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 575

System / cell line: sequencing ✕ Assay: type ✕ Clear

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

Full-text index only

emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

streptococcus pyogenes emm values multilocus emm comparative
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

PMID 31114675 · PMC6505635 · F1000Research · 2019 · 7 claims · 4 setups

Has reproduction · 90

pysradb provides a command-line interface to query metadata and download raw sequencing data from NCBI SRA using the SRAdb SQLite database.

sra-deposited pc3 sra tissues metadata polya assays
Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

Has reproduction · 97

Paramutation between R and S HPT epialleles occurs only in tetraploid (RRSS) F2 progeny, not in diploid (RS) F2 progeny, reducing the ratio of hygromycin-resistant plants below Mendelian expectation.

diploid 14-day-old tetraploid type hygromycin small crispr-cas9
Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

PMID 41792273 · PMC13096493 · Communications biology · 2026 · 7 claims · 6 setups

Full-text index only

cAMP-pulse signaling during early development induces transcriptome synchronicity at the single-cell level and morphological synchronicity at the multicellular level; its absence compromises synchronicity despite continued development.

discoideum single-cell scrna-seq dissecting
Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

PMID 11161376 · PMC2363715 · British journal of cancer · 2001 · 6 claims · 4 setups

Full-text index only

No SRC codon 531 mutation was detected in any of 155 Italian colorectal cancer cases (171 tissue specimens, primary tumours and liver metastases)

colorectal liver scalar subset pcr-rflp direct
Whole genome amplification and de novo assembly of single bacterial cells.

PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

Full-text index only

FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

prochlorococcus single-cell seven sag genome spike-in amplification
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

PMID 34551434 · PMC8501979 · Nucleic acids research · 2021 · 6 claims · 4 setups

Has reproduction · 75

rNTP incorporation is preferentially found on the leading strand in yeast cells expressing wild-type replicative DNA polymerases

saccharomyces model ribose-seq emriboseq rhii-hyden-seq
scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data.

PMID 41982479 · PMC13075984 · Bioinformatics advances · 2026 · 7 claims · 4 setups

Full-text index only

scGeno, a categorical HMM, infers chromosome-level genotype states in mixed-genotype organisms by modeling sequential single-cell allelic expression ratios along chromosomes

wild-type dnmt1 synthetic embryo single-cell posterior down-sampling
Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

Has reproduction · 55

Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls

midbrain single microglia substantia single-cell scenic monocle
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

Full-text index only

None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

genomic case-control nramp1 type sanger snp microsatellite
A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

PMID 18618024 · PMC2453075 · PLoS neglected tropical diseases · 2008 · 7 claims · 8 setups

Full-text index only

ETR-D sequencing allows accurate, single-step identification of MTC species, circumventing the expensive polyphasic approach.

mtc tuberculosis phenotypic pcr mptr
InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.

PMID 42109251 · PMC13158666 · Nucleic acids research · 2026 · 8 claims · 6 setups

Full-text index only

InSituPREP is a computational framework that quantifies proximity-associated gene programs across multiple analytical layers (binary contacts, graded distance, density, triplets, RNA velocity) in 3D single-cell spatial data

breast adjacent exseq-imaged exseq-derived expansion 16s scrna-seq
Mutation patterns of mtDNA: empirical inferences for the coding region.

PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

Full-text index only

Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

extended-family same direct electropherogram molecular
p53 tumor suppressor gene mutations in fibroblast-like synoviocytes from erosion synovium and non-erosion synovium in rheumatoid arthritis.

PMID 15642132 · PMC1064878 · Arthritis research & therapy · 2005 · 8 claims · 4 setups

Full-text index only

p53 mutation frequency and type do not differ significantly between erosion and non-erosion FLS

fibroblast-like matched snap-frozen p53 elisa pcr
Genetic variation in PARL influences mitochondrial content.

PMID 19862556 · PMC2829432 · Human genetics · 2010 · 7 claims · 5 setups

Full-text index only

PARL is a key regulator of mitochondrial integrity and function and plays a role in cellular apoptosis

genomic nuclear parl pcr snp real-time
Hypogonadotropic hypogonadism due to a novel missense mutation in the first extracellular loop of the neurokinin B receptor.

PMID 19755480 · PMC4306717 · The Journal of clinical endocrinology and metabolism · 2009 · 8 claims · 4 setups

Full-text index only

Homozygosity for a novel TACR3 His148Leu mutation causes normosmic isolated hypogonadotropic hypogonadism (nIHH) in three siblings

blood hek293a bosc serum sanger calcium confocal
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

Full-text index only

A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

PMID 28789673 · PMC5549432 · BMC research notes · 2017 · 7 claims · 7 setups

Full-text index only

Gene and transcript abundances of bacterial type III secretion system (T3SS) genes are positively correlated with methane yield in sheep

rumen reassembled succinivibrio dextrinosolvens metagenomic metatranscriptomic 16s
Loss of Chromosome Y Associates With Altered Immune Cell Trajectories and X-Inactivation Features.

PMID 42070154 · PMC13135724 · Aging cell · 2026 · 8 claims · 5 setups

Full-text index only

LOY has cell type-specific effects on immune cells, with the highest prevalence in classical monocytes, that vary along differentiation trajectories

peripheral blood classical cd4+ single-cell snp differential
Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 8 claims · 5 setups

Has reproduction · 77

Microbial keystone species and gut microbiota composition are highly variable during pathological development of BPSD in AD

appswe app gut 16s random open

Experiments

Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development.

Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

Whole genome amplification and de novo assembly of single bacterial cells.

Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polymerases.

scGeno: a Hidden Markov Model approach to denoise chromosome-scale genotypes from single-cell data.

Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species.

InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.

Mutation patterns of mtDNA: empirical inferences for the coding region.

p53 tumor suppressor gene mutations in fibroblast-like synoviocytes from erosion synovium and non-erosion synovium in rheumatoid arthritis.

Genetic variation in PARL influences mitochondrial content.

Hypogonadotropic hypogonadism due to a novel missense mutation in the first extracellular loop of the neurokinin B receptor.

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

Loss of Chromosome Y Associates With Altered Immune Cell Trajectories and X-Inactivation Features.

Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.