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 336

Assay: real ✕ Clear

Influence of two vaccination campaigns on genetic diversity of invasive Neisseria meningitidis isolates in northern Spain (1997-2008).

PMID 20041148 · PMC2794534 · PloS one · 2009 · 7 claims · 7 setups

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Overall diversity of the invasive meningococcal population, measured by ST/clonal complex frequencies, allele numbers, polymorphic sites, and index of association, remained relatively constant throughout the 12-year study period despite the two vaccination campaigns.

invasive non-serogroupable meningitidis mlst latex real-time pcr
omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

PMID 41582216 · PMC12837286 · Genome biology · 2026 · 8 claims · 6 setups

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omnideconv is an R package providing a unified interface to twelve second-generation deconvolution methods (AutoGeneS, BayesPrism, Bseq-SC, Bisque, CDseq, CIBERSORTx, CPM, DWLS, MOMF, MuSiC, SCDC, Scaden)

blood-derived pbmc blood spleen bulk scrna-seq pseudo-bulk
DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

PMID 41663685 · PMC12996496 · Communications biology · 2026 · 7 claims · 6 setups

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DANST, a deconvolution framework using deep domain adversarial neural networks, achieves superior cell-type deconvolution accuracy compared with existing methods on human and mouse benchmark datasets

heart cortex visual brain spatial cell-type
Virus variant quantification with Orthanq.

PMID 41639627 · PMC12930645 · BMC bioinformatics · 2026 · 8 claims · 6 setups

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Orthanq performs identification and uncertainty-aware quantification of known virus variants of any virus species, including in samples with mixed infections

simulated real mixture sequencing sequencing-based pangenome variant
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

PMID 15854232 · PMC1142514 · BMC genomics · 2005 · 8 claims · 2 setups

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Correlations between qRT-PCR and microarray data are generally strong, especially when identical transcripts are targeted by both methods (r = 0.89 for fold-change).

pediatric same oligonucleotide quantitative
Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

Has reproduction · 68

scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

raw real-world expressed gene deep
scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

PMID 41632596 · PMC12866930 · Briefings in bioinformatics · 2026 · 8 claims · 6 setups

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scGACL, a GAN integrated with multi-scale contrastive learning, is proposed to overcome the over-smoothing problem in scRNA-seq imputation

simulated real-world scrna-seq scrna-seq clustering gene
Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 5 claims · 6 setups

Has reproduction

SLDP selects a subset of WGS variants using GWAS prior information (P-value threshold) combined with LD pruning (r2) to improve genomic prediction accuracy.

duroc discovery training real low-coverage genome-wide genomic
TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

Has reproduction · 84

TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

fischer computational transcriptomic same bulk gan-based autoencoder
ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

PMID 41790830 · PMC12991369 · PLoS computational biology · 2026 · 7 claims · 4 setups

Has reproduction · 83

ConNIS provides an analytic probability distribution for the length of the longest insertion-free sequence within a gene, given gene length and expected insertion count.

synthetic four real tradis simulation semi-synthetic real-world
All systems GO for understanding mouse gene function.

PMID 15610553 · PMC549721 · Journal of biology · 2004 · 7 claims · 4 setups

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Quantitative, multivariate cross-tissue expression measurements are powerfully predictive of gene function

diverse tissues computational dye-swap reverse-transcription-coupled support
Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.

PMID 16001973 · PMC1183194 · BMC cancer · 2005 · 6 claims · 5 setups

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The number of significantly differentially expressed probesets induced by each drug correlates with the known clinical therapeutic response rate of that drug in fibrosarcoma

ht1080 ht1080-derived oligonucleotide quantitative gene
Insights into the physiology of childbirth using transcriptomics.

PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

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Labor results in a change in the transcriptome in each component of the uterus studied

uterine lower microarray quantitative re-analysis
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

simulated real apoe igf2 cubic pairwise haplotype
HIV-1 sequence evolution in vivo after superinfection with three viral strains.

PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

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gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

blood seminal pbmcs biological strain-specific bulk in-house
Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

PMID 17704778 · PMC2872770 · Nature genetics · 2007 · 8 claims · 6 setups

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Mutations in UPF3B cause syndromic (Lujan-Fryns syndrome, FG syndrome) and nonsyndromic X-linked mental retardation

probands lymphoblastoid lcls tissues gene quantitative cycloheximide
Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

PMID 17594496 · PMC1934370 · BMC genomics · 2007 · 8 claims · 7 setups

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125I-IUdR-induced DNA damage alters expression of only a limited subset of genes in primary human cells

ag09319 gm05388 nhfk whole-genome quantitative dna-associated
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative

Experiments

Influence of two vaccination campaigns on genetic diversity of invasive Neisseria meningitidis isolates in northern Spain (1997-2008).

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

DANST enables cell-type deconvolution in spatial transcriptomics using deep domain adversarial neural networks.

Virus variant quantification with Orthanq.

Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?

Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

ConNIS and labeling instability: New statistical methods for improving the detection of essential genes in TraDIS libraries.

All systems GO for understanding mouse gene function.

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

Response rate of fibrosarcoma cells to cytotoxic drugs on the expression level correlates to the therapeutic response rate of fibrosarcomas and is mediated by regulation of apoptotic pathways.

Insights into the physiology of childbirth using transcriptomics.

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

HIV-1 sequence evolution in vivo after superinfection with three viral strains.

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

Effects of DNA-targeted ionizing radiation produced by 5-[125I]iodo-2'-deoxyuridine on global gene expression in primary human cells.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).