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 755

Assay: clustering ✕ Clear

Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia.

PMID 19691824 · PMC2732614 · Virology journal · 2009 · 7 claims · 5 setups

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HBV/B and HBV/C are the dominant genotypes among HBsAg-positive blood donors in Makassar

serum hbv pre-s genotype-specific nested complete
Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr
Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

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A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

bidirectional across high-quality nascent comparative eqtl
NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

PMID 41710890 · PMC12909245 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Dysidea avara has a chromosome-level genome assembly of 575 Mb, N50 41 Mb, 162 scaffolds, and 15 chromosomes.

dysidea avara translated nlrs long-read hi-c genome
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
Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

PMID 41852645 · PMC12993812 · PNAS nexus · 2026 · 8 claims · 8 setups

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The Tokara Islands population is a cryptic species new to science, morphologically similar to but genetically distinct from Ijima's Leaf Warbler on the Izu Islands

museum ijimae phylloscopidae genome-wide morphometric bioacoustic whole-genome
A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development.

PMID 41957362 · PMC13066550 · Nature communications · 2026 · 8 claims · 7 setups

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A 3 bp deletion or a 1 bp insertion in the Enh13 SOX9 binding site causes complete XX female-to-male sex reversal in adult homozygous mice

c57bl6 6-week-old 6-week e12.5 crispr-cas9 gross immunostaining
Much ado about nothing: modeling amino acid replacement with predicted protein structures.

PMID 42036821 · PMC13171170 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 7 setups

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AFSM was constructed from over 660,000 structural alignments across ~21,000 proteins (297 InterPro families), following the BLOSUM log-odds methodology.

proteins balibase pfam cath structural sequence remote
Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

PMID 41419303 · PMC13151493 · Gut · 2026 · 8 claims · 8 setups

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KC-Cpa1 mice show markedly increased pancreatic remodelling, fibrosis and metaplastic/PanIN lesion formation compared with KC mice

pancreas cre acinar scrna-seq histology bulk single-cell
Sequential RNA polymerase II activation drives human hematopoiesis.

PMID 41520338 · PMC13067999 · Cell reports · 2026 · 7 claims · 7 setups

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sciCUT&Tag2in1 enables simultaneous single-cell combinatorial-indexing profiling of Pol II occupancy (Ser5/Ser2-phospho CTD) together with histone modifications (H3K4me1-2-3 or H3K27me3) in up to 50,000 cells per experiment

g-csf-mobilized cd34+ 10-donor lineage-depleted scicut&tag2in1 individual souporcell
Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

PMID 41532847 · PMC13056296 · Cancer discovery · 2026 · 8 claims · 8 setups

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High-depth targeted sequencing of >1,500 IM samples from six countries identified 47 significantly mutated driver genes, including ARID1A, KRAS/MAPK pathway genes, and PIGR

subset matched saliva hek293t high-depth whole-genome genome-wide
Rtf1-dependent transcriptional pausing regulates cardiogenesis.

PMID 41537425 · PMC12807453 · eLife · 2026 · 8 claims · 7 setups

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Rtf1 activity is essential for differentiation of the myocardial lineage from mesoderm

zebrafish embryo embryonic mescs crispr situ shrna
IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

PMID 41559031 · PMC12819398 · Cell discovery · 2026 · 8 claims · 8 setups

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Aging reduces hASC self-renewal, lineage plasticity (adipogenic/osteogenic differentiation), and in vivo tissue repair efficacy

i-hascs full-thickness nude hascs edu scratch adipogenic
Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109.

PMID 41571773 · PMC12929570 · Communications biology · 2026 · 8 claims · 4 setups

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EMP activation (increased vimentin, decreased E-cadherin) is associated with advanced histologic grade in canine mammary carcinomas

archived canine cmc same immunohistochemistry sequencing
Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

PMID 41574606 · PMC12892883 · JCI insight · 2026 · 8 claims · 8 setups

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Chondrocyte-specific (Col2a1-Cre-driven) expression of the p.R594H Trpv4 mutation reproduces the human TRPV4 skeletal dysplasia phenotype in mice, including short stature, long bone and craniofacial abnormalities, and vertebral defects.

col2a1-cre proximal growth cervical radiography histology rnascope
Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

PMID 41578129 · PMC12932634 · NPJ breast cancer · 2026 · 8 claims · 7 setups

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Identified 30 isolated tumor cells (ITCs) in a clinically metastasis-negative tumor-draining lymph node, representing the initial metastatic seeding event, spanning ~200 μm

dissected same tumor xenium-derived bulk enzymatic whole-genome
Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.

PMID 41611829 · PMC12894973 · Communications biology · 2026 · 7 claims · 8 setups

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TGF-β induced EMT in MCF10A cells follows two broad paths that arise from coupling between cell cycle and EMT at either the G1 or G2/M phase

mcf10a scrna-seq vector pseudotime
Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups

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446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways

carotid degs six bulk kegg logistic
Stem cell-associated osteogenic deficiency causes craniofacial deformities with progeroid accumulation of prelamin A.

PMID 41632539 · PMC13041684 · JCI insight · 2026 · 8 claims · 8 setups

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Lmna L648R mutation causes multiple suture craniosynostosis (AF, PF, COR) occurring under low bone density, contrasting with conventional synostosis caused by excessive ossification

skull calvarial suture p7-p10 micro-ct h&e brdu
Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

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OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

tcga-luad geo lung single-cell bulk ssgsea cibersort

Experiments

Hepatitis B virus genotypes/subgenotypes in voluntary blood donors in Makassar, South Sulawesi, Indonesia.

Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

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

Discovering and protecting cryptic biodiversity: A case study of a previously undescribed, vulnerable bird species in Japan.

A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development.

Much ado about nothing: modeling amino acid replacement with predicted protein structures.

Hereditary chronic pancreatitis induced plasticity cooperates with mutant Kras in early pancreatic carcinogenesis.

Sequential RNA polymerase II activation drives human hematopoiesis.

Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

Rtf1-dependent transcriptional pausing regulates cardiogenesis.

IGF2BP3-dependent glutamine/BCAA metabolic rewiring rejuvenates aged human adipose-derived stem cells for enhanced tissue regeneration.

Epithelial-mesenchymal plasticity and immunosuppression in canine carcinomas reveals cross-species upregulation of CD109.

Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

Spatial gene expression analysis reveals drivers of extremely early lymph node metastasis in breast cancer.

Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.

Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

Stem cell-associated osteogenic deficiency causes craniofacial deformities with progeroid accumulation of prelamin A.

Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.