation with RAC1/CDC42 and PAK1.

Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

Functional effects of KCNE3 mutation and its role in the development of Brugada syndrome.

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.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints.

Disturbed interaction of p21-rac with mutated p67-phox causes chronic granulomatous disease.

From genomes to systems.

Spinocerebellar ataxia type 23: a genetic update.

Systematic prediction of human membrane receptor interactions.

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