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 71

System / cell line: derived ✕ Assay: relative ✕ Clear

Efficacy assessment of SNP sets for genome-wide disease association studies.

PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

hapmap affymetrix illumina genome-wide swept comparative
Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

Has reproduction

m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

paired hl-60 gene aml nanopore functional kaplan-meier
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

Has reproduction · 54

In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

analysis microarray rna-seq quantitative
Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

PMID 17895983 · PMC1976591 · PloS one · 2007 · 8 claims · 5 setups

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Sequencing of complete mtDNA genomes in 23 pediatric patients identified 27 significant variants (12 novel, 15 known) associated with mitochondrial encephalomyopathies.

blood-derived lymphocytes maternal wild-type complete respiratory pcr-rflp
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

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The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

falciparum berghei nano-lc-ms targeted gene
Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

PMID 19768705 · PMC3030255 · Electrophoresis · 2009 · 8 claims · 8 setups

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Commercial plasma-derived FVIII/VWF concentrates contain significant amounts of non-FVIII/VWF plasma proteins as impurities

plasma-derived octanate sec fviii sds-page size-exclusion lc-esi-ms
Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

PMID 40472802 · PMC12171563 · EBioMedicine · 2025 · 6 claims · 7 setups

Has reproduction · 83

AI-derived radiological clustering identifies stage II CRC patients with significantly different survival benefit from adjuvant chemotherapy

stage patients tumour whole-tumour radiomics bulk cellular
Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

Has reproduction · 68

The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

ht29-derived ht29 nod rna-seq faire-qpcr chip-seq
The distribution of SNPs in human gene regulatory regions.

PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

gene mammalian promoter experimentally genome-wide computational binding
Characterization of the placental macrophage secretome: implications for antiviral activity.

PMID 19070362 · PMC2947718 · Placenta · 2009 · 7 claims · 5 setups

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PM and MDM secrete different soluble proteins, some of which may contribute to decreased HIV-1 replication in PM

placental seldi-tof sds-page western
Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

peripheral wecare atm mutation case-control variant
Bcipep: a database of B-cell epitopes.

PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

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Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

synthetic antigenic anti-peptide sequence
BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

PMID 16417652 · PMC1413985 · Breast cancer research : BCR · 2006 · 8 claims · 7 setups

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BOADICEA predicts accurately the number of BRCA1 and BRCA2 mutations across family groups and discriminates well between carriers and noncarriers

french-canadian families brca1-positive same targeted full-length multiplex
Widely variable endogenous retroviral methylation levels in human placenta.

PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

term placenta genome bisulfite rt-pcr genome-wide
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

PMID 19763269 · PMC2741593 · PLoS pathogens · 2009 · 8 claims · 7 setups

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Viral escape from autologous Nab occurred repeatedly (cyclically) throughout the first two years of infection in two subtype C-infected subjects despite high-titer Nab responses.

hiv-1 longitudinal 0-month single pseudovirus single site-directed
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
Patterns of evolutionary constraints on genes in humans.

PMID 18840274 · PMC2587479 · BMC evolutionary biology · 2008 · 7 claims · 6 setups

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BaseDiver, a novel framework integrating GERP score and derived allele frequency (DAF) at nonsynonymous coding SNPs, can classify GO functional categories by patterns of evolutionary constraint

mammalian hapmap panther significant comparative population chi-square
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.

PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups

Has reproduction · 43

N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management

rice ir64 recombinant bulk biomass relative

Experiments

Efficacy assessment of SNP sets for genome-wide disease association studies.

Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

Heterotachy in mammalian promoter evolution.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

Multimodal data integration for biologically-relevant artificial intelligence to guide adjuvant chemotherapy in stage II colorectal cancer.

Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

The distribution of SNPs in human gene regulatory regions.

Characterization of the placental macrophage secretome: implications for antiviral activity.

Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

Bcipep: a database of B-cell epitopes.

BRCA1 and BRCA2 mutation predictions using the BOADICEA and BRCAPRO models and penetrance estimation in high-risk French-Canadian families.

Widely variable endogenous retroviral methylation levels in human placenta.

Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.

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

Patterns of evolutionary constraints on genes in humans.

Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.