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 15

System / cell line: lines ✕ Assay: linear ✕ Clear

Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes.

PMID 18715113 · PMC2517618 · PLoS medicine · 2008 · 8 claims · 4 setups

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A linear one-compartment mathematical model can relate secreted blood tumor biomarker levels to tumor burden/size at steady state

ovarian serum model culture clinical mathematical
A pharmacogene database enhanced by the 1000 Genomes Project.

PMID 19745786 · PMC2935084 · Pharmacogenetics and genomics · 2009 · 7 claims · 4 setups

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The database provides a convenient portal for immediate utilization of newly released 1000 Genomes Project (KGP) data in pharmacogenetic studies

ceu hapmap lymphoblastoid genotype-phenotype whole-genome low-coverage
Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

PMID 19116668 · PMC2605564 · PloS one · 2008 · 7 claims · 6 setups

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ASE is more robust than total gene expression approaches to environmental variation and trans-acting genetic factors, giving a cleaner representation of cis-acting effects.

hapmap combined coriell ceu allele-specific linear one-sample
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Genetic architecture of natural variation of cardiac performance from flies to humans.

PMID 36383075 · PMC9668334 · eLife · 2022 · 8 claims · 7 setups

Has reproduction · 74

Natural genetic variation significantly influences cardiac performance traits (rhythmicity and contractility) across 167 DGRP lines

drosophila dgrp gene induced high-speed genome-wide epistasis
Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

Has reproduction · 50

A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

epithelial-based tcga gdsc muscle-invasive differential co-expression signature
Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

PMID 33999949 · PMC8158866 · PLoS pathogens · 2021 · 8 claims · 8 setups

Has reproduction · 80

MCPyV generates two circular RNAs (circALTO1, circALTO2) spanning the early region/ALTO ORF, detectable in VP-MCC cell lines and patient tumors

mcpyv-infected vp-mcc waga mcc rna-seq inverse qrt-pcr
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

PMID 18366618 · PMC2386070 · BMC genomics · 2008 · 8 claims · 7 setups

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RMT removes the random noise component of the gene expression correlation matrix by testing its eigenvalue statistics against a null hypothesis derived from a truly random correlation matrix

yeast liver eight-node microarray k-means hybrid
Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.

PMID 35953471 · PMC9372134 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 83

ATX1, ATX2, and ATXR7 redundantly mediate H3K4 monomethylation genome-wide

arabidopsis chip-seq western random
Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance.

PMID 16168060 · PMC1249558 · BMC biotechnology · 2005 · 8 claims · 6 setups

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Increased gDNA input into the MDA WGA reaction increases the proportion of double-stranded and human-specific PCR-amplifiable wgaDNA and improves genotyping performance.

lymphoblastoid gdna ntc wgadna quantification displacement str
Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

PMID 20174676 · PMC3087299 · Molecular bioSystems · 2010 · 8 claims · 8 setups

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Cellular response to a signal is assumed to involve only specific TRN modules (conditionally active subnetworks) rather than the entire network, providing quantitative tractability

yeast specified normal coli chip-on-chip chip-sequencing correlation-based
Mathematical models in mammalian cell biology.

PMID 18638360 · PMC2530880 · Genome biology · 2008 · 8 claims · 8 setups

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A point mutation in the circadian Per2 gene causes familial advanced sleep phase syndrome (FASPS) via a phosphorylation defect that alters PER2 stability and subcellular localization.

culture skin hela mammalian live-cell confocal phosphoprotein
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 90

Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

vero calu-3 genes direct pcr poly

Experiments

Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes.

A pharmacogene database enhanced by the 1000 Genomes Project.

Validating discovered Cis-acting regulatory genetic variants: application of an allele specific expression approach to HapMap populations.

Population genomics of human gene expression.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Genetic architecture of natural variation of cardiac performance from flies to humans.

Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

Genome-wide survey of allele-specific splicing in humans.

Transcription network construction for large-scale microarray datasets using a high-performance computing approach.

Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.

Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance.

Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Mathematical models in mammalian cell biology.

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.