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 681

System / cell line: frequency ✕ Clear

Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

PMID 41644766 · PMC12956596 · Nature immunology · 2026 · 8 claims · 7 setups

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A subset of 23 highly expanded, CSF-enriched CD8+ T cell clonotypes exists predominantly in the CSF of the MS/CIS cohort.

paired cd8+ cd4+ csf single-cell differential pseudotime
A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.

PMID 41673035 · PMC13002930 · Scientific data · 2026 · 8 claims · 7 setups

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Generated a chromosome-scale, phased reference genome of Argania spinosa using PacBio HiFi long reads combined with Hi-C scaffolding

argania pacbio assembled pacbio hi-c rna-seq
The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

PMID 41686183 · PMC12988592 · Cancer immunology research · 2026 · 7 claims · 7 setups

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CD79A is a reliable transcriptomic/protein quantifier of B lymphocytes across differentiation stages, unlike CD19/CD20 whose expression changes upon activation

healthy tcga luad til-b flow bulk single-cell
Blood-based epigenetic instability linked to human aging and disease.

PMID 41690920 · PMC13018287 · Nature communications · 2026 · 7 claims · 8 setups

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31,744 unmethylated (and 6143 methylated) CpG loci in blood show highly consistent, stable methylation in young healthy individuals and are defined as Epigenetically Stable Loci (ESLs)

blood normal paired aml illumina whole-genome methylation
Modeling nascent transcription from chromatin landscape and structure with CLASTER.

PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

embryonic mescs chromatin k562 eu-seq chip-seq micro-c
Segzoo: a turnkey system that summarizes genome annotations.

PMID 42087325 · PMC13189851 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 4 setups

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Segzoo is a turnkey system that automates downloading of reference data and running of analyses to summarize SAGA genome annotations, requiring only a BED-format annotation file as input

embryonic segway chip-seq segway segtools
BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

PMID 42164079 · PMC13183670 · Bioinformatics advances · 2026 · 8 claims · 5 setups

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BLIT provides a unified R6-based framework for seamless integration of command-line bioinformatics tools within R, replacing fragile string-based system() calls.

core circrna clinical europe unit pipeline production
A workflow reproducibility scale for automatic validation of biological interpretation results.

PMID 37150537 · PMC10164546 · GigaScience · 2022 · 8 claims · 4 setups

Has reproduction · 100

Comparing output files by checksum alone is insufficient to verify reproducibility, since checksums can differ even when the underlying biological interpretation is unchanged

nf-core sam vcf workflow checksum biological workflow
The association between headache and Val158Met polymorphism in the catechol-O-methyltransferase gene: the HUNT Study.

PMID 16688411 · PMC3451703 · The journal of headache and pain · 2006 · 7 claims · 3 setups

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No association was found between COMT Val158Met polymorphism and migraine in a population-based sample.

peripheral population hunt genotyping structured extraction
SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

PMID 17971856 · PMC2034603 · PloS one · 2007 · 8 claims · 3 setups

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SiDCoN is a spreadsheet-based application that simulates Ballele and logR plots for all known types of DNA copy number change, with or without stromal contamination, for up to 5000 SNP data points and up to 3 combined aberrations

sidcon real mixtures snp re-analysis
Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.

PMID 41777052 · PMC13010820 · Genome biology and evolution · 2026 · 8 claims · 3 setups

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tRNA genes and their flanking regions show signatures of high historical transcription-associated mutagenesis (TAM) combined with strong purifying selection on the gene body

reference strains computational population full-length
Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

PMID 37572656 · PMC10576612 · Immunity · 2023 · 8 claims · 8 setups

Has reproduction · 68

Arg1 is highly and specifically induced in lung CD4+ T cells during in vivo influenza infection

flow-sort-purified lung cd4+ congenically rna-seq flow expression
Social and ethical implications of genomics, race, ethnicity, and health inequities.

PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

population prostate non-small-cell breast genome-wide gene somatic
Getting started in computational immunology.

PMID 18769677 · PMC2518523 · PLoS computational biology · 2008 · 8 claims · 7 setups

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Affinity maturation is driven by cycles of somatic hypermutation and affinity-dependent selection acting on B cell Ig receptors.

splenic lymphocytes lymph secondary flow microdissection intravital
Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

PMID 39592593 · PMC11599844 · Nature communications · 2024 · 8 claims · 2 setups

Has reproduction · 90

Weak selection conferred by HSC variation created before birth can reliably yield clonal hematopoiesis later in life, demonstrated via shared prenatal circulation of monozygotic (MZ) twins.

blood simulated fluctuating single-cell
Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

PMID 9197534 · PMC5921420 · Japanese journal of cancer research : Gann · 1997 · 5 claims · 2 setups

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Germline BRCA1 mutations were detected in 7 of 19 Japanese cancer families (4 breast-ovarian, 3 site-specific ovarian)

genomic tumor single-strand loss
Subfunctionalization of duplicated genes as a transition state to neofunctionalization.

PMID 15831095 · PMC1112588 · BMC evolutionary biology · 2005 · 8 claims · 2 setups

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Subfunctionalization plays an important role in duplicate gene retention but functions as a transition state leading to neofunctionalization rather than as a terminal fate.

model lattice
Mass spectrometry-based proteomic analyses of contact lens deposition.

PMID 18334948 · PMC2254969 · Molecular vision · 2008 · 8 claims · 2 setups

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Silicone hydrogel contact lenses deposit substantially less total protein than traditional soft (non-silicone) lens materials

worn bradford nano-lc-ms
Genes influencing coagulation and the risk of aneurysmal subarachnoid hemorrhage, and subsequent complications of secondary cerebral ischemia and rebleeding.

PMID 19826759 · PMC2815293 · Acta neurochirurgica · 2010 · 6 claims · 2 setups

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Carriers of the factor XIII subunit B His95Arg polymorphism have an increased risk of aneurysmal SAH

dutch aneurysmal pcr-based clinical
Physical and nutrient stimuli differentially modulate gut motility patterns, gut transit rate, and transcriptome in an agastric fish, the ballan wrasse.

PMID 33571240 · PMC7877642 · PloS one · 2021 · 8 claims · 2 setups

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Intestinal stretch generated by inert cellulose causes faster evacuation of digesta from the anterior intestine than digestible protein and lipid

intestine bulbous time-lapse sequencing

Experiments

Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.

The Presence of CD11c+ B Cells with Potent Effector Memory Phenotype in Lung Adenocarcinoma Correlates with Overall Patient Survival.

Blood-based epigenetic instability linked to human aging and disease.

Modeling nascent transcription from chromatin landscape and structure with CLASTER.

Segzoo: a turnkey system that summarizes genome annotations.

BLIT: an R package for seamless integration of command-line bioinformatics tool universe.

A workflow reproducibility scale for automatic validation of biological interpretation results.

The association between headache and Val158Met polymorphism in the catechol-O-methyltransferase gene: the HUNT Study.

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.

Loss of CD4(+) T cell-intrinsic arginase 1 accelerates Th1 response kinetics and reduces lung pathology during influenza infection.

Social and ethical implications of genomics, race, ethnicity, and health inequities.

Getting started in computational immunology.

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life.

Mutational analysis of BRCA1 gene in ovarian and breast-ovarian cancer families in Japan.

Subfunctionalization of duplicated genes as a transition state to neofunctionalization.

Mass spectrometry-based proteomic analyses of contact lens deposition.

Genes influencing coagulation and the risk of aneurysmal subarachnoid hemorrhage, and subsequent complications of secondary cerebral ischemia and rebleeding.

Physical and nutrient stimuli differentially modulate gut motility patterns, gut transit rate, and transcriptome in an agastric fish, the ballan wrasse.