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: cell-line ✕ Assay: growth ✕ Clear

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
Backseat drivers take the wheel.

PMID 18068625 · PMC2705833 · Cancer cell · 2007 · 8 claims · 8 setups

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Systematic resequencing combined with functional validation can distinguish rare driver FLT3 mutations from passenger mutations in AML patients negative for known activating mutations

pretreatment baf3 additional normal targeted baf3 immunoprecipitation
Chips to hits.

PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups

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Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping

individual yeast pools lncap cell-based affymetrix automated
Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

PMID 7577470 · PMC2033929 · British journal of cancer · 1995 · 8 claims · 4 setups

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Homozygous deletion of both p15 and p16 occurred in 7 of 13 (54%) independent bladder cancer cell lines tested

bladder pcr pcr cytogenetic arbitrary
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual
Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas.

PMID 18790768 · PMC2651569 · Molecular cancer therapeutics · 2008 · 8 claims · 6 setups

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CDK4 mutations (K22Q, R24C, R24L) alone do not confer resistance to the BRAF inhibitor SB590885

melanoma metastatic wm39 451lu mtt pcr array
Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

one nci60 cerevisiae cancer multidimensional cellular two-color
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

PMID 35729113 · PMC9213456 · Nature communications · 2022 · 7 claims · 5 setups

Has reproduction · 84

Developed a python-based, scalable model creation and simulation pipeline that converts structured text files into an SBML-standard model and is high-performance/cloud-computing ready.

sparced mcf10a deterministic hybrid comparison
Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

nsclc 293t il-3-independent mutational site-directed cytokine-independence
Utilization of genomic signatures to identify phenotype-specific drugs.

PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

nci-60 breast mda-mb-231 signature-drug gene signature
Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups

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Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors

ht1080 coli ht1080-derived synthetic novo gel transposition
Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

PMID 19929607 · PMC2931417 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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Serine/threonine phosphorylation widely functions to modulate protein-protein interactions (PPIs) across signaling systems

hela jurkat exposed yeast quantitative antibody-based analog-sensitive
Systems biology and the host response to viral infection.

PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

lung cd4 rhesus kshv microarray quantitative genomic
Advances in the study of SR protein family.

PMID 15626328 · PMC5172405 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 8 setups

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SR proteins promote assembly of the early splicesome via protein-protein interactions in their RS-domain that recruit components of the splicing machinery.

nuclear bovine drosophila caenorhabditis selex rna-binding splicing
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative
With the finished human genome in hand, what next?

PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups

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Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.

domestic saccharomyces systemic schistosoma comparative functional genetic
Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.

PMID 35547750 · PMC9065207 · Theranostics · 2022 · 8 claims · 8 setups

Has reproduction · 68

THBS2 is a tumor size-independent biomarker that robustly predicts post-surgical OS and RFS in multiple independent early-stage LUAD cohorts

tcga paired thbs2+ scrna-seq wgcna scrna-seq gsea

Experiments

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

Backseat drivers take the wheel.

Chips to hits.

Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

Increased cyclin D1 expression can mediate BRAF inhibitor resistance in BRAF V600E-mutated melanomas.

Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

Phenotypic variation meets systems biology.

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.

Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

Utilization of genomic signatures to identify phenotype-specific drugs.

Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.

Phosphoproteomics by mass spectrometry: insights, implications, applications and limitations.

Systems biology and the host response to viral infection.

Advances in the study of SR protein family.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

With the finished human genome in hand, what next?

Multi-scale integrative analyses identify THBS2(+) cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma.