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 30

System / cell line: whole-genome ✕ Assay: promoter ✕ Clear

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

Full-text index only

P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

vivax genome comparative microsatellite
Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

Has reproduction

Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

nasal aggregated genes differentially whole-genome methylation tiling
A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.

PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups

Has reproduction · 54

A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS

domestic re-sampled hek293t yak whole-genome pcr dual-luciferase
Genome-wide DNA hypermethylation opposes healing in patients with chronic wounds by impairing epithelial-mesenchymal transition.

PMID 35819852 · PMC9433101 · The Journal of clinical investigation · 2022 · 8 claims · 8 setups

Has reproduction · 68

Chronic wound-edge tissue shows genome-wide DNA hypermethylation compared with unwounded skin

chronic wound-edge unwounded ischemic whole-genome bisulfite bulk
The genome of the ant Tetramorium bicarinatum reveals a tandem organization of venom peptides genes allowing the prediction of their regulatory and evolutionary profiles.

PMID 38245722 · PMC10800049 · BMC genomics · 2024 · 8 claims · 8 setups

Has reproduction · 100

44 venom peptide genes were identified, distributed across four of the eleven chromosomes and organized in tandem repeat clusters.

tetramorium bicarinatum vpg venom whole-genome blast gene
Viruses take center stage in cellular evolution.

PMID 16787527 · PMC1779534 · Genome biology · 2006 · 8 claims · 6 setups

Full-text index only

A large poxvirus-like dsDNA virus may have become the eukaryotic nucleus after being taken in by an ancestral cell (viral eukaryogenesis)

acanthamoeba coccolithovirus nucleocytoplasmic dsdna whole-genome phylogenetic comparative
Genetic diversity among five T4-like bacteriophages.

PMID 16716236 · PMC1524935 · Virology journal · 2006 · 8 claims · 8 setups

Full-text index only

A core set of 82 conserved genes (T4-like genes) is present in all five genomes analyzed, clustered in large collinear blocks.

bacteriophages five conserved aeh1 genome orf trna
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

Has reproduction · 91

A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

yeonsan ogye_1.1 locus tissues whole-genome genome structural
Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

Has reproduction · 80

The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

mpm mesomics whole-genome bulk methylation
Bench-to-bedside review: fulfilling promises of the Human Genome Project.

PMID 12133180 · PMC137447 · Critical care (London, England) · 2002 · 8 claims · 4 setups

Full-text index only

Most common diseases and many drug responses are influenced by inherited genetic variation

haemophilus genome septic genomic whole-genome snp large-scale
The field of tissue injury in the lung and airway.

PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

Full-text index only

Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific
DDBJ in collaboration with mass-sequencing teams on annotation.

PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups

Full-text index only

DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data

chimpanzee silkworm mus homo whole-chromosome whole-genome cage
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.

PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 63

Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date

pigs sscrofa11.1 pig domestic whole-genome tandem repeat
Heterotachy in mammalian promoter evolution.

PMID 16683025 · PMC1449885 · PLoS genetics · 2006 · 8 claims · 5 setups

Full-text index only

The rate of promoter evolution relative to control sequences is not consistent between or within mammalian lineages over time (heterotachy)

promoter ancient chimpanzee comparative ancient micro-indel
Ecotype diversity and conversion in Photobacterium profundum strains.

PMID 24824441 · PMC4019646 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 77

No single gene restricts the environmental niche of each bathytype; instead a set of strain-specific genetic features confers depth-specific stress tolerance (temperature, pressure, nutrients).

photobacterium profundum predicted orthologous whole-genome pulsed-field comparative
Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

PMID 41540108 · PMC13004696 · Nature medicine · 2026 · 7 claims · 7 setups

Full-text index only

GPRC5D antigenic drift/mutational events occurred in 68.4% of relapsed cases following anti-GPRC5D TCE therapy (13/19 evaluable patients)

cd138+ pbmcs cohort bulk single-cell targeted
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
Critical care: applying genomics to inflammation outcomes.

PMID 16330338 · PMC1314943 · Environmental health perspectives · 2005 · 8 claims · 6 setups

Full-text index only

Genetic factors drive key aspects of an individual's inflammatory outcome after trauma, burns, or sepsis

leukocytes whole-blood healthy peripheral genomewide whole-genome microarray
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

Full-text index only

aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.

PMID 41515103 · PMC12787715 · Plants (Basel, Switzerland) · 2026 · 8 claims · 8 setups

Full-text index only

295 AP2/ERF transcription factor genes were identified and classified in the S. scabra genome

scabra representative hmm rna-seq qpcr

Experiments

Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

Viruses take center stage in cellular evolution.

Genetic diversity among five T4-like bacteriophages.

Bench-to-bedside review: fulfilling promises of the Human Genome Project.

The field of tissue injury in the lung and airway.

DDBJ in collaboration with mass-sequencing teams on annotation.

Heterotachy in mammalian promoter evolution.

Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.

Critical care: applying genomics to inflammation outcomes.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

Genome- and Transcriptome-Wide Characterization of AP2/ERF Transcription Factor Superfamily Reveals Their Relevance in Stylosanthes scabra Vogel Under Water Deficit Stress.