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 35

Assay: repeated ✕ Clear

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

PMID 18598366 · PMC2474618 · BMC bioinformatics · 2008 · 7 claims · 6 setups

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Experimentally measured protein-protein interaction sub-networks are not random samples of their parent networks.

yeast drosophila networks dppi reanalysis computer repeated
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

PMID 19653838 · PMC3819565 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 8 claims · 5 setups

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A subset of probesets (3,414) shows 4-hour test-retest reliability exceeding r=0.70 for detecting individual differences in gene expression.

blood edta reliably genome-wide twin sub-type
MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

PMID 33849057 · PMC8266615 · Nucleic acids research · 2021 · 8 claims · 7 setups

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MrHAMER yields >1000s of viral genomes per sample at 99.9% accuracy

psg3.1 transcribed double-stranded mrhamer transcription reverse mrhamer
Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.

PMID 41784373 · PMC13055366 · Microbiology spectrum · 2026 · 8 claims · 6 setups

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Significant taxonomic and functional differences exist between the gut microbiota of wild and captive-bred European hares

fecal gut mag mags shotgun alpha differential
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

PMID 19801557 · PMC2780952 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2009 · 6 claims · 3 setups

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An SVM trained on 69 binary features of known PID genes can accurately classify PID vs non-PID genes and predict novel candidate PID genes

genome training svm support leave-one-out sensitivity
A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

PMID 19772600 · PMC2765429 · Journal of translational medicine · 2009 · 7 claims · 3 setups

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The naive Bayes model with the wrapper-based feature selection approach performed best among all predictive models tested for distinguishing CFS from controls.

subjects naive svm c4.5
Comprehensive benchmarking of large language models for RNA secondary structure prediction.

PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

Has reproduction · 88

Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

archiveii bprna large-scale secondary cross-family self-supervised
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

PMID 34742227 · PMC8572424 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 53

Current (recent) effective population size is equal to or less than 50 fish in all analysed farmed populations

turbot gilthead european common rad genotype decay
Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

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Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

hela post-mitotic pulsed fluorescence selective
Coffee, caffeine-related genes, and Parkinson's disease: a case-control study.

PMID 18759349 · PMC4554698 · Movement disorders : official journal of the Movement Disorder Society · 2008 · 8 claims · 5 setups

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Coffee drinking (ever/never or by cups/day) was not associated with PD susceptibility

blood-derived subjects matched genomic snp structured conditional
A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

family k4425 embryonic scn9a-n641y linkage copy deletion
CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

PMID 41231245 · PMC13053056 · Cancer research · 2026 · 7 claims · 7 setups

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CanSig is a comprehensive benchmarking tool for evaluating computational methods that identify shared transcriptional signatures in cancer from scRNA-seq data

neftel kim scrna-seq same scrna-seq ground-truth robustness
DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

PMID 41704565 · PMC12907731 · NAR genomics and bioinformatics · 2026 · 7 claims · 5 setups

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DoBSeqWF, a Nextflow-based pipeline, processes pooled DoBSeq sequencing data through alignment, variant calling, machine-learning-based filtering, and variant pinpointing/assignment to individuals.

individual pooled individuals gatk-called whole-genome overlapped simulated
Vitamin C Conditioning Generates Tumor-Targeting CAR T Cells with Superior Cytotoxicity and Fitness in a Posttransplant Lymphoproliferative Disorder Tumor Model.

PMID 41416402 · PMC13136873 · Molecular cancer therapeutics · 2026 · 8 claims · 8 setups

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VitC conditioning enhances transduction efficiency and proliferative capacity, yielding a higher yield of CD4+ and CD8+ CAR19-Ts

cd3+ je6-1 car19-ts coculture flow nf-κb cytotoxicity

Experiments

Deducing topology of protein-protein interaction networks from experimentally measured sub-networks.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution.

Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.

Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach.

A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data.

Comprehensive benchmarking of large language models for RNA secondary structure prediction.

Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.

Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

Coffee, caffeine-related genes, and Parkinson's disease: a case-control study.

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data.

DoBSeqWF: a framework for sensitive detection of individual genetic variation in pooled sequencing data.

Vitamin C Conditioning Generates Tumor-Targeting CAR T Cells with Superior Cytotoxicity and Fitness in a Posttransplant Lymphoproliferative Disorder Tumor Model.