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 455

System / cell line: cohort ✕ Clear

PCR-free method detects high frequency of genomic instability in prostate cancer.

PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

blood normal prostate matched pcr-free degenerate-pcr blastn
Reconstructing Indian population history.

PMID 19779445 · PMC2842210 · Nature · 2009 · 8 claims · 8 setups

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Most Indian populations descend from a mixture of two ancient, genetically divergent populations: ANI (close to Middle Easterners, Central Asians, Europeans) and ASI (as distinct from ANI and East Asians as those are from each other).

indian pairs gujarati genome-wide principal fst-based
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
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

PMID 19761607 · PMC2759961 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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2LOmb performs an omnibus permutation test on ensembles of two-locus analyses via a four-step algorithm (two-locus analysis, permutation test, global p-value determination, progressive ensemble search)

simulated same snp type two-locus 2lomb benchmark
Replication by the Epistasis Project of the interaction between the genes for IL-6 and IL-10 in the risk of Alzheimer's disease.

PMID 19698145 · PMC2744667 · Journal of neuroinflammation · 2009 · 8 claims · 4 setups

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IL6 rs2069837 AA x IL10 rs1800871 CC interaction is associated with increased AD risk (synergy factor 1.63)

blood-derived pooled snp genome-wide logistic
Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

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RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic
Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

PMID 39649097 · PMC11621083 · Frontiers in genetics · 2024 · 7 claims · 8 setups

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HJURP is a significant prognostic biomarker in LUAD, with high expression associated with increased risk of overall survival death across four independent cohorts

tcga-luad best brain advanced bulk kaplan-meier pearson
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime
MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

PMID 39805182 · PMC11780959 · Translational oncology · 2025 · 6 claims · 8 setups

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A C3 PCLAF+ tumor cell subtype identified by scRNA-seq shows high proliferation/differentiation potential and is linked to aggressive tumor behavior and poor prognosis in HR+BC

hr+bc mda-mb-361 tcga scrna-seq cellchat pyscenic
metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

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metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

simulated selected gut mags novo binning pangenome-based
CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

PMID 41630911 · PMC12860730 · iScience · 2026 · 8 claims · 8 setups

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CTCF and cohesin (RAD21) remain co-bound to DNA throughout interphase, including during the S (replication) phase, in HeLa cells

hela tumors flow chromatin frap
Disruption of tRNA threonylation triggers RIG-I mediated anti-tumour immune response.

PMID 41735308 · PMC13043769 · Nature communications · 2026 · 8 claims · 8 setups

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OSGEP is the catalytic subunit of the KEOPS complex responsible for t6A modification at position 37 of cytoplasmic tRNAs, and its loss causes the highest protein aggregation among 45 screened tRNA-modifying enzymes in melanoma cells

mm117 b16f10 b16f10-derived c57bl esirna shrna rna-seq
Segmented filamentous bacteria are worldwide human gut commensals.

PMID 41786702 · PMC13153320 · Nature communications · 2026 · 8 claims · 8 setups

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Identification and morphological/genomic characterization of a novel human SFB species, Anisomitus miae (Human-SFB-ML), from Malian/Gambian/Kenyan fecal samples, displaying SFB-specific morphology including the attachment tip structure

fecal sfb human-sfb-ml publicly pacbio maximum gram
Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

PMID 41792463 · PMC13084053 · EMBO molecular medicine · 2026 · 7 claims · 8 setups

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Combining cfDNA methylome (EwingSign) and fragmentome analysis detects all clinically confirmed relapse events in EwS/CIC patients

plasma cfdna t7-mbd-seq ichorcna fragment
VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

PMID 41820368 · PMC13121600 · Nature communications · 2026 · 8 claims · 8 setups

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CBFB (CBF-β) is a synthetic lethal interactor of VHL in ccRCC cell lines

786o ccrcc tcga genome-wide competitive immunoblot
DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

PMID 42021404 · PMC13251264 · Clinical epigenetics · 2026 · 7 claims · 5 setups

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DNA methylation profiles at hospital admission differ among disease trajectory groups (TGs) and are associated with subsequent disease progression.

pbmcs blood immune end-stage targeted rna-seq mass
Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

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Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

synchronized falciparum blood microsphere bulk exflagellation
Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

PMID 41419303 · PMC13151493 · Gut · 2026 · 8 claims · 8 setups

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KC-Cpa1 mice show markedly increased pancreatic remodelling, fibrosis and metaplastic/PanIN lesion formation compared with KC mice

pancreas cre acinar scrna-seq histology bulk single-cell
YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

PMID 41431390 · PMC13040214 · Cancer prevention research (Philadelphia, Pa.) · 2026 · 7 claims · 8 setups

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YAP1 nuclear localization and mRNA expression significantly increase in luminal epithelial cells (LEp) with increased age and with genetic risk for breast cancer (e.g., BRCA1/2 mutation carriers)

breast hmec post-stasis 184d-p16sh ihc bulk odds
Multi-Omic Profiling of T Cell-Mediated Rejection After Kidney Transplantation Reveals B Cell Receptor Repertoire Expansion and Its Prognostic Relevance.

PMID 41467897 · PMC12752722 · FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026 · 8 claims · 8 setups

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The BCR repertoire, particularly the IgG isotype, is significantly expanded in TCMR compared to stable renal function (STA) across independent renal transplant cohorts

kidney healthy lp-1 bcr bulk triple

Experiments

PCR-free method detects high frequency of genomic instability in prostate cancer.

Reconstructing Indian population history.

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

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.

Replication by the Epistasis Project of the interaction between the genes for IL-6 and IL-10 in the risk of Alzheimer's disease.

Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

Holliday junction recognition protein (HJURP) could reflect the clinical outcomes of lung adenocarcinoma patients, and impact the choice of precision therapy.

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

MAZ-mediated tumor progression and immune evasion in hormone receptor-positive breast cancer: Targeting tumor microenvironment and PCLAF+ subtype-specific therapy.

metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

Disruption of tRNA threonylation triggers RIG-I mediated anti-tumour immune response.

Segmented filamentous bacteria are worldwide human gut commensals.

Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.

VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

YAP1 Dysfunction Promotes Molecular Properties Linked to Breast Cancer Susceptibility.

Multi-Omic Profiling of T Cell-Mediated Rejection After Kidney Transplantation Reveals B Cell Receptor Repertoire Expansion and Its Prognostic Relevance.